On the vanishing of the t-term in the short-time expansion of the diffusion coefficient for oscillating gradients in diffusion NMR

NASA Astrophysics Data System (ADS)

Laun, Frederik B.; Demberg, Kerstin; Nagel, Armin M.; Uder, Micheal; Kuder, Tristan A.

2017-11-01

Nuclear magnetic resonance (NMR) diffusion measurements can be used to probe porous structures or biological tissues by means of the random motion of water molecules. The short-time expansion of the diffusion coefficient in powers of sqrt(t), where t is the diffusion time related to the duration of the diffusion-weighting magnetic field gradient profile, is universally connected to structural parameters of the boundaries restricting the diffusive motion. The sqrt(t)-term is proportional to the surface to volume ratio. The t-term is related to permeability and curvature. The short time expansion can be measured with two approaches in NMR-based diffusion experiments: First, by the use of diffusion encodings of short total duration and, second, by application of oscillating gradients of long total duration. For oscillating gradients, the inverse of the oscillation frequency becomes the relevant time scale. The purpose of this manuscript is to show that the oscillating gradient approach is blind to the t-term. On the one hand, this prevents fitting of permeability and curvature measures from this term. On the other hand, the t-term does not bias the determination of the sqrt(t)-term in experiments.

Mode-coupling theoretical analysis of transport and relaxation properties of liquid dimethylimidazolium chloride

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Koda, S.

2010-03-01

The mode-coupling theory for molecular liquids based on the interaction-site model is applied to a representative molecular ionic liquid, dimethylimidazolium chloride, and dynamic properties such as shear viscosity, self-diffusion coefficients, reorientational relaxation time, electric conductivity, and dielectric relaxation spectrum are analyzed. Molecular dynamics (MD) simulation is also performed on the same system for comparison. The theory captures the characteristics of the dynamics of the ionic liquid qualitatively, although theoretical relaxation times are several times larger than those from the MD simulation. Large relaxations are found in the 100 MHz region in the dispersion of the shear viscosity and the dielectric relaxation, in harmony with various experiments. The relaxations of the self-diffusion coefficients are also found in the same frequency region. The dielectric relaxation spectrum is divided into the contributions of the translational and reorientational modes, and it is demonstrated that the relaxation in the 100 MHz region mainly stems from the translational modes. The zero-frequency electric conductivity is close to the value predicted by the Nernst-Einstein equation in both MD simulation and theoretical calculation. However, the frequency dependence of the electric conductivity is different from those of self-diffusion coefficients in that the former is smaller than the latter in the gigahertz-terahertz region, which is compensated by the smaller dispersion of the former in the 100 MHz region. The analysis of the theoretical calculation shows that the difference in their frequency dependence is due to the different contribution of the short- and long-range liquid structures.

Short-time dynamics of monomers and dimers in quasi-two-dimensional colloidal mixtures.

PubMed

Sarmiento-Gómez, Erick; Villanueva-Valencia, José Ramón; Herrera-Velarde, Salvador; Ruiz-Santoyo, José Arturo; Santana-Solano, Jesús; Arauz-Lara, José Luis; Castañeda-Priego, Ramón

2016-07-01

We report on the short-time dynamics in colloidal mixtures made up of monomers and dimers highly confined between two glass plates. At low concentrations, the experimental measurements of colloidal motion agree well with the solution of the Navier-Stokes equation at low Reynolds numbers; the latter takes into account the increase in the drag force on a colloidal particle due to wall-particle hydrodynamic forces. More importantly, we find that the ratio of the short-time diffusion coefficient of the monomer and that of the center of mass of the dimmer is almost independent of both the dimer molar fraction, x_{d}, and the total packing fraction, ϕ, up to ϕ≈0.5. At higher concentrations, this ratio displays a small but systematic increase. A similar physical scenario is observed for the ratio between the parallel and the perpendicular components of the short-time diffusion coefficients of the dimer. This dynamical behavior is corroborated by means of molecular dynamics computer simulations that include explicitly the particle-particle hydrodynamic forces induced by the solvent. Our results suggest that the effects of colloid-colloid hydrodynamic interactions on the short-time diffusion coefficients are almost identical and factorable in both species.

Quantifying TEMPO Redox Polymer Charge Transport toward the Organic Radical Battery.

PubMed

Karlsson, Christoffer; Suga, Takeo; Nishide, Hiroyuki

2017-03-29

To design new and better organic active battery materials in a rational fashion, fundamental parameters of the charge transport must be studied. Herein we report on the electronic conductivity by electron diffusion in a TEMPO-containing redox polymer, and the reorganization energy of the TEMPO self-exchange in an organic solvent is determined for the first time. The electronic conductivity was 8.5 μS/cm at E 0 and corresponded to a redox hopping mechanism. The apparent electron diffusion coefficient was 1.9 × 10 -9 cm 2 /s at room temperature, and at short times the ion diffusion was limiting with a diffusion coefficient of 6.5 × 10 -10 cm 2 /s. The reorganization energy was determined to be 1.01 eV, indicating a rather polar chemical environment for the TEMPO groups. The implications for the usage of this type of materials in organic energy storage are discussed. As conductivity through 10 μm was demonstrated, we show that, if sufficient swellability can be ensured, charge can be transported through several micrometer thick layers in a battery electrode without any conducting additive.

Using tobacco mosaic virus to probe enhanced surface diffusion of molecular glasses.

PubMed

Zhang, Yue; Potter, Richard; Zhang, William; Fakhraai, Zahra

2016-11-09

Recent studies have shown that diffusion on the surface of organic glasses can be many orders of magnitude faster than bulk diffusion. Developing new probes that can readily measure surface diffusion can help study the effect of parameters such as chemical structure, intermolecular interaction, molecules' shape and size on the enhanced surface diffusion. In this study, we develop a novel probe that significantly simplifies these types of studies. Tobacco mosaic virus (TMV) is used as probe particle to measure surface diffusion coefficient of molecular glass N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD). The evolution of the meniscus formed around TMV is probed as a function of time at various temperatures. TMV has a well-defined, mono-dispersed, cylindrical shape, with a large aspect-ratio (average diameter of 16.6 nm, length of 300 nm). As such, the shape of the meniscus around the center of TMV is semi-two dimensional, which compared to using a nanosphere as probe, increases the driving force for meniscus formation and simplifies the analysis of surface diffusion. We show that under these conditions, after a short transient time the shape of the meniscus is self-similar, allowing accurate determination of the surface diffusion coefficient. Measurements at various temperatures are then performed to investigate the temperature dependence of the surface diffusion coefficient. It is found that surface diffusion is greatly enhanced in TPD and has a lower activation barrier compared to the bulk counterpart. These observations are consistent with previous studies of surface diffusion on molecular glasses, demonstrating the accuracy of this method.

Velocity and stress autocorrelation decay in isothermal dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Chaudhri, Anuj; Lukes, Jennifer R.

2010-02-01

The velocity and stress autocorrelation decay in a dissipative particle dynamics ideal fluid model is analyzed in this paper. The autocorrelation functions are calculated at three different friction parameters and three different time steps using the well-known Groot/Warren algorithm and newer algorithms including self-consistent leap-frog, self-consistent velocity Verlet and Shardlow first and second order integrators. At low friction values, the velocity autocorrelation function decays exponentially at short times, shows slower-than exponential decay at intermediate times, and approaches zero at long times for all five integrators. As friction value increases, the deviation from exponential behavior occurs earlier and is more pronounced. At small time steps, all the integrators give identical decay profiles. As time step increases, there are qualitative and quantitative differences between the integrators. The stress correlation behavior is markedly different for the algorithms. The self-consistent velocity Verlet and the Shardlow algorithms show very similar stress autocorrelation decay with change in friction parameter, whereas the Groot/Warren and leap-frog schemes show variations at higher friction factors. Diffusion coefficients and shear viscosities are calculated using Green-Kubo integration of the velocity and stress autocorrelation functions. The diffusion coefficients match well-known theoretical results at low friction limits. Although the stress autocorrelation function is different for each integrator, fluctuates rapidly, and gives poor statistics for most of the cases, the calculated shear viscosities still fall within range of theoretical predictions and nonequilibrium studies.

Self-diffusion of electrolyte species in model battery electrodes using Magic Angle Spinning and Pulsed Field Gradient Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Tambio, Sacris Jeru; Deschamps, Michaël; Sarou-Kanian, Vincent; Etiemble, Aurélien; Douillard, Thierry; Maire, Eric; Lestriez, Bernard

2017-09-01

Lithium-ion batteries are electrochemical storage devices using the electrochemical activity of the lithium ion in relation to intercalation compounds owing to mass transport phenomena through diffusion. Diffusion of the lithium ion in the electrode pores has been poorly understood due to the lack of experimental techniques for measuring its self-diffusion coefficient in porous media. Magic-Angle Spinning, Pulsed Field Gradient, Stimulated-Echo Nuclear Magnetic Resonance (MAS-PFG-STE NMR) was used here for the first time to measure the self-diffusion coefficients of the electrolyte species in the LP30 battery electrolyte (i.e. a 1 M solution of LiPF6 dissolved in 1:1 Ethylene Carbonate - Dimethyl Carbonate) in model composites. These composite electrodes were made of alumina, carbon black and PVdF-HFP. Alumina's magnetic susceptibility is close to the measured magnetic susceptibility of the LP30 electrolyte thereby limiting undesirable internal field gradients. Interestingly, the self-diffusion coefficient of lithium ions decreases with increasing carbon content. FIB-SEM was used to describe the 3D geometry of the samples. The comparison between the reduction of self-diffusion coefficients as measured by PFG-NMR and as geometrically derived from FIB/SEM tortuosity values highlights the contribution of specific interactions at the material/electrolyte interface on the lithium transport properties.

Electrokinetic and hydrodynamic properties of charged-particles systems. From small electrolyte ions to large colloids

NASA Astrophysics Data System (ADS)

Nägele, G.; Heinen, M.; Banchio, A. J.; Contreras-Aburto, C.

2013-11-01

Dynamic processes in dispersions of charged spherical particles are of importance both in fundamental science, and in technical and bio-medical applications. There exists a large variety of charged-particles systems, ranging from nanometer-sized electrolyte ions to micron-sized charge-stabilized colloids. We review recent advances in theoretical methods for the calculation of linear transport coefficients in concentrated particulate systems, with the focus on hydrodynamic interactions and electrokinetic effects. Considered transport properties are the dispersion viscosity, self- and collective diffusion coefficients, sedimentation coefficients, and electrophoretic mobilities and conductivities of ionic particle species in an external electric field. Advances by our group are also discussed, including a novel mode-coupling-theory method for conduction-diffusion and viscoelastic properties of strong electrolyte solutions. Furthermore, results are presented for dispersions of solvent-permeable particles, and particles with non-zero hydrodynamic surface slip. The concentration-dependent swelling of ionic microgels is discussed, as well as a far-reaching dynamic scaling behavior relating colloidal long- to short-time dynamics.

Effective temperatures and the breakdown of the Stokes-Einstein relation for particle suspensions.

PubMed

Mendoza, Carlos I; Santamaría-Holek, I; Pérez-Madrid, A

2015-09-14

The short- and long-time breakdown of the classical Stokes-Einstein relation for colloidal suspensions at arbitrary volume fractions is explained here by examining the role that confinement and attractive interactions play in the intra- and inter-cage dynamics executed by the colloidal particles. We show that the measured short-time diffusion coefficient is larger than the one predicted by the classical Stokes-Einstein relation due to a non-equilibrated energy transfer between kinetic and configuration degrees of freedom. This transfer can be incorporated in an effective kinetic temperature that is higher than the temperature of the heat bath. We propose a Generalized Stokes-Einstein relation (GSER) in which the effective temperature replaces the temperature of the heat bath. This relation then allows to obtain the diffusion coefficient once the viscosity and the effective temperature are known. On the other hand, the temporary cluster formation induced by confinement and attractive interactions of hydrodynamic nature makes the long-time diffusion coefficient to be smaller than the corresponding one obtained from the classical Stokes-Einstein relation. Then, the use of the GSER allows to obtain an effective temperature that is smaller than the temperature of the heat bath. Additionally, we provide a simple expression based on a differential effective medium theory that allows to calculate the diffusion coefficient at short and long times. Comparison of our results with experiments and simulations for suspensions of hard and porous spheres shows an excellent agreement in all cases.

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.

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.

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.

Magnetic orientation of nontronite clay in aqueous dispersions and its effect on water diffusion.

PubMed

Abrahamsson, Christoffer; Nordstierna, Lars; Nordin, Matias; Dvinskikh, Sergey V; Nydén, Magnus

2015-01-01

The diffusion rate of water in dilute clay dispersions depends on particle concentration, size, shape, aggregation and water-particle interactions. As nontronite clay particles magnetically align parallel to the magnetic field, directional self-diffusion anisotropy can be created within such dispersion. Here we study water diffusion in exfoliated nontronite clay dispersions by diffusion NMR and time-dependant 1H-NMR-imaging profiles. The dispersion clay concentration was varied between 0.3 and 0.7 vol%. After magnetic alignment of the clay particles in these dispersions a maximum difference of 20% was measured between the parallel and perpendicular self-diffusion coefficients in the dispersion with 0.7 vol% clay. A method was developed to measure water diffusion within the dispersion in the absence of a magnetic field (random clay orientation) as this is not possible with standard diffusion NMR. However, no significant difference in self-diffusion coefficient between random and aligned dispersions could be observed. Copyright © 2014 Elsevier Inc. All rights reserved.

Memory effects in funnel ratchet of self-propelled particles

NASA Astrophysics Data System (ADS)

Hu, Cai-Tian; Wu, Jian-Chun; Ai, Bao-Quan

2017-05-01

The transport of self-propelled particles with memory effects is investigated in a two-dimensional periodic channel. Funnel-shaped barriers are regularly arrayed in the channel. Due to the asymmetry of the barriers, the self-propelled particles can be rectified. It is found that the memory effects of the rotational diffusion can strongly affect the rectified transport. The memory effects do not always break the rectified transport, and there exists an optimal finite value of correlation time at which the rectified efficiency takes its maximal value. We also find that the optimal values of parameters (the self-propulsion speed, the translocation diffusion coefficient, the rotational noise intensity, and the self-rotational diffusion coefficient) can facilitate the rectified transport. When introducing a finite load, particles with different self-propulsion speeds move to different directions and can be separated.

Diffusion NMR methods applied to xenon gas for materials study

NASA Technical Reports Server (NTRS)

Mair, R. W.; Rosen, M. S.; Wang, R.; Cory, D. G.; Walsworth, R. L.

2002-01-01

We report initial NMR studies of (i) xenon gas diffusion in model heterogeneous porous media and (ii) continuous flow laser-polarized xenon gas. Both areas utilize the pulsed gradient spin-echo (PGSE) techniques in the gas phase, with the aim of obtaining more sophisticated information than just translational self-diffusion coefficients--a brief overview of this area is provided in the Introduction. The heterogeneous or multiple-length scale model porous media consisted of random packs of mixed glass beads of two different sizes. We focus on observing the approach of the time-dependent gas diffusion coefficient, D(t) (an indicator of mean squared displacement), to the long-time asymptote, with the aim of understanding the long-length scale structural information that may be derived from a heterogeneous porous system. We find that D(t) of imbibed xenon gas at short diffusion times is similar for the mixed bead pack and a pack of the smaller sized beads alone, hence reflecting the pore surface area to volume ratio of the smaller bead sample. The approach of D(t) to the long-time limit follows that of a pack of the larger sized beads alone, although the limiting D(t) for the mixed bead pack is lower, reflecting the lower porosity of the sample compared to that of a pack of mono-sized glass beads. The Pade approximation is used to interpolate D(t) data between the short- and long-time limits. Initial studies of continuous flow laser-polarized xenon gas demonstrate velocity-sensitive imaging of much higher flows than can generally be obtained with liquids (20-200 mm s-1). Gas velocity imaging is, however, found to be limited to a resolution of about 1 mm s-1 owing to the high diffusivity of gases compared with liquids. We also present the first gas-phase NMR scattering, or diffusive-diffraction, data, namely flow-enhanced structural features in the echo attenuation data from laser-polarized xenon flowing through a 2 mm glass bead pack. c2002 John Wiley & Sons, Ltd.

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.

Brownian motion of boomerang colloidal particles.

PubMed

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan V; Sun, Kai; Wei, Qi-Huo

2013-10-18

We investigate the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short-time faster to long-time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to the superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.

Brownian Motion of Boomerang Colloidal Particles

NASA Astrophysics Data System (ADS)

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan V.; Sun, Kai; Wei, Qi-Huo

2013-10-01

We investigate the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short-time faster to long-time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to the superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.

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.

Damage and recovery characteristics of lithium-containing solar cells.

NASA Technical Reports Server (NTRS)

Faith, T. J.

1971-01-01

Damage and recovery characteristics were measured on lithium-containing solar cells irradiated by 1-MeV electrons. Empirical expressions for cell recovery time, diffusion-length damage coefficient immediately after irradiation, and diffusion-length damage coefficient after recovery were derived using results of short-circuit current, diffusion-length, and reverse-bias capacitance measurements. The damage coefficients were expressed in terms of a single lithium density parameter, the lithium gradient. A fluence dependence was also established, this dependence being the same for both the immediate-post-irradiation and post-recovery cases. Cell recovery rates were found to increase linearly with lithium gradient.

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.

Anomalous Diffusion of Water in Lamellar Membranes Formed by Pluronic Polymers

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Ohl, Michael; Han, Youngkyu; Smith, Gregory; Do, Changwoo; Biology; Soft-Matter Division, Oak Ridge National Laboratory Team; Julich CenterNeutron Science Team

Water diffusion is playing an important role in polymer systems. We calculated the water diffusion coefficient at different layers along z-direction which is perpendicular to the lamellar membrane formed by Pluronic block copolymers (L62: (EO6-PO34-EO6)) with the molecular dynamics simulation trajectories. Water molecules at bulk layers are following the normal diffusion, while that at hydration layers formed by polyethylene oxide (PEO) and hydrophobic layers formed by polypropylene oxide (PPO) are following anomalous diffusion. We find that although the subdiffusive regimes at PEO layers and PPO layers are the same, which is the fractional Brownian motion, however, the dynamics are different, i.e. diffusion at the PEO layers is much faster than that at the PPO layers, and meanwhile it exhibits a normal diffusive approximation within a short time period which is governed by the localized free self-diffusion, but becomes subdiffusive after t >8 ps, which is governed by the viscoelastic medium. The Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy; and Zhe Zhang gratefully acknowledges financial support from Julich Center for Neutron Science.

Diffusion and Electric Mobility of KCI within Isolated Cuticles of Citrus aurantium 1

PubMed Central

Tyree, Melvin T.; Wescott, Charles R.; Tabor, Christopher A.; Morse, Anne D.

1992-01-01

Fick's second law has been used to predict the time course of electrical conductance change in isolated cuticles following the rapid change in bathing solution (KCI) from concentration C to 0.1 C. The theoretical time course is dependent on the coefficient of diffusion of KCI in the cuticle and the cuticle thickness. Experimental results, obtained from cuticles isolated from sour orange (Citrus aurantium), fit with a diffusion model of an isolated cuticle in which about 90% of the conductance change following a solution change is due to salts diffusing from polar pores in the wax, and 10% of the change is due to salt diffusion from the wax. Short and long time constants for the washout of KCI were found to be 0.11 and 3.8 hours, respectively. These time constants correspond to KCI diffusion coefficients of 1 × 10−15 and 3 × 10−17 square meters per second, respectively. The larger coefficient is close to the diffusion coefficient for water in polar pores of Citrus reported elsewhere (M Becker, G Kerstiens, J Schönherr [1986] Trees 1: 54-60). This supports our interpretation of the washout kinetics of KCI following a change in concentration of bathing solution. PMID:16668971

Saturation of the lower-hybrid-drift instability by mode coupling

NASA Technical Reports Server (NTRS)

Drake, J. F.; Guzdar, P. N.; Huba, J. D.

1983-01-01

A nonlinear mode-coupling theory of the lower-hybrid-drift instability is presented. It is found that the instability saturates by transferring energy from the growing, long wavelength modes to the damped, short wavelength modes. The saturation energy, mean square of the potential fluctuations, and diffusion coefficient are calculated self-consistently.

Optimal estimation of diffusion coefficients from single-particle trajectories

NASA Astrophysics Data System (ADS)

Vestergaard, Christian L.; Blainey, Paul C.; Flyvbjerg, Henrik

2014-02-01

How does one optimally determine the diffusion coefficient of a diffusing particle from a single-time-lapse recorded trajectory of the particle? We answer this question with an explicit, unbiased, and practically optimal covariance-based estimator (CVE). This estimator is regression-free and is far superior to commonly used methods based on measured mean squared displacements. In experimentally relevant parameter ranges, it also outperforms the analytically intractable and computationally more demanding maximum likelihood estimator (MLE). For the case of diffusion on a flexible and fluctuating substrate, the CVE is biased by substrate motion. However, given some long time series and a substrate under some tension, an extended MLE can separate particle diffusion on the substrate from substrate motion in the laboratory frame. This provides benchmarks that allow removal of bias caused by substrate fluctuations in CVE. The resulting unbiased CVE is optimal also for short time series on a fluctuating substrate. We have applied our estimators to human 8-oxoguanine DNA glycolase proteins diffusing on flow-stretched DNA, a fluctuating substrate, and found that diffusion coefficients are severely overestimated if substrate fluctuations are not accounted for.

Molecular dynamics simulations of propane in slit shaped silica nano-pores: direct comparison with quasielastic neutron scattering experiments.

PubMed

Gautam, Siddharth; Le, Thu; Striolo, Alberto; Cole, David

2017-12-13

Molecular motion under confinement has important implications for a variety of applications including gas recovery and catalysis. Propane confined in mesoporous silica aerogel as studied using quasielastic neutron scattering (QENS) showed anomalous pressure dependence in its diffusion coefficient (J. Phys. Chem. C, 2015, 119, 18188). Molecular dynamics (MD) simulations are often employed to complement the information obtained from QENS experiments. Here, we report an MD simulation study to probe the anomalous pressure dependence of propane diffusion in silica aerogel. Comparison is attempted based on the self-diffusion coefficients and on the time scales of the decay of the simulated intermediate scattering functions. While the self-diffusion coefficients obtained from the simulated mean squared displacement profiles do not exhibit the anomalous pressure dependence observed in the experiments, the time scales of the decay of the intermediate scattering functions calculated from the simulation data match the corresponding quantities obtained in the QENS experiment and thus confirm the anomalous pressure dependence of the diffusion coefficient. The origin of the anomaly in pressure dependence lies in the presence of an adsorbed layer of propane molecules that seems to dominate the confined propane dynamics at low pressure, thereby lowering the diffusion coefficient. Further, time scales for rotational motion obtained from the simulations explain the absence of rotational contribution to the QENS spectra in the experiments. In particular, the rotational motion of the simulated propane molecules is found to exhibit large angular jumps at lower pressure. The present MD simulation work thus reveals important new insights into the origin of anomalous pressure dependence of propane diffusivity in silica mesopores and supplements the information obtained experimentally by QENS data.

Symmetry of the gradient profile as second experimental dimension in the short-time expansion of the apparent diffusion coefficient as measured with NMR diffusometry.

PubMed

Laun, Frederik Bernd; Kuder, Tristan Anselm; Zong, Fangrong; Hertel, Stefan; Galvosas, Petrik

2015-10-01

The time-dependent apparent diffusion coefficient as measured by pulsed gradient NMR can be used to estimate parameters of porous structures including the surface-to-volume ratio and the mean curvature of pores. In this work, the short-time diffusion limit and in particular the influence of the temporal profile of diffusion gradients on the expansion as proposed by Mitra et al. (1993) is investigated. It is shown that flow-compensated waveforms, i.e. those whose first moment is zero, are blind to the term linear in observation time, which is the term that is proportional to mean curvature and surface permeability. A gradient waveform that smoothly interpolates between flow-compensated and bipolar waveform is proposed and the degree of flow-compensation is used as a second experimental dimension. This two-dimensional ansatz is shown to yield an improved precision when characterizing the confining domain. This technique is demonstrated with simulations and in experiments performed with cylindrical capillaries of 100 μm radius. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

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.

Brownian Motion of Boomerang Colloidal Particles

NASA Astrophysics Data System (ADS)

Wei, Qi-Huo; Konya, Andrew; Wang, Feng; Selinger, Jonathan V.; Sun, Kai; Chakrabarty, Ayan

2014-03-01

We present experimental and theoretical studies on the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short-time faster to long-time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to the superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.

Understanding of Relationship between Phospholipid Membrane Permeability and Self-Diffusion Coefficients of Some Drugs and Biologically Active Compounds in Model Solvents.

PubMed

Blokhina, Svetlana V; Volkova, Tatyana V; Golubev, Vasiliy A; Perlovich, German L

2017-10-02

In this work we measured self-diffusion coefficients of 5 drugs (aspirin, caffeine, ethionamide, salicylic acid, and paracetamol) and 11 biologically active compounds of similar structure in deuterated water and 1-octanol by NMR. It has been found that an increase in the van der Waals volume of the molecules of the studied substances result in reduction of their diffusion mobility in both solvents. The analysis of the experimental data showed the influence of chemical nature and structural isomerization of the molecules on the diffusion mobility. Apparent permeability coefficients of the studied compounds were determined using an artificial phospholipid membrane made of egg lecithin as a model of in vivo absorption. Distribution coefficients in 1-octanol/buffer pH 7.4 system were measured. For the first time the model of the passive diffusion through the phospholipid membrane was validated based on the experimental data. To this end, the passive diffusion was considered as an additive process of molecule passage through the aqueous boundary layer before the membrane and 1-octanol barrier simulating the lipid layer of the membrane.

The Shape of Protein Crowders is a Major Determinant of Protein Diffusion

PubMed Central

Balbo, Jessica; Mereghetti, Paolo; Herten, Dirk-Peter; Wade, Rebecca C.

2013-01-01

As a model for understanding how molecular crowding influences diffusion and transport of proteins in cellular environments, we combined experimental and theoretical approaches to study the diffusion of proteins in highly concentrated protein solutions. Bovine serum albumin and γ-Globulin were chosen as molecular crowders and as tracers. These two proteins are representatives of the main types of plasma protein and have different shapes and sizes. Solutions consisting of one or both proteins were studied. The self-diffusion coefficients of the fluorescently labeled tracer proteins were measured by means of fluorescence correlation spectroscopy at a total protein concentration of up to 400 g/L. γ-Globulin is found to have a stronger influence as a crowder on the tracer self-diffusion coefficient than Bovine serum albumin. Brownian dynamics simulations show that the excluded volume and the shape of the crowding protein have a significantly stronger influence on translational and rotational diffusion coefficients, as well as transient oligomerization, than hydrodynamic or direct interactions. Anomalous subdiffusion, which is not observed at the experimental fluorescence correlation spectroscopy timescales (>100 μs), appears only at very short timescales (<1 μs) in the simulations due to steric effects of the proteins. We envision that the combined experimental and computational approach employed here can be developed to unravel the different biophysical contributions to protein motion and interaction in cellular environments by systematically varying protein properties such as molecular weight, size, shape, and electrostatic interactions. PMID:23561534

Measurement of hyperpolarized gas diffusion at very short time scales

PubMed Central

Carl, Michael; Wilson Miller, G.; Mugler, John P.; Rohrbaugh, Scott; Tobias, William A.; Cates, Gordon D.

2007-01-01

We present a new pulse sequence for measuring very-short-time-scale restricted diffusion of hyperpolarized noble gases. The pulse sequence is based on concatenating a large number of bipolar diffusion-sensitizing gradients to increase the diffusion attenuation of the MR signal while maintaining a fundamentally short diffusion time. However, it differs in several respects from existing methods that use oscillating diffusion gradients for this purpose. First, a wait time is inserted between neighboring pairs of gradient pulses; second, consecutive pulse pairs may be applied along orthogonal axes; and finally, the diffusion-attenuated signal is not simply read out at the end of the gradient train but is periodically sampled during the wait times between neighboring pulse pairs. The first two features minimize systematic differences between the measured (apparent) diffusion coefficient and the actual time-dependent diffusivity, while the third feature optimizes the use of the available MR signal to improve the precision of the diffusivity measurement in the face of noise. The benefits of this technique are demonstrated using theoretical calculations, Monte-Carlo simulations of gas diffusion in simple geometries, and experimental phantom measurements in a glass sphere containing hyperpolarized 3He gas. The advantages over the conventional single-bipolar approach were found to increase with decreasing diffusion time, and thus represent a significant step toward making accurate surface-to-volume measurements in the lung airspaces. PMID:17936048

Using the Ab Initio Molecular Dynamics Method for Simulating the Peculiarities in the Temperature Dependence of Liquid Bismuth Properties

NASA Astrophysics Data System (ADS)

Yuryev, A. A.; Gelchinski, B. R.; Vatolin, N. A.

2018-03-01

The specific features pertinent to the temperature dependence of the electronic and atomic properties of liquid bismuth that have been observed in experiments are investigated according to the ab initio molecular dynamics method using the SIESTA open software package. The density of electronic states, the radial distribution function of atoms, and the self-diffusion coefficient are calculated for the temperature range from the melting point equal to 545 K to 1500 K. The calculated data are in good agreement with the experimental data. It is found that the position of the first peak in the radial distribution function of atoms and the self-diffusion coefficient are characterized by a nonmonotonic dependence under the conditions of superheating by approximately 150 K above the melting temperature. In the authors' opinion, this dependence feature is attributed to a change in the liquid short-range order structure.

Dynamics of proteins: Light scattering study of dilute and dense colloidal suspensions of eye lens homogenates

NASA Astrophysics Data System (ADS)

Giannopoulou, A.; Aletras, A. J.; Pharmakakis, N.; Papatheodorou, G. N.; Yannopoulos, S. N.

2007-11-01

We report a dynamic light scattering study on protein suspensions of bovine lens homogenates at conditions (pH and ionic strength) similar to the physiological ones. Light scattering data were collected at two temperatures, 20 and 37°C, over a wide range of concentrations from the very dilute limit up to the dense regime approaching the physiological lens concentration. A comparison with experimental data from intact bovine lenses was advanced, revealing differences between dispersions and lenses at similar concentrations. In the dilute regime, two scattering entities were detected and identified with the long-time self-diffusion modes of α-crystallins and their aggregates, which naturally exist in lens nucleus. Upon increasing protein concentration, significant changes in time correlation function were observed starting at ˜75mgml-1, where a new mode originating from collective diffusive motions becomes visible. Self-diffusion coefficients are temperature insensitive, whereas the collective diffusion coefficient depends strongly on temperature revealing a reduction of the net repulsive interparticle forces with decreasing temperature. While there are no rigorous theoretical approaches on particle diffusion properties for multicomponent, nonideal hard sphere polydispersed systems, as the suspensions studied here, a discussion of the volume fraction dependence of the long-time self-diffusion coefficient in the context of existing theoretical approaches was undertaken. This study is purported to provide some insight into the complex light scattering pattern of intact lenses and the interactions between the constituent proteins that are responsible for lens transparency. This would lead to understand basic mechanisms of specific protein interactions that lead to lens opacification (cataract) under pathological conditions.

Removing the barrier to the calculation of activation energies: Diffusion coefficients and reorientation times in liquid water.

PubMed

Piskulich, Zeke A; Mesele, Oluwaseun O; Thompson, Ward H

2017-10-07

General approaches for directly calculating the temperature dependence of dynamical quantities from simulations at a single temperature are presented. The method is demonstrated for self-diffusion and OH reorientation in liquid water. For quantities which possess an activation energy, e.g., the diffusion coefficient and the reorientation time, the results from the direct calculation are in excellent agreement with those obtained from an Arrhenius plot. However, additional information is obtained, including the decomposition of the contributions to the activation energy. These results are discussed along with prospects for additional applications of the direct approach.

Expanding the calculation of activation volumes: Self-diffusion in liquid water

NASA Astrophysics Data System (ADS)

Piskulich, Zeke A.; Mesele, Oluwaseun O.; Thompson, Ward H.

2018-04-01

A general method for calculating the dependence of dynamical time scales on macroscopic thermodynamic variables from a single set of simulations is presented. The approach is applied to the pressure dependence of the self-diffusion coefficient of liquid water as a particularly useful illustration. It is shown how the activation volume associated with diffusion can be obtained directly from simulations at a single pressure, avoiding approximations that are typically invoked.

Calibration-free concentration analysis for an analyte prone to self-association.

PubMed

Imamura, Hiroshi; Honda, Shinya

2017-01-01

Calibration-free concentration analysis (CFCA) based on surface plasmon resonance uses the diffusion coefficient of an analyte to determine the concentration of that analyte in a bulk solution. In general, CFCA is avoided when investigating analytes prone to self-association, as the heterogeneous diffusion coefficient results in a loss of precision. The derivation for self-association of the analyte was presented here. By using the diffusion coefficient for the monomeric state, CFCA provides the lowest possible concentration even though the analyte is self-associated. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

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.

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.

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).

Application of pulsed-gradient Fourier transform nuclear magnetic resonance to the study of self-diffusion of phospholipid vesicles.

PubMed

McDonald, G G; Vanderkooi, J M

1975-05-20

A pulsed-gradient Fourier transform nuclear magnetic resonance (NMR) technique was appplied to the study of diffusion of phospholipid vesicles. The diffusion coefficient of dimyristoyllecithin vesicles (DML) in a D2O-phospahte buffer at 37 degrees is D = 1.9 TIMES 10(-6) cm2/sec. In a solution made viscous by DNA addition, the diffusion coefficient of DML vesicles was 3.5 times 10(-7) cm2/sec. These values compare favorably with the diffusion rate for liposomes as determined by ultracentrifugation and by Stokes law calculation. The data suggest that DML diffusion is controlled primarily by whole liposome migration as opposed to movement of individual molecules within the liposome, liposome rotation, or fast exchange between lecithin molecules in solution and in vesicles.

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.

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.

Effects of Diffusion Time on Short-Range Hyperpolarized 3He Diffusivity Measurements in Emphysema

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

Gierada, David S.; Woods, Jason C.; Bierhals, Andrew J.

2009-09-28

Purpose: To characterize the effect of diffusion time on short-range hyperpolarized 3He MR diffusion measurements across a wide range of emphysema severity. Materials and Methods: 3He diffusion MR imaging was performed on 19 lungs or lobes resected from 18 subjects with varying degrees of emphysema using 3 diffusion times (1.6 msec, 5 msec, and 10 msec) at constant b value. Emphysema severity was quantified as the mean apparent diffusion coefficient (ADC) and as the percentage of pixels with ADC higher than multiple thresholds from 0.30-0.55 cm2/sec (ADC index). Quantitative histology (mean linear intercept) was obtained in 10 of the lungmore » specimens from 10 of the subjects. Results: The mean ADCs with diffusion times of 1.6, 5.0, and 10.0 msec were 0.46, 0.40, and 0.37 cm2/sec, respectively (P <0.0001, ANOVA). There was no relationship between the ADC magnitude and the effect of diffusion time on ADC values. Mean linear intercept correlated with ADC (r=0.91-0.94, P<0.001) and ADC index (r=0.78-0.92, P<0.01) at all diffusion times.« less

Divergence of the long-wavelength collective diffusion coefficient in quasi-one- and quasi-two-dimensional colloidal suspensions.

PubMed

Lin, Binhua; Cui, Bianxiao; Xu, Xinliang; Zangi, Ronen; Diamant, Haim; Rice, Stuart A

2014-02-01

We report the results of experimental studies of the short-time-long-wavelength behavior of collective particle displacements in quasi-one-dimensional (q1D) and quasi-two-dimensional (q2D) colloid suspensions. Our results are reported via the q → 0 behavior of the hydrodynamic function H(q) that relates the effective collective diffusion coefficient D(e)(q), with the static structure factor S(q) and the self-diffusion coefficient of isolated particles D(0): H(q) ≡ D(e)(q)S(q)/D(0). We find an apparent divergence of H(q) as q → 0 with the form H(q) ∝ q(-γ) (1.7 < γ < 1.9) for both q1D and q2D colloid suspensions. Given that S(q) does not diverge as q → 0 we infer that D(e)(q) does. This behavior is qualitatively different from that of the three-dimensional H(q) and D(e)(q) as q → 0, and the divergence is of a different functional form from that predicted for the diffusion coefficient in one-component one-dimensional and two-dimensional fluids not subject to boundary conditions that define the dimensionality of the system. We provide support for the contention that the boundary conditions that define a confined system play a very important role in determining the long-wavelength behavior of the collective diffusion coefficient from two sources: (i) the results of simulations of H(q) and D(e)(q) in quasi-1D and quasi-2D systems and (ii) verification, using data from the work of Lin, Rice and Weitz [Phys. Rev. E 51, 423 (1995)], of the prediction by Bleibel et al., arXiv:1305.3715, that D(e)(q) for a monolayer of colloid particles constrained to lie in the interface between two fluids diverges as q(-1) as q → 0.

Self-diffusion of Si and O in diopside-anorthite melt at high pressures

NASA Astrophysics Data System (ADS)

Tinker, David; Lesher, Charles E.; Hutcheon, Ian D.

2003-01-01

Self-diffusion coefficients for Si and O in Di 58An 42 liquid were measured from 1 to 4 GPa and temperatures from 1510 to 1764°C. Glass starting powders enriched in 18O and 28Si were mated to isotopically normal glass powders to form simple diffusion couples, and self-diffusion experiments were conducted in the piston cylinder device (1 and 2 GPa) and in the multianvil apparatus (3.5 and 4 GPa). Profiles of 18O/ 16O and 29,30Si/ 28Si were measured using secondary ion mass spectrometry. Self-diffusion coefficients for O (D(O)) are slightly greater than self-diffusion coefficients for Si (D(Si)) and are often the same within error. For example, D(O) = 4.20 ± 0.42 × 10 -11 m 2/s and D(Si) = 3.65 ± 0.37 × 10 -11 m 2/s at 1 GPa and 1662°C. Activation energies for self-diffusion are 215 ± 13 kJ/mol for O and 227 ± 13 kJ/mol for Si. Activation volumes for self-diffusion are -2.1 ± 0.4 cm 3/mol and -2.3 ± 0.4 cm 3/mol for O and Si, respectively. The similar self-diffusion coefficients for Si and O, similar activation energies, and small, negative activation volumes are consistent with Si and O transport by a cooperative diffusion mechanism, most likely involving the formation and disassociation of a high-coordinated intermediate species. The small absolute magnitudes of the activation volumes imply that Di 58An 42 liquid is close to a transition from negative to positive activation volume, and Adam-Gibbs theory suggests that this transition is linked to the existence of a critical fraction (˜0.6) of bridging oxygen.

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.

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles

NASA Astrophysics Data System (ADS)

Banchio, Adolfo J.; Heinen, Marco; Holmqvist, Peter; Nägele, Gerhard

2018-04-01

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, fc(q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of fc(q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with fc(q, t), there is indication of long-time exponential decay of fc(q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of fc(q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for fc(q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, fs(q, t), and its non-Gaussian parameter α2(t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from fc(q, t) is theoretically validated.

Oxygen self-diffusion in diopside with application to cooling rate determinations

NASA Astrophysics Data System (ADS)

Farver, John R.

1989-04-01

The kinetics of oxygen self-diffusion in a natural diopside have been measured over the temperature range 700-1250°C. Experiments were run under hydrothermal conditions using 18O-enriched water. Profiles of 18O/( 16O+ 18O) versus depth into the crystal were obtained using an ion microprobe. At 1000 bars (100 MPa) confining pressure, the Arrhenius relation for diffusion parallel to the c crystallographic direction yields a pre-exponential factor ( D0) = 1.5 × 10 -6 cm 2/s and an activation energy ( Q) = 54 ± 5 kcal/g-atom O (226 kJ/g-atom O) over the temperature range of the experiments. Diffusion coefficients parallel to the c crystallographic direction are ≈ 100 times greater than perpendicular to c. The oxygen self-diffusion coefficient obtained for diopside is ≈ 1000 times less than that for diffusion in feldspars, and ≈ 100 times less than that for quartz at 800°C, transport parallel to the c axis. Closure temperatures calculated for oxygen diffusional exchange in natural diopside are significantly higher than for quartz or feldspars. Measurable oxygen isotope exchange in diopside by diffusion would require geological settings with very high temperatures maintained for very long durations. The oxygen diffusional exchange kinetics in diopside presented in this paper find important applications in studies of meteoric hydrothermal circulation systems and the time-temperature history of high-grade regionally metamorphosed terrains. Examples considered include the Outer Unlayered Gabbro, Cuillins Gabbro Complex, Isle of Skye, Scotland, and the granulite-grade Turpentine Hill Metamorphics near Einasleigh, Queensland, Australia.

Molecular dynamics study of nanodroplet diffusion on smooth solid surfaces

NASA Astrophysics Data System (ADS)

Niu, Zhao-Xia; Huang, Tao; Chen, Yong

2018-10-01

We perform molecular dynamics simulations of Lennard-Jones particles in a canonical ensemble to study the diffusion of nanodroplets on smooth solid surfaces. Using the droplet-surface interaction to realize a hydrophilic or hydrophobic surface and calculating the mean square displacement of the center-of-mass of the nanodroplets, the random motion of nanodroplets could be characterized by shorttime subdiffusion, intermediate-time superdiffusion, and long-time normal diffusion. The short-time subdiffusive exponent increases and almost reaches unity (normal diffusion) with decreasing droplet size or enhancing hydrophobicity. The diffusion coefficient of the droplet on hydrophobic surfaces is larger than that on hydrophilic surfaces.

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.

Self-diffusion and conductivity in an ultracold strongly coupled plasma: Calculation by the method of molecular dynamics

NASA Astrophysics Data System (ADS)

Zelener, B. B.; Zelener, B. V.; Manykin, E. A.; Bronin, S. Ya; Bobrov, A. A.; Khikhlukha, D. R.

2018-01-01

We present results of calculations by the method of molecular dynamics of self-diffusion and conductivity of electron and ion components of ultracold plasma in a comparison with available theoretical and experimental data. For the ion self-diffusion coefficient, good agreement was obtained with experiments on ultracold plasma. The results of the calculation of self-diffusion also agree well with other calculations performed for the same values of the coupling parameter, but at high temperatures. The difference in the results of the conductivity calculations on the basis of the current autocorrelation function and on the basis of the diffusion coefficient is discussed.

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.

Surface-to-volume ratio mapping of tumor microstructure using oscillating gradient diffusion weighted imaging

PubMed Central

Reynaud, Olivier; Winters, Kerryanne Veronica; Hoang, Dung Minh; Wadghiri, Youssef Zaim; Novikov, Dmitry S; Kim, Sungheon Gene

2015-01-01

Purpose To disentangle the free diffusivity (D0) and cellular membrane restrictions, via their surface-to-volume ratio (S/V), using the frequency-dependence of the diffusion coefficient D(ω), measured in brain tumors in the short diffusion-time regime using oscillating gradients (OGSE). Methods In vivo and ex vivo OGSE experiments were performed on mice bearing the GL261 murine glioma model (n=10) to identify the relevant time/frequency (t/ω) domain where D(ω) linearly decreases with ω−1/2. Parametric maps (S/V, D0) are compared to conventional DWI metrics. The impact of frequency range and temperature (20°C vs. 37°C) on S/V and D0 is investigated ex vivo. Results The validity of the short diffusion-time regime is demonstrated in vivo and ex vivo. Ex vivo measurements confirm that the purely geometric restrictions embodied in S/V are independent from temperature and frequency range, while the temperature dependence of the free diffusivity D0 is similar to that of pure water. Conclusion Our results suggest that D(ω) in the short diffusion-time regime can be used to uncouple the purely geometric restriction effect, such as S/V, from the intrinsic medium diffusivity properties, and provides a non-empirical and objective way to interpret frequency/time-dependent diffusion changes in tumors in terms of objective biophysical tissue parameters. PMID:26207354

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.

Study on the effect of Cd-diffusion annealing on the electrical properties of CdZnTe

NASA Astrophysics Data System (ADS)

Wanwan, Li; Zechun, Cao; Bin, Zhang; Feng, Zhan; Hongtao, Liu; Wenbin, Sang; Jiahua, Min; Kang, Sun

2006-06-01

In order to meet the requirements for the device design of radiation detectors, CdZnTe (or Cd 1-xZn xTe) crystals grown by Vertical Bridgman Method often need subsequent annealing to increase their resistivity. The nature of this treatment is a diffusion process. Thus, it is meaningful to relate the change of resistivity to the diffusion parameters. A model correlating resistivity and conduction type of CdZnTe with the main diffusion parameter—diffusion coefficient—is put forward in this paper. Combining the model with the analysis of our experimental data, DCd=1.464×10 -10, 1.085×10 -11 and 4.167×10 -13 cm 2/s are the values of Cd self-diffusion coefficient in Cd 0.9Zn 0.1Te at 1073, 973 and 873 K, respectively. The data coincide closely with the Cd self-diffusion coefficient in CdTe provided by different authors [E.D. Jones, N.M. Stewart, Self-diffusion of cadmium in cadmium telluride, J. Crystal Growth 84 (1987) 289-294; P.M. Borsenberger, D.A. Stevenson, J. Phys. Chem. Solids 29 (1968) 1277; R.C. Whelan, D. Shaw, in: D.G. Thomas (Ed.), II -VI Semiconductor Compounds, Benjamin, New York, 1967, p. 451]. With the data, the effects of annealing time on the change of resistivity and conduction type for Cd 0.9Zn 0.1Te wafers, which are annealed in saturated Cd vapor at 1073, 973 and 873 K, were simulated, and good consistency was found. This work suggests an alternative way to obtain the diffusion coefficient in semiconductor materials and also enables ones to analyze the diffusion process quantitatively and predict the annealing results.

Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

2018-01-01

We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

Self-diffusion Coefficient and Structure of Binary n-Alkane Mixtures at the Liquid-Vapor Interfaces.

PubMed

Chilukoti, Hari Krishna; Kikugawa, Gota; Ohara, Taku

2015-10-15

The self-diffusion coefficient and molecular-scale structure of several binary n-alkane liquid mixtures in the liquid-vapor interface regions have been examined using molecular dynamics simulations. It was observed that in hexane-tetracosane mixture hexane molecules are accumulated in the liquid-vapor interface region and the accumulation intensity decreases with increase in a molar fraction of hexane in the examined range. Molecular alignment and configuration in the interface region of the liquid mixture change with a molar fraction of hexane. The self-diffusion coefficient in the direction parallel to the interface of both tetracosane and hexane in their binary mixture increases in the interface region. It was found that the self-diffusion coefficient of both tetracosane and hexane in their binary mixture is considerably higher in the vapor side of the interface region as the molar fraction of hexane goes lower, which is mostly due to the increase in local free volume caused by the local structure of the liquid in the interface region.

Effect of zone size on the convergence of exact solutions for diffusion in single phase systems with planar, cylindrical or spherical geometry

NASA Technical Reports Server (NTRS)

Unnam, J.; Tenney, D. R.

1981-01-01

Exact solutions for diffusion in single phase binary alloy systems with constant diffusion coefficient and zero-flux boundary condition have been evaluated to establish the optimum zone size of applicability. Planar, cylindrical and spherical interface geometry, and finite, singly infinite, and doubly infinite systems are treated. Two solutions are presented for each geometry, one well suited to short diffusion times, and one to long times. The effect of zone-size on the convergence of these solutions is discussed. A generalized form of the diffusion solution for doubly infinite systems is proposed.

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles.

PubMed

Banchio, Adolfo J; Heinen, Marco; Holmqvist, Peter; Nägele, Gerhard

2018-04-07

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, f c (q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of f c (q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with f c (q, t), there is indication of long-time exponential decay of f c (q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of f c (q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for f c (q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, f s (q, t), and its non-Gaussian parameter α 2 (t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from f c (q, t) is theoretically validated.

Time delay can facilitate coherence in self-driven interacting-particle systems

NASA Astrophysics Data System (ADS)

Sun, Yongzheng; Lin, Wei; Erban, Radek

2014-12-01

Directional switching in a self-propelled particle model with delayed interactions is investigated. It is shown that the average switching time is an increasing function of time delay. The presented results are applied to studying collective animal behavior. It is argued that self-propelled particle models with time delays can explain the state-dependent diffusion coefficient measured in experiments with locust groups. The theory is further generalized to heterogeneous groups where each individual can respond to its environment with a different time delay.

Ion-Exchanged Waveguides for Signal Processing Applications - A Novel Electrolytic Process.

DTIC Science & Technology

1987-03-07

were constructed of aluminium : the thermo- limitations in the melt are not expected to dominate couple sheath was stainless steel. the exchange rate...silver ion, D is its T, C0 , and t) with Schott 8011 glass (left) and a Fisher self-diffusion coefficient, and t is the time of diffusion. microscope

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.

Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes.

PubMed

Kondratyuk, Nikolay D; Norman, Genri E; Stegailov, Vladimir V

2016-11-28

Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description.

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.

Selectivity and self-diffusion of CO2 and H2 in a mixture on a graphite surface

PubMed Central

Trinh, Thuat T.; Vlugt, Thijs J. H.; Hägg, May-Britt; Bedeaux, Dick; Kjelstrup, Signe

2013-01-01

We performed classical molecular dynamics (MD) simulations to understand the mechanism of adsorption from a gas mixture of CO2 and H2 (mole fraction of CO2 = 0.30) and diffusion along a graphite surface, with the aim to help enrich industrial off-gases in CO2, separating out H2. The temperature of the system in the simulation covered typical industrial conditions for off-gas treatment (250–550 K). The interaction energy of single molecules CO2 or H2 on graphite surface was calculated with classical force fields (FFs) and with Density Functional Theory (DFT). The results were in good agreement. The binding energy of CO2 on graphite surface is three times larger than that of H2. At lower temperatures, the selectivity of CO2 over H2 is five times larger than at higher temperatures. The position of the dividing surface was used to explain how the adsorption varies with pore size. In the temperature range studied, the self-diffusion coefficient of CO2 is always smaller than of H2. The temperature variation of the selectivities and the self-diffusion coefficient imply that the carbon molecular sieve membrane can be used for gas enrichment of CO2. PMID:24790965

Numerical convergence of the self-diffusion coefficient and viscosity obtained with Thomas-Fermi-Dirac molecular dynamics.

PubMed

Danel, J-F; Kazandjian, L; Zérah, G

2012-06-01

Computations of the self-diffusion coefficient and viscosity in warm dense matter are presented with an emphasis on obtaining numerical convergence and a careful evaluation of the standard deviation. The transport coefficients are computed with the Green-Kubo relation and orbital-free molecular dynamics at the Thomas-Fermi-Dirac level. The numerical parameters are varied until the Green-Kubo integral is equal to a constant in the t→+∞ limit; the transport coefficients are deduced from this constant and not by extrapolation of the Green-Kubo integral. The latter method, which gives rise to an unknown error, is tested for the computation of viscosity; it appears that it should be used with caution. In the large domain of coupling constant considered, both the self-diffusion coefficient and viscosity turn out to be well approximated by simple analytical laws using a single effective atomic number calculated in the average-atom model.

Numerical convergence of the self-diffusion coefficient and viscosity obtained with Thomas-Fermi-Dirac molecular dynamics

NASA Astrophysics Data System (ADS)

Danel, J.-F.; Kazandjian, L.; Zérah, G.

2012-06-01

Computations of the self-diffusion coefficient and viscosity in warm dense matter are presented with an emphasis on obtaining numerical convergence and a careful evaluation of the standard deviation. The transport coefficients are computed with the Green-Kubo relation and orbital-free molecular dynamics at the Thomas-Fermi-Dirac level. The numerical parameters are varied until the Green-Kubo integral is equal to a constant in the t→+∞ limit; the transport coefficients are deduced from this constant and not by extrapolation of the Green-Kubo integral. The latter method, which gives rise to an unknown error, is tested for the computation of viscosity; it appears that it should be used with caution. In the large domain of coupling constant considered, both the self-diffusion coefficient and viscosity turn out to be well approximated by simple analytical laws using a single effective atomic number calculated in the average-atom model.

Langevin equation with fluctuating diffusivity: A two-state model

NASA Astrophysics Data System (ADS)

Miyaguchi, Tomoshige; Akimoto, Takuma; Yamamoto, Eiji

2016-07-01

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

Reduction of Diffusion-Weighted Imaging Contrast of Acute Ischemic Stroke at Short Diffusion Times.

PubMed

Baron, Corey Allan; Kate, Mahesh; Gioia, Laura; Butcher, Kenneth; Emery, Derek; Budde, Matthew; Beaulieu, Christian

2015-08-01

Diffusion-weighted imaging (DWI) of tissue water is a sensitive and specific indicator of acute brain ischemia, where reductions of the diffusion of tissue water are observed acutely in the stroke lesion core. Although these diffusion changes have been long attributed to cell swelling, the precise nature of the biophysical mechanisms remains uncertain. The potential cause of diffusion reductions after stroke was investigated using an advanced DWI technique, oscillating gradient spin-echo DWI, that enables much shorter diffusion times and can improve specificity for alterations of structure at the micron level. Diffusion measurements in the white matter lesions of patients with acute ischemic stroke were reduced by only 8% using oscillating gradient spin-echo DWI, in contrast to a 37% decrease using standard DWI. Neurite beading has recently been proposed as a mechanism for the diffusion changes after ischemic stroke with some ex vivo evidence. To explore whether beading could cause such differential results, simulations of beaded cylinders and axonal swelling were performed, yielding good agreement with experiment. Short diffusion times result in dramatically reduced diffusion contrast of human stroke. Simulations implicate a combination of neuronal beading and axonal swelling as the key structural changes leading to the reduced apparent diffusion coefficient after stroke. © 2015 American Heart Association, Inc.

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.

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

Precise Inference and Characterization of Structural Organization (PICASO) of tissue from molecular diffusion

PubMed Central

Ning, Lipeng; Özarslan, Evren; Westin, Carl-Fredrik; Rathi, Yogesh

2017-01-01

Inferring the microstructure of complex media from the diffusive motion of molecules is a challenging problem in diffusion physics. In this paper, we introduce a novel representation of diffusion MRI (dMRI) signal from tissue with spatially-varying diffusivity using a diffusion disturbance function. This disturbance function contains information about the (intra-voxel) spatial fluctuations in diffusivity due to restrictions, hindrances and tissue heterogeneity of the underlying tissue substrate. We derive the short- and long-range disturbance coefficients from this disturbance function to characterize the tissue structure and organization. Moreover, we provide an exact relation between the disturbance coefficients and the time-varying moments of the diffusion propagator, as well as their relation to specific tissue microstructural information such as the intra-axonal volume fraction and the apparent axon radius. The proposed approach is quite general and can model dMRI signal for any type of gradient sequence (rectangular, oscillating, etc.) without using the Gaussian phase approximation. The relevance of the proposed PICASO model is explored using Monte-Carlo simulations and in-vivo dMRI data. The results show that the estimated disturbance coefficients can distinguish different types of microstructural organization of axons. PMID:27751940

Precise Inference and Characterization of Structural Organization (PICASO) of tissue from molecular diffusion.

PubMed

Ning, Lipeng; Özarslan, Evren; Westin, Carl-Fredrik; Rathi, Yogesh

2017-02-01

Inferring the microstructure of complex media from the diffusive motion of molecules is a challenging problem in diffusion physics. In this paper, we introduce a novel representation of diffusion MRI (dMRI) signal from tissue with spatially-varying diffusivity using a diffusion disturbance function. This disturbance function contains information about the (intra-voxel) spatial fluctuations in diffusivity due to restrictions, hindrances and tissue heterogeneity of the underlying tissue substrate. We derive the short- and long-range disturbance coefficients from this disturbance function to characterize the tissue structure and organization. Moreover, we provide an exact relation between the disturbance coefficients and the time-varying moments of the diffusion propagator, as well as their relation to specific tissue microstructural information such as the intra-axonal volume fraction and the apparent axon radius. The proposed approach is quite general and can model dMRI signal for any type of gradient sequence (rectangular, oscillating, etc.) without using the Gaussian phase approximation. The relevance of the proposed PICASO model is explored using Monte-Carlo simulations and in-vivo dMRI data. The results show that the estimated disturbance coefficients can distinguish different types of microstructural organization of axons. Copyright © 2016 Elsevier Inc. All rights reserved.

A theoretical model for the collective motion of proteins by means of principal component analysis

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2011-02-01

A coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations have been studied for the Bovine Pancreatic Trypsin Inhibitor. We analyzed the stability of the method by studying structural fluctuations of the C a atoms obtained from a 20 ns molecular dynamics simulation. Subsequently, the dynamics of the collective coordinates of protein were characterized by calculating the dynamical friction coefficient and diffusion coefficients along with time-dependent correlation functions of collective coordinates. A dual diffusion behavior was observed with a fast relaxation time of short diffusion regime 0.2-0.4 ps and slow relaxation time of long diffusion about 1-2 ps. In addition, we observed a power law decay of dynamical friction coefficient with exponent for the first five collective coordinates varying from -0.746 to -0.938 for the real part and from -0.528 to -0.665 for its magnitude. It was found that only the first ten collective coordinates are responsible for configuration transitions occurring on time scale longer than 50 ps.

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.

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.

Diffusion of oxygen in cork.

PubMed

Lequin, Sonia; Chassagne, David; Karbowiak, Thomas; Simon, Jean-Marc; Paulin, Christian; Bellat, Jean-Pierre

2012-04-04

This work reports measurements of effective oxygen diffusion coefficient in raw cork. Kinetics of oxygen transfer through cork is studied at 298 K thanks to a homemade manometric device composed of two gas compartments separated by a cork wafer sample. The first compartment contains oxygen, whereas the second one is kept under dynamic vacuum. The pressure decrease in the first compartment is recorded as a function of time. The effective diffusion coefficient D(eff) is obtained by applying Fick's law to transient state using a numerical method based on finite differences. An analytical model derived from Fick's law applied to steady state is also proposed. Results given by these two methods are in close agreement with each other. The harmonic average of the effective diffusion coefficients obtained from the distribution of 15 cork wafers of 3 mm thickness is 1.1 × 10(-9) m(2) s(-1) with a large distribution over four decades. The statistical analysis of the Gaussian distribution obtained on a 3 mm cork wafer is extrapolated to a 48 mm cork wafer, which length corresponds to a full cork stopper. In this case, the probability density distribution gives a mean value of D(eff) equal to 1.6 × 10(-9) m(2) s(-1). This result shows that it is possible to obtain the effective diffusion coefficient of oxygen through cork from short time (few days) measurements performed on a thin cork wafer, whereas months are required to obtain the diffusion coefficient for a full cork stopper. Permeability and oxygen transfer rate are also calculated for comparison with data from other studies.

Evaporation, diffusion and self-assembly at drying interfaces.

PubMed

Roger, K; Sparr, E; Wennerström, H

2018-04-18

Water evaporation from complex aqueous solutions leads to the build-up of structure and composition gradients at their interface with air. We recently introduced an experimental setup for quantitatively studying such gradients and discussed how structure formation can lead to a self-regulation mechanism for controlling water evaporation through self-assembly. Here, we provide a detailed theoretical analysis using an advection/diffusion transport equation that takes into account thermodynamically non-ideal conditions and we directly relate the theoretical description to quantitative experimental data. We derive that the concentration profile develops according to a general square root of time scaling law, which fully agrees with experimental observations. The evaporation rate notably decreases with time as t-1/2, which shows that diffusion in the liquid phase is the rate limiting step for this system, in contrast to pure water evaporation. For the particular binary system that was investigated experimentally, which is composed of water and a sugar-based surfactant (α-dodecylmaltoside), the interfacial layer consists in a sequence of liquid crystalline phases of different mesostructures. We extract values for mutual diffusion coefficients of lamellar, hexagonal and micellar cubic phases, which are consistent with previously reported values and simple models. We thus provide a method to estimate the transport properties of oriented mesophases. The macroscopic humidity-independence of the evaporation rate up to 85% relative humidities is shown to result from both an extremely low mutual diffusion coefficient and the large range of water activities corresponding to relative humidities below 85%, at which the lamellar phase exists. Such a humidity self-regulation mechanism is expected for a large variety of complex system.

Multiple echo multi-shot diffusion sequence.

PubMed

Chabert, Steren; Galindo, César; Tejos, Cristian; Uribe, Sergio A

2014-04-01

To measure both transversal relaxation time (T2 ) and diffusion coefficients within a single scan using a multi-shot approach. Both measurements have drawn interest in many applications, especially in skeletal muscle studies, which have short T2 values. Multiple echo single-shot schemes have been proposed to obtain those variables simultaneously within a single scan, resulting in a reduction of the scanning time. However, one problem with those approaches is the associated long echo read-out. Consequently, the minimum achievable echo time tends to be long, limiting the application of these sequences to tissues with relatively long T2 . To address this problem, we propose to extend the multi-echo sequences using a multi-shot approach, so that to allow shorter echo times. A multi-shot dual-echo EPI sequence with diffusion gradients and echo navigators was modified to include independent diffusion gradients in any of the two echoes. The multi-shot approach allows us to drastically reduce echo times. Results showed a good agreement for the T2 and mean diffusivity measurements with gold standard sequences in phantoms and in vivo data of calf muscles from healthy volunteers. A fast and accurate method is proposed to measure T2 and diffusion coefficients simultaneously, tested in vitro and in healthy volunteers. Copyright © 2013 Wiley Periodicals, Inc.

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

DCE-MRI-Derived Volume Transfer Constant (Ktrans) and DWI Apparent Diffusion Coefficient as Predictive Markers of Short- and Long-Term Efficacy of Chemoradiotherapy in Patients With Esophageal Cancer.

PubMed

Ye, Zhi-Min; Dai, Shu-Jun; Yan, Feng-Qin; Wang, Lei; Fang, Jun; Fu, Zhen-Fu; Wang, Yue-Zhen

2018-01-01

This study aimed to evaluate both the short- and long-term efficacies of chemoradiotherapy in relation to the treatment of esophageal cancer . This was achieved through the use of dynamic contrast-enhanced magnetic resonance imaging-derived volume transfer constant and diffusion weighted imaging-derived apparent diffusion coefficient . Patients with esophageal cancer were assigned into the sensitive and resistant groups based on respective efficacies in chemoradiotherapy. Dynamic contrast-enhanced magnetic resonance imaging and diffusion weighted imaging were used to measure volume transfer constant and apparent diffusion coefficient, while computed tomography was used to calculate tumor size reduction rate. Pearson correlation analyses were conducted to analyze correlation between volume transfer constant, apparent diffusion coefficient, and the tumor size reduction rate. Receiver operating characteristic curve was constructed to analyze the short-term efficacy of volume transfer constant and apparent diffusion coefficient, while Kaplan-Meier curve was employed for survival rate analysis. Cox proportional hazard model was used for the risk factors for prognosis of patients with esophageal cancer. Our results indicated reduced levels of volume transfer constant, while increased levels were observed in ADC min , ADC mean , and ADC max following chemoradiotherapy. A negative correlation was determined between ADC min , ADC mean , and ADC max , as well as in the tumor size reduction rate prior to chemoradiotherapy, whereas a positive correlation was uncovered postchemoradiotherapy. Volume transfer constant was positively correlated with tumor size reduction rate both before and after chemoradiotherapy. The 5-year survival rate of patients with esophageal cancer having high ADC min , ADC mean , and ADC max and volume transfer constant before chemoradiotherapy was greater than those with respectively lower values. According to the Cox proportional hazard model, ADC mean , clinical stage, degree of differentiation, and tumor stage were all confirmed as being independent risk factors in regard to the prognosis of patients with EC. The findings of this study provide evidence suggesting that volume transfer constant and apparent diffusion coefficient as being tools allowing for the evaluation of both the short- and long-term efficacies of chemoradiotherapy esophageal cancer treatment.

Hydrodynamic effects on phase transition in active matter

NASA Astrophysics Data System (ADS)

Gidituri, Harinadha; Akella, V. S.; Panchagnula, Mahesh; Vedantam, Srikanth; Multiphase flow physics lab Team

2017-11-01

Organized motion of active (self-propelled) objects are ubiquitous in nature. The objective of this study to investigate the effect of hydrodynamics on the coherent structures in active and passive particle mixtures. We use a mesoscopic method Dissipative Particle Dynamics (DPD). The system shows three different states viz. meso-turbulent (disordered state), polar flock and vortical (ordered state) for different values of activity and volume fraction of active particles. From our numerical simulations we construct a phase diagram between activity co-efficient, volume fraction and viscosity of the passive fluid. Transition from vortical to polar is triggered by increasing the viscosity of passive fluid which causes strong short-range hydrodynamic interactions. However, as the viscosity of the fluid decreases, both vortical and meso-turbulent states transition to polar flock phase. We also calculated the diffusion co-efficients via mean square displacement (MSD) for passive and active particles. We observe ballistic and diffusive regimes in the present system.

Coastal Atmosphere and Sea Time Series (CoASTS)

NASA Technical Reports Server (NTRS)

Hooker, Stanford B. (Editor); Firestone, Elaine R. (Editor); Berthon, Jean-Francoise; Zibordi, Giuseppe; Doyle, John P.; Grossi, Stefania; vanderLinde, Dirk; Targa, Cristina; McClain, Charles R. (Technical Monitor)

2002-01-01

In this document, the first three years of a time series of bio-optical marine and atmospheric measurements are presented and analyzed. These measurements were performed from an oceanographic tower in the northern Adriatic Sea within the framework of the Coastal Atmosphere and Sea Time Series (CoASTS) project, an ocean color calibration and validation activity. The data set collected includes spectral measurements of the in-water apparent (diffuse attenuation coefficient, reflectance, Q-factor, etc.) and inherent (absorption and scattering coefficients) optical properties, as well as the concentrations of the main optical components (pigment and suspended matter concentrations). Clear seasonal patterns are exhibited by the marine quantities on which an appreciable short-term variability (on the order of a half day to one day) is superimposed. This short-term variability is well correlated with the changes in salinity at the surface resulting from the southward transport of freshwater coming from the northern rivers. Concentrations of chlorophyll alpha and total suspended matter span more than two orders of magnitude. The bio-optical characteristics of the measurement site pertain to both Case-I (about 64%) and Case-II (about 36%) waters, based on a relationship between the beam attenuation coefficient at 660nm and the chlorophyll alpha concentration. Empirical algorithms relating in-water remote sensing reflectance ratios and optical components or properties of interest (chlorophyll alpha, total suspended matter, and the diffuse attenuation coefficient) are presented.

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.

Counterion self-diffusion in polyelectrolyte solutions

NASA Astrophysics Data System (ADS)

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

1997-12-01

The self-diffusion coefficient of 0953-8984/9/50/019/img1, tetra-methylammonium 0953-8984/9/50/019/img2, tetra-ethylammonium 0953-8984/9/50/019/img3, tetra-propylammonium 0953-8984/9/50/019/img4 and tetra-butylammonium 0953-8984/9/50/019/img5 in solutions of the weak polymethacrylic acid (PMA) were measured with PFG NMR. No additional salt was present in any of the experiments. The polyion concentration and degree of neutralization were varied. The maximum relative counterion self-diffusion coefficient against polyion concentration, that was reported earlier, was observed for both alkali and tetra-alkylammonium 0953-8984/9/50/019/img6 counterions. We propose that the maximum is due to the combination of the obstruction by the polyion and the changing counterion distribution at increasing polyion concentration. An explanation of this proposal is offered in terms of the Poisson - Boltzmann - Smoluchowski (PBS) model for polyelectrolytes. Qualitative agreement of this model with experiment was found for the dependence of the counterion self-diffusion coefficient on the degree of neutralization of the polyion, on counterion radius and on polyion concentration, over a concentration range from 0.01 to 1 0953-8984/9/50/019/img7. Adaption of the theoretical obstruction, to fit the self-diffusion data of the solvent, also greatly improves the model predictions on the counterion self-diffusion.

Hepatocellular carcinoma: short-term reproducibility of apparent diffusion coefficient and intravoxel incoherent motion parameters at 3.0T.

PubMed

Kakite, Suguru; Dyvorne, Hadrien; Besa, Cecilia; Cooper, Nancy; Facciuto, Marcelo; Donnerhack, Claudia; Taouli, Bachir

2015-01-01

To evaluate short-term test-retest and interobserver reproducibility of IVIM (intravoxel incoherent motion) diffusion parameters and ADC (apparent diffusion coefficient) of hepatocellular carcinoma (HCC) and liver parenchyma at 3.0T. In this prospective Institutional Review Board (IRB)-approved study, 11 patients were scanned twice using a free-breathing single-shot echo-planar-imaging, diffusion-weighted imaging (DWI) sequence using 4 b values (b = 0, 50, 500, 1000 s/mm(2)) and IVIM DWI using 16 b values (0-800 s/mm(2)) at 3.0T. IVIM parameters (D: true diffusion coefficient, D*: pseudodiffusion coefficient, PF: perfusion fraction) and ADC (using 4 b and 16 b) were calculated. Short-term test-retest and interobserver reproducibility of IVIM parameters and ADC were assessed by measuring correlation coefficient, coefficient of variation (CV), and Bland-Altman limits of agreements (BA-LA). Fifteen HCCs were assessed in 10 patients. Reproducibility of IVIM metrics in HCC was poor for D* and PF (mean CV 60.6% and 37.3%, BA-LA: -161.6% to 135.3% and -66.2% to 101.0%, for D* and PF, respectively), good for D and ADC (CV 19.7% and <16%, BA-LA -57.4% to 36.3% and -38.2 to 34.1%, for D and ADC, respectively). Interobserver reproducibility was on the same order of test-retest reproducibility except for PF in HCC. Reproducibility of diffusion parameters was better in liver parenchyma compared to HCC. Poor reproducibility of D*/PF and good reproducibility for D/ADC were observed in HCC and liver parenchyma. These findings may have implications for trials using DWI in HCC. © 2014 Wiley Periodicals, Inc.

A model for self-diffusion of guanidinium-based ionic liquids: a molecular simulation study.

PubMed

Klähn, Marco; Seduraman, Abirami; Wu, Ping

2008-11-06

We propose a novel self-diffusion model for ionic liquids on an atomic level of detail. The model is derived from molecular dynamics simulations of guanidinium-based ionic liquids (GILs) as a model case. The simulations are based on an empirical molecular mechanical force field, which has been developed in our preceding work, and it relies on the charge distribution in the actual liquid. The simulated GILs consist of acyclic and cyclic cations that were paired with nitrate and perchlorate anions. Self-diffusion coefficients are calculated at different temperatures from which diffusive activation energies between 32-40 kJ/mol are derived. Vaporization enthalpies between 174-212 kJ/mol are calculated, and their strong connection with diffusive activation energies is demonstrated. An observed formation of cavities in GILs of up to 6.5% of the total volume does not facilitate self-diffusion. Instead, the diffusion of ions is found to be determined primarily by interactions with their immediate environment via electrostatic attraction between cation hydrogen and anion oxygen atoms. The calculated average time between single diffusive transitions varies between 58-107 ps and determines the speed of diffusion, in contrast to diffusive displacement distances, which were found to be similar in all simulated GILs. All simulations indicate that ions diffuse by using a brachiation type of movement: a diffusive transition is initiated by cleaving close contacts to a coordinated counterion, after which the ion diffuses only about 2 A until new close contacts are formed with another counterion in its vicinity. The proposed diffusion model links all calculated energetic and dynamic properties of GILs consistently and explains their molecular origin. The validity of the model is confirmed by providing an explanation for the variation of measured ratios of self-diffusion coefficients of cations and paired anions over a wide range of values, encompassing various ionic liquid classes as well as the simulated GILs. The proposed diffusion model facilitates the qualitative a priori prediction of the impact of ion modifications on the diffusive characteristics of new ionic liquids.

Kinetics of proton migration in liquid water.

PubMed

Chen, Hanning; Voth, Gregory A; Agmon, Noam

2010-01-14

We have utilized multistate empirical valence bond (MS-EVB3) simulations of protonated liquid water to calculate the relative mean-square displacement (MSD) and the history-independent time correlation function, c(t), of the hydrated proton center of excess charge (CEC) with respect to the water molecule on which it has initially resided. The MSD is nonlinear for the first 15 ps, suggesting that the relative diffusion coefficient increases from a small value, D(0), at short separations to its larger bulk value, D(infinity), at large separations. With the ensuing distance-dependent diffusion coefficient, D(r), the time dependence of both the MSD and c(t) agrees quantitatively with the solution of a diffusion equation for reversible geminate recombination. This suggests that the relative motion of the CEC is not independent from the nearby water molecules, in agreement with theoretical and experimental observations that large water clusters participate in the mechanism of proton mobility.

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.

Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules

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

Li, Derek D.; Greenfield, Michael L., E-mail: greenfield@egr.uri.edu

2014-01-21

The dynamics properties of a new “next generation” model asphalt system that represents SHRP AAA-1 asphalt using larger molecules than past models is studied using molecular simulation. The system contains 72 molecules distributed over 12 molecule types that range from nonpolar branched alkanes to polar resins and asphaltenes. Molecular weights range from 290 to 890 g/mol. All-atom molecular dynamics simulations conducted at six temperatures from 298.15 to 533.15 K provide a wealth of correlation data. The modified Kohlrausch-Williams-Watts equation was regressed to reorientation time correlation functions and extrapolated to calculate average rotational relaxation times for individual molecules. The rotational relaxationmore » rate of molecules decreased significantly with increasing size and decreasing temperature. Translational self-diffusion coefficients followed an Arrhenius dependence. Similar activation energies of ∼42 kJ/mol were found for all 12 molecules in the model system, while diffusion prefactors spanned an order of magnitude. Viscosities calculated directly at 533.15 K and estimated at lower temperatures using the Debye-Stokes-Einstein relationship were consistent with experimental data for asphalts. The product of diffusion coefficient and rotational relaxation time showed only small changes with temperature above 358.15 K, indicating rotation and translation that couple self-consistently with viscosity. At lower temperatures, rotation slowed more than diffusion.« less

MUTUAL DIFFUSION OF PAIRS OF RARE GASES AT DIFFERENT TEMPERATURES

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

Srivastava, B.N.; Srivastava, K.P.

1959-04-01

The eoefficient of mutual diffusion of the binary gas mixtures Ne--Ar, Ar--Krs and Ne--Kr has been determined at 0, 15, 30s and 45 C. Diffusion is allowed to take place between two diffusion bulbs through a precision capillary tube and samples of gas are withdrawn from one bulb at different times and analyzed by a differential conductivity analyzer. From the experimentally determined values of the diffusion coefficient at different temperatures the unlike interaction parameters for the above gas pairs have been calculated by two different methods on the Lennard-Jones I2:6 model. These values of the force parameters are found tomore » be in good agreement with those obtained from the usual combination rules and also from the thermal diffusion data following the method of Srivastava and Madan. These values are found to reproduce the experimental data on mutual diffusion quite satisfactorily. With Kelvin's method, these data have also been utilized to calculate the self-diffusion coefficient of neon, argons and krypton. (auth)« less

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.

NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions.

PubMed

Bai, Ruiliang; Basser, Peter J; Briber, Robert M; Horkay, Ferenc

2014-03-15

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca 2+ and Na + . Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na + on the mobility of water molecules was practically undetectable. By contrast, addition of Ca 2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced.

Effect of nonlinear absorption on self focusing of short laser pulse in a plasma

NASA Astrophysics Data System (ADS)

Kumar, Ashok

2012-06-01

Paraxial theory of self focusing of short pulse laser in a plasma under transient and saturating effects of nonlinearity and nonlinear absorption is developed. The absorption is averaged over the cross-section of the beam and is different for different time segments of the pulse. The electron temperature includes cumulative effect of previous history of temporal profile of pulse intensity, however, the ambipolar diffusion is taken to be faster than the heating time. The relaxation effect causes self-distortion of the pulse temporal profile where as the nonlinear absorption weakens self focusing. For the pulses of duration comparable to the electron ion collision time, the front part of the pulse gets defocused where as the latter part undergoes periodic self focusing.

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.

Reduced xenon diffusion for quantitative lung study--the role of SF(6)

NASA Technical Reports Server (NTRS)

Mair, R. W.; Hoffmann, D.; Sheth, S. A.; Wong, G. P.; Butler, J. P.; Patz, S.; Topulos, G. P.; Walsworth, R. L.

2000-01-01

The large diffusion coefficients of gases result in significant spin motion during the application of gradient pulses that typically last a few milliseconds in most NMR experiments. In restricted environments, such as the lung, this rapid gas diffusion can lead to violations of the narrow pulse approximation, a basic assumption of the standard Stejskal-Tanner NMR method of diffusion measurement. We therefore investigated the effect of a common, biologically inert buffer gas, sulfur hexafluoride (SF(6)), on (129)Xe NMR and diffusion. We found that the contribution of SF(6) to (129)Xe T(1) relaxation in a 1:1 xenon/oxygen mixture is negligible up to 2 bar of SF(6) at standard temperature. We also measured the contribution of SF(6) gas to (129)Xe T(2) relaxation, and found it to scale inversely with pressure, with this contribution approximately equal to 1 s for 1 bar SF(6) pressure and standard temperature. Finally, we found the coefficient of (129)Xe diffusion through SF(6) to be approximately 4.6 x 10(-6) m(2)s(-1) for 1 bar pressure of SF(6) and standard temperature, which is only 1.2 times smaller than the (129)Xe self diffusion coefficient for 1 bar (129)Xe pressure and standard temperature. From these measurements we conclude that SF(6) will not sufficiently reduce (129)Xe diffusion to allow accurate surface-area/volume ratio measurements in human alveoli using time-dependent gas diffusion NMR.

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.

Diffusion of multi-isotopic chemical species in molten silicates

NASA Astrophysics Data System (ADS)

Watkins, James M.; Liang, Yan; Richter, Frank; Ryerson, Frederick J.; DePaolo, Donald J.

2014-08-01

Diffusion experiments in a simplified Na2O-CaO-SiO2 liquid system are used to develop a general formulation for the fractionation of Ca isotopes during liquid-phase diffusion. Although chemical diffusion is a well-studied process, the mathematical description of the effects of diffusion on the separate isotopes of a chemical element is surprisingly underdeveloped and uncertain. Kinetic theory predicts a mass dependence on isotopic mobility, but it is unknown how this translates into a mass dependence on effective binary diffusion coefficients, or more generally, the chemical diffusion coefficients that are housed in a multicomponent diffusion matrix. Our experiments are designed to measure Ca mobility, effective binary diffusion coefficients, the multicomponent diffusion matrix, and the effects of chemical diffusion on Ca isotopes in a liquid of single composition. We carried out two chemical diffusion experiments and one self-diffusion experiment, all at 1250 °C and 0.7 GPa and using a bulk composition for which other information is available from the literature. The self-diffusion experiment is used to determine the mobility of Ca in the absence of diffusive fluxes of other liquid components. The chemical diffusion experiments are designed to determine the effect on Ca isotope fractionation of changing the counter-diffusing component from fast-diffusing Na2O to slow-diffusing SiO2. When Na2O is the main counter-diffusing species, CaO diffusion is fast and larger Ca isotopic effects are generated. When SiO2 is the main counter-diffusing species, CaO diffusion is slow and smaller Ca isotopic effects are observed. In both experiments, the liquid is initially isotopically homogeneous, and during the experiment Ca isotopes become fractionated by diffusion. The results are used as a test of a new general expression for the diffusion of isotopes in a multicomponent liquid system that accounts for both self diffusion and the effects of counter-diffusing species. Our results show that (1) diffusive isotopic fractionations depend on the direction of diffusion in composition space, (2) diffusive isotopic fractionations scale with effective binary diffusion coefficient, as previously noted by Watkins et al. (2011), (3) self-diffusion is not decoupled from chemical diffusion, (4) self diffusion can be faster than or slower than chemical diffusion and (5) off-diagonal terms in the chemical diffusion matrix have isotopic mass-dependence. The results imply that relatively large isotopic fractionations can be generated by multicomponent diffusion even in the absence of large concentration gradients of the diffusing element. The new formulations for isotope diffusion can be tested with further experimentation and provide an improved framework for interpreting mass-dependent isotopic variations in natural liquids.

Pulsed field gradient magic angle spinning NMR self-diffusion measurements in liquids

NASA Astrophysics Data System (ADS)

Viel, Stéphane; Ziarelli, Fabio; Pagès, Guilhem; Carrara, Caroline; Caldarelli, Stefano

2008-01-01

Several investigations have recently reported the combined use of pulsed field gradient (PFG) with magic angle spinning (MAS) for the analysis of molecular mobility in heterogeneous materials. In contrast, little attention has been devoted so far to delimiting the role of the extra force field induced by sample rotation on the significance and reliability of self-diffusivity measurements. The main purpose of this work is to examine this phenomenon by focusing on pure liquids for which its impact is expected to be largest. Specifically, we show that self-diffusion coefficients can be accurately determined by PFG MAS NMR diffusion measurements in liquids, provided that specific experimental conditions are met. First, the methodology to estimate the gradient uniformity and to properly calibrate its absolute strength is briefly reviewed and applied on a MAS probe equipped with a gradient coil aligned along the rotor spinning axis, the so-called 'magic angle gradient' coil. Second, the influence of MAS on the outcome of PFG MAS diffusion measurements in liquids is investigated for two distinct typical rotors of different active volumes, 12 and 50 μL. While the latter rotor led to totally unreliable results, especially for low viscosity compounds, the former allowed for the determination of accurate self-diffusion coefficients both for fast and slowly diffusing species. Potential implications of this work are the possibility to measure accurate self-diffusion coefficients of sample-limited mixtures or to avoid radiation damping interferences in NMR diffusion measurements. Overall, the outlined methodology should be of interest to anyone who strives to improve the reliability of MAS diffusion studies, both in homogeneous and heterogeneous media.

Nonlinear Landau damping in the ionosphere

NASA Technical Reports Server (NTRS)

Kiwamoto, Y.; Benson, R. F.

1978-01-01

A model is presented to explain the non-resonant waves which give rise to the diffuse resonance observed near 3/2 f sub H by the Alouette and ISIS topside sounders, where f sub H is the ambient electron cyclotron frequency. In a strictly linear analysis, these instability driven waves will decay due to Landau damping on a time scale much shorter than the observed time duration of the diffuse resonance. Calculations of the nonlinear wave particle coupling coefficients, however, indicate that the diffuse resonance wave can be maintained by the nonlinear Landau damping of the sounder stimulated 2f sub H wave. The time duration of the diffuse resonance is determined by the transit time of the instability generated and nonlinearly maintained diffuse resonance wave from the remote short lived hot region back to the antenna. The model is consistent with the Alouette/ISIS observations, and clearly demonstrates the existence of nonlinear wave-particle interactions in the ionosphere.

Unexpected perturbations training improves balance control and voluntary stepping times in older adults - a double blind randomized control trial.

PubMed

Kurz, Ilan; Gimmon, Yoav; Shapiro, Amir; Debi, Ronen; Snir, Yoram; Melzer, Itshak

2016-03-04

Falls are common among elderly, most of them occur while slipping or tripping during walking. We aimed to explore whether a training program that incorporates unexpected loss of balance during walking able to improve risk factors for falls. In a double-blind randomized controlled trial 53 community dwelling older adults (age 80.1±5.6 years), were recruited and randomly allocated to an intervention group (n = 27) or a control group (n = 26). The intervention group received 24 training sessions over 3 months that included unexpected perturbation of balance exercises during treadmill walking. The control group performed treadmill walking with no perturbations. The primary outcome measures were the voluntary step execution times, traditional postural sway parameters and Stabilogram-Diffusion Analysis. The secondary outcome measures were the fall efficacy Scale (FES), self-reported late life function (LLFDI), and Performance-Oriented Mobility Assessment (POMA). Compared to control, participation in intervention program that includes unexpected loss of balance during walking led to faster Voluntary Step Execution Times under single (p = 0.002; effect size [ES] =0.75) and dual task (p = 0.003; [ES] = 0.89) conditions; intervention group subjects showed improvement in Short-term Effective diffusion coefficients in the mediolateral direction of the Stabilogram-Diffusion Analysis under eyes closed conditions (p = 0.012, [ES] = 0.92). Compared to control there were no significant changes in FES, LLFDI, and POMA. An intervention program that includes unexpected loss of balance during walking can improve voluntary stepping times and balance control, both previously reported as risk factors for falls. This however, did not transferred to a change self-reported function and FES. ClinicalTrials.gov NCT01439451 .

Concentration dependence of lipopolymer self-diffusion in supported bilayer membranes

PubMed Central

Zhang, Huai-Ying; Hill, Reghan J.

2011-01-01

Self-diffusion coefficients of poly(ethylene glycol)2k-derivatized lipids (DSPE-PEG2k-CF) in glass-supported DOPC phospholipid bilayers are ascertained from quantitative fluorescence recovery after photobleaching (FRAP). We developed a first-order reaction–diffusion model to ascertain the bleaching constant, mobile fraction and lipopolymer self-diffusion coefficient Ds at concentrations in the range c ≈ 0.5–5 mol%. In contrast to control experiments with 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl) (ammonium salt) (DOPE-NBD) in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), the lipopolymer self-diffusion coefficient decreases monotonically with increasing concentration, without a distinguishing mushroom-to-brush transition. Our data yield a correlation Ds = D0/(1 + αc), where D0 ≈ 3.36 µm2 s−1 and α ≈ 0.56 (with c expressed as a mole percent). Interpreting the dilute limit with the Scalettar–Abney–Owicki statistical mechanical theory for transmembrane proteins yields an effective disc radius ae ≈ 2.41 nm. On the other hand, the Bussell–Koch–Hammer theory, which includes hydrodynamic interactions, yields ae ≈ 2.92 nm. As expected, both measures are smaller than the Flory radius of the 2 kDa poly(ethylene glycol) (PEG) chains, RF ≈ 3.83 nm, and significantly larger than the nominal radius of the phospholipid heads, al ≈ 0.46 nm. The diffusion coefficient at infinite dilution D0 was interpreted using the Evans–Sackmann theory, furnishing an inter-leaflet frictional drag coefficient bs ≈ 1.33 × 108 N s m−3. Our results suggest that lipopolymer interactions are dominated by the excluded volume of the PEG-chain segments, with frictional drag dominated by the two-dimensional bilayer hydrodynamics. PMID:20504804

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.

Predicting First Traversal Times for Virions and Nanoparticles in Mucus with Slowed Diffusion

PubMed Central

Erickson, Austen M.; Henry, Bruce I.; Murray, John M.; Klasse, Per Johan; Angstmann, Christopher N.

2015-01-01

Particle-tracking experiments focusing on virions or nanoparticles in mucus have measured mean-square displacements and reported diffusion coefficients that are orders of magnitude smaller than the diffusion coefficients of such particles in water. Accurate description of this subdiffusion is important to properly estimate the likelihood of virions traversing the mucus boundary layer and infecting cells in the epithelium. However, there are several candidate models for diffusion that can fit experimental measurements of mean-square displacements. We show that these models yield very different estimates for the time taken for subdiffusive virions to traverse through a mucus layer. We explain why fits of subdiffusive mean-square displacements to standard diffusion models may be misleading. Relevant to human immunodeficiency virus infection, using computational methods for fractional subdiffusion, we show that subdiffusion in normal acidic mucus provides a more effective barrier against infection than previously thought. By contrast, the neutralization of the mucus by alkaline semen, after sexual intercourse, allows virions to cross the mucus layer and reach the epithelium in a short timeframe. The computed barrier protection from fractional subdiffusion is some orders of magnitude greater than that derived by fitting standard models of diffusion to subdiffusive data. PMID:26153713

Thermodynamic assessment of oxygen diffusion in non-stoichiometric UO2±x from experimental data and Frenkel pair modeling

NASA Astrophysics Data System (ADS)

Berthinier, C.; Rado, C.; Chatillon, C.; Hodaj, F.

2013-02-01

The self and chemical diffusion of oxygen in the non-stoichiometric domain of the UO2 compound is analyzed from the point of view of experimental determinations and modeling from Frenkel pair defects. The correlation between the self-diffusion and the chemical diffusion coefficients is analyzed using the Darken coefficient calculated from a thermodynamic description of the UO2±x phase. This description was obtained from an optimization of thermodynamic and phase diagram data and modeling with different point defects, including the Frenkel pair point defects. The proposed diffusion coefficients correspond to the 300-2300 K temperature range and to the full composition range of the non stoichiometric UO2 compound. These values will be used for the simulation of the oxidation and ignition of the uranium carbide in different oxygen atmospheres that starts at temperatures as low as 400 K.

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.

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.

Effect of hydrodynamic interactions on the diffusion of integral membrane proteins: diffusion in plasma membranes.

PubMed Central

Bussell, S J; Koch, D L; Hammer, D A

1995-01-01

Tracer diffusion coefficients of integral membrane proteins (IMPs) in intact plasma membranes are often much lower than those found in blebbed, organelle, and reconstituted membranes. We calculate the contribution of hydrodynamic interactions to the tracer, gradient, and rotational diffusion of IMPs in plasma membranes. Because of the presence of immobile IMPs, Brinkman's equation governs the hydrodynamics in plasma membranes. Solutions of Brinkman's equation enable the calculation of short-time diffusion coefficients of IMPs. There is a large reduction in particle mobilities when a fraction of them is immobile, and as the fraction increases, the mobilities of the mobile particles continue to decrease. Combination of the hydrodynamic mobilities with Monte Carlo simulation results, which incorporate excluded area effects, enable the calculation of long-time diffusion coefficients. We use our calculations to analyze results for tracer diffusivities in several different systems. In erythrocytes, we find that the hydrodynamic theory, when combined with excluded area effects, closes the gap between existing theory and experiment for the mobility of band 3, with the remaining discrepancy likely due to direct obstruction of band 3 lateral mobility by the spectrin network. In lymphocytes, the combined hydrodynamic-excluded area theory provides a plausible explanation for the reduced mobility of sIg molecules induced by binding concanavalin A-coated platelets. However, the theory does not explain all reported cases of "anchorage modulation" in all cell types in which receptor mobilities are reduced after binding by concanavalin A-coated platelets. The hydrodynamic theory provides an explanation of why protein lateral mobilities are restricted in plasma membranes and why, in many systems, deletion of the cytoplasmic tail of a receptor has little effect on diffusion rates. However, much more data are needed to test the theory definitively. We also predict that gradient and tracer diffusivities are the same to leading order. Finally, we have calculated rotational diffusion coefficients in plasma membranes. They decrease less rapidly than translational diffusion coefficients with increasing protein immobilization, and the results agree qualitatively with the limited experimental data available. PMID:7612825

Bond lifetime and diffusion coefficient in colloids with short-range interactions.

PubMed

Ndong Mintsa, E; Germain, Ph; Amokrane, S

2015-03-01

We use molecular dynamics simulations to study the influence of short-range structures in the interaction potential between hard-sphere-like colloidal particles. Starting from model potentials and effective potentials in binary mixtures computed from the Ornstein-Zernike equations, we investigate the influence of the range and strength of a possible tail beyond the usual core repulsion or the presence of repulsive barriers. The diffusion coefficient and mean "bond" lifetimes are used as indicators of the effect of this structure on the dynamics. The existence of correlations between the variations of these quantities with the physical parameters is discussed to assess the interpretation of dynamics slowing down in terms of long-lived bonds. We also discuss the question of a universal behaviour determined by the second virial coefficient B ((2)) and the interplay of attraction and repulsion. While the diffusion coefficient follows the B ((2)) law for purely attractive tails, this is no longer true in the presence of repulsive barriers. Furthermore, the bond lifetime shows a dependence on the physical parameters that differs from that of the diffusion coefficient. This raises the question of the precise role of bonds on the dynamics slowing down in colloidal gels.

Theory of Transport of Long Polymer Molecules through Carbon Nanotube Channels

NASA Technical Reports Server (NTRS)

Wei, Chenyu; Srivastava, Deepak

2003-01-01

A theory of transport of long chain polymer molecules through carbon nanotube (CNT) channels is developed using Fokker-Planck equation and direct molecular dynamics (MD) simulations. The mean transport or translocation time tau is found to depend on the chemical potential energy, entropy and diffusion coefficient. A power law dependence tau approx. N(sup 2)is found where N is number of monomers in a molecule. For 10(exp 5)-unit long polyethylene molecules, tau is estimated to be approx. 1micro-s. The diffusion coefficient of long polymer molecules inside CNTs, like that of short ones, are found to be few orders of magnitude larger than in ordinary silicate based zeolite systems.

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.

Self-diffusion of charged colloidal tracer spheres in transparent porous glass media: Effect of ionic strength and pore size

NASA Astrophysics Data System (ADS)

Kluijtmans, Sebastiaan G. J. M.; de Hoog, Els H. A.; Philipse, Albert P.

1998-05-01

The influence of charge on diffusion in porous media was studied for fluorescent colloidal silica spheres diffusing in a porous glass medium. The bicontinuous porous silica glasses were optically matched with an organic solvent mixture in which both glass and tracers are negatively charged. Using fluorescence recovery after photobleaching, the long-time self-diffusion coefficient DSL of the confined silica particles was monitored in situ as a function of the ionic strength and particle to pore size ratio. At high salt concentration DSL reaches a relatively high plateau value, which depends on the particle to pore size ratio. This plateau value is unexpectedly higher than the value found for uncharged silica spheres in these porous glasses, but still significantly smaller than the free particle bulk diffusion coefficient of the silica spheres. At low salt concentration DSL reduces markedly, up to the point where colloids are nearly immobilized. This peculiar retardation probably originates from potential traps and barriers at pore intersections due to deviations from cylinder symmetry in the double layer interactions between tracers and pore walls. This indicates that diffusion of charged particles in tortuous porous media may be very different from transport in long capillaries without such intersections.

NMR Water Self–Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions

PubMed Central

Bai, Ruiliang; Basser, Peter J.; Briber, Robert M.; Horkay, Ferenc

2013-01-01

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca2+ and Na+. Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na+ on the mobility of water molecules was practically undetectable. By contrast, addition of Ca2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced. PMID:24409001

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.

Brownian motion of arbitrarily shaped particles in two dimensions.

PubMed

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan V; Sun, Kai; Wei, Qi-Huo

2014-11-25

We implement microfabricated boomerang particles with unequal arm lengths as a model for nonsymmetric particles and study their Brownian motion in a quasi-two-dimensional geometry by using high-precision single-particle motion tracking. We show that because of the coupling between translation and rotation, the mean squared displacements of a single asymmetric boomerang particle exhibit a nonlinear crossover from short-time faster to long-time slower diffusion, and the mean displacements for fixed initial orientation are nonzero and saturate out at long times. The measured anisotropic diffusion coefficients versus the tracking point position indicate that there exists one unique point, i.e., the center of hydrodynamic stress (CoH), at which all coupled diffusion coefficients vanish. This implies that in contrast to motion in three dimensions where the CoH exists only for high-symmetry particles, the CoH always exists for Brownian motion in two dimensions. We develop an analytical model based on Langevin theory to explain the experimental results and show that among the six anisotropic diffusion coefficients only five are independent because the translation-translation coupling originates from the translation-rotation coupling. Finally, we classify the behavior of two-dimensional Brownian motion of arbitrarily shaped particles into four groups based on the particle shape symmetry group and discussed potential applications of the CoH in simplifying understanding of the circular motions of microswimmers.

Fluid transport in partially filled porous sol-gel silica glass

NASA Astrophysics Data System (ADS)

D'orazio, Franco; Bhattacharja, Sankar; Halperin, William P.; Gerhardt, Rosario

1990-10-01

Measurements of low-frequency ac electrical conductivity of a porous glass filled with different amounts of a saline solution are compared with the self-diffusion coefficient of water measured in the same sample, reported previously [F. D'Orazio et al., Phys. Rev. Lett. 63, 43 (1989)]. The two transport parameters are consistently related through the Einstein relation under saturation conditions. A more complex picture is revealed for the unsaturated sample, since the presence of a vapor phase enhances the self-diffusion coefficient. Conductivity experiments allow an independent assessment of the contribution to self-diffusion from the liquid phase. However, a comparison between the two experiments indicates that the role of the vapor phase is not well understood.

HIGH-TEMPERATURE, SHORT-TIME SULFATION OF CALCIUM- BASED SORBENTS. 1. THEORETICAL SULFATION MODEL

EPA Science Inventory

A mathematical model for the sulfation of CaO is developed around the overlapping grain concept. The potential influence of high mass-transfer rates from simultaneous calcination of CaCO3 or Ca(OH)2 is incorporated in the mass-transfer coefficient for SO2 diffusion to the partic...

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

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

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

2010-08-15

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

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

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

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

PubMed

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

2002-06-01

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

Is the wall of a cellulose fiber saturated with liquid whether or not permeable with CO2 dissolved molecules? Application to bubble nucleation in champagne wines.

PubMed

Liger-Belair, Gérard; Topgaard, Daniel; Voisin, Cédric; Jeandet, Philippe

2004-05-11

In this paper, the transversal diffusion coefficient D perpendicular of CO2 dissolved molecules through the wall of a hydrated cellulose fiber was approached, from the liquid bulk diffusion coefficient of CO2 dissolved molecules modified by an obstruction factor. The porous network between the cellulose microfibrils of the fiber wall was assumed being saturated with liquid. We retrieved information from previous NMR experiments on the self-diffusion of water in cellulose fibers to reach an order of magnitude for the transversal diffusion coefficient of CO2 molecules through the fiber wall. A value of about D perpendicular approximately 0.2D0 was proposed, D0 being the diffusion coefficient of CO2 molecules in the liquid bulk. Because most of bubble nucleation sites in a glass poured with carbonated beverage are cellulose fibers cast off from paper or cloth which floated from the surrounding air, or remaining from the wiping process, this result directly applies to the kinetics of carbon dioxide bubble formation from champagne and sparkling wines. If the cellulose fiber wall was impermeable with regard to CO2 dissolved molecules, it was suggested that the kinetics of bubbling would be about three times less than it is.

Modelling oxygen self-diffusion in UO 2 under pressure

DOE PAGES

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

2015-10-22

Access to values for oxygen self-diffusion over a range of temperatures and pressures in UO 2 is important to nuclear fuel applications. Here, elastic and expansivity data are used in the framework of a thermodynamic model, the cBΩ model, to derive the oxygen self-diffusion coefficient in UO 2 over a range of pressures (0–10 GPa) and temperatures (300–1900 K). Furthermore, the significant reduction in oxygen self-diffusion as a function of increasing hydrostatic pressure, and the associated increase in activation energy, is identified.

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

PubMed Central

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

2012-01-01

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

Pitch-angle diffusion of electrons through growing and propagating along a magnetic field electromagnetic wave in Earth's radiation belts

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

Choi, C.-R., E-mail: crchoi@kaist.ac.kr; Dokgo, K.; Min, K.-W.

The diffusion of electrons via a linearly polarized, growing electromagnetic (EM) wave propagating along a uniform magnetic field is investigated. The diffusion of electrons that interact with the growing EM wave is investigated through the autocorrelation function of the parallel electron acceleration in several tens of electron gyration timescales, which is a relatively short time compared with the bounce time of electrons between two mirror points in Earth's radiation belts. Furthermore, the pitch-angle diffusion coefficient is derived for the resonant and non-resonant electrons, and the effect of the wave growth on the electron diffusion is discussed. The results can bemore » applied to other problems related to local acceleration or the heating of electrons in space plasmas, such as in the radiation belts.« less

Diffusion in thorium carbide: A first-principles study

NASA Astrophysics Data System (ADS)

Pérez Daroca, D.; Llois, A. M.; Mosca, H. O.

2015-12-01

The prediction of the behavior of Th compounds under irradiation is an important issue for the upcoming Generation-IV nuclear reactors. The study of self-diffusion and hetero-diffusion is a central key to fulfill this goal. As a first approach, we obtained, by means of first-principles methods, migration and activation energies of Th and C atoms self-diffusion and diffusion of He atoms in ThC. We also calculate diffusion coefficients as a function of temperature.

A monte carlo study of restricted diffusion: Implications for diffusion MRI of prostate cancer.

PubMed

Gilani, Nima; Malcolm, Paul; Johnson, Glyn

2017-04-01

Diffusion MRI is used frequently to assess prostate cancer. The prostate consists of cellular tissue surrounding fluid filled ducts. Here, the diffusion properties of the ductal fluid alone were studied. Monte Carlo simulations were used to investigate ductal residence times to determine whether ducts can be regarded as forming a separate compartment and whether ductal radius could determine the Apparent Diffusion Coefficient (ADC) of the ductal fluid. Random walks were simulated in cavities. Average residence times were estimated for permeable cavities. Signal reductions resulting from application of a Stejskal-Tanner pulse sequence were calculated in impermeable cavities. Simulations were repeated for cavities of different radii and different diffusion times. Residence times are at least comparable with diffusion times even in relatively high grade tumors. ADCs asymptotically approach theoretical limiting values. At large radii and short diffusion times, ADCs are similar to free diffusion. At small radii and long diffusion times, ADCs are reduced toward zero, and kurtosis approaches a value of -1.2. Restricted diffusion in cavities of similar sizes to prostate ducts may reduce ductal ADCs. This may contribute to reductions in total ADC seen in prostate cancer. Magn Reson Med 77:1671-1677, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Lateral diffusion in model membranes is independent of the size of the hydrophobic region of molecules.

PubMed Central

Balcom, B J; Petersen, N O

1993-01-01

We have systematically investigated the probe size and shape dependence of lateral diffusion in model dimyristoyl phosphatidylcholine membranes. Linear hydrophobic polymers, which differ in length by an order of magnitude, were used to explore the effect on the lateral diffusion coefficient of hydrodynamic restrictions in the bilayer interior. The polymers employed are isoprenoid alcohols--citronellol, solanesol, and dolichol. Tracer lateral diffusion coefficients were measured by fluorescence photobleaching recovery. Despite the large difference in lengths, the nitrobenzoxadiazole labelled alcohols all diffuse at the rate of lipid self-diffusion (5.0 x 10(-12) m2 s-1, 29 degrees C) in the liquid crystal phase. Companion measurements in isotropic polymer solution, in gel phase lipid membranes and with nonpolar fluorescent polyaromatic hydrocarbons, show a marked dependence of the lateral diffusion coefficient on the probe molecule size. Our results in the liquid crystal phase are in accord with free area theory which asserts that lateral diffusion in the membrane is restricted by the surface-free area. Probe molecules which are significantly longer than the host phospholipid, seven times longer in the case of dolichol, are still restricted in their lateral motion by the surface properties of the bilayer in the liquid crystal phase. Fluorescence quenching experiments indicate that the nitrobenzoxadiazole label does not reside at the aqueous interface, although it must reside in close proximity according to the diffusion measurements. PMID:8218892

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.

Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: numerical study.

PubMed

Nardecchia, Ilaria; Spinelli, Lionel; Preto, Jordane; Gori, Matteo; Floriani, Elena; Jaeger, Sebastien; Ferrier, Pierre; Pettini, Marco

2014-08-01

The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is shown that when the particles are uniformly distributed throughout the accessible space, the self-diffusion coefficient is always lowered by the considered interparticle interactions, irrespective of their attractive or repulsive character. This fact is also confirmed by a simple model to compute the correction to the Brownian diffusion coefficient due to the interactions among the particles. These interactions are also responsible for the onset of dynamical chaos and an associated chaotic diffusion which still follows an Einstein-Fick-like law for the mean-square displacement as a function of time. Transitional phenomena are observed for Coulomb-electrostatic (repulsive) and dipole-electrodynamic (attractive) interactions considered both separately and in competition. The outcomes reported in this paper clearly indicate a feasible experimental method to probe the activation of resonant electrodynamic interactions among biomolecules.

Interface Defect States and Charge Transport Properties in Low-Cost Photovoltaic Devices made from Scalable Deposition Methods

NASA Astrophysics Data System (ADS)

Marin, Andrew; Munoz-Rojas, David; Iza, Diana; Gershon, Talia; MacManus-Driscoll, Judith

2011-03-01

In-plane (parallel to the substrate) polymer diffusion at and near interfaces has significant implications for polymeric surfactants used in tertiary oil recovery, exfoliation of clay sheets in polymer nano-composites, and several other high technology applications. Here, we report a study on the in-plane diffusion of whole polymer chains confined between interfaces using fluorescence recovery after photobleaching. Adapted from quantitative biology, FRAP provides a platform to independently study the effect of temperature, molecular weight, and film thickness on in-plane diffusion of polymers confined between interfaces. Fluorescently labeled polymers were synthesized, spin coated onto quartz substrates and the self-diffusion coefficient was measured by irreversibly photobleaching fluorophores in a pre-defined pattern and monitoring recovery of fluorescence over time. Preliminary results indicate that for thick films the diffusion coefficient is consistent with bulk values. The authors would like to thank the Gates-Cambridge Trust and the International Copper Association.

The effect of recombination under short-circuit conditions on the determination of charge transport properties in nanostructured photoelectrodes.

PubMed

Villanueva-Cab, J; Anta, J A; Oskam, G

2016-01-28

We report on the commonly unaccounted for process of recombination under short-circuit conditions in nanostructured photoelectrodes with special attention to the charge collection efficiency. It is observed that when recombination under short circuit conditions is significant, small perturbation methods overestimate the charge-collection efficiency, which is related to the inaccurate determination of the electron diffusion coefficient and diffusion length.

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.

Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

PubMed Central

Skolnick, Jeffrey

2016-01-01

An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes. PMID:27634243

Nonmonotonic diffusion in crowded environments

PubMed Central

Putzel, Gregory Garbès; Tagliazucchi, Mario; Szleifer, Igal

2015-01-01

We study the diffusive motion of particles among fixed spherical crowders. The diffusers interact with the crowders through a combination of a hard-core repulsion and a short-range attraction. The long-time effective diffusion coefficient of the diffusers is found to depend non-monotonically on the strength of their attraction to the crowders. That is, for a given concentration of crowders, a weak attraction to the crowders enhances diffusion. We show that this counterintuitive fact can be understood in terms of the mesoscopic excess chemical potential landscape experienced by the diffuser. The roughness of this excess chemical potential landscape quantitatively captures the nonmonotonic dependence of the diffusion rate on the strength of crowder-diffuser attraction; thus it is a purely static predictor of dynamic behavior. The mesoscopic view given here provides a unified explanation for enhanced diffusion effects that have been found in various systems of technological and biological interest. PMID:25302920

Self-diffusion in a stochastically heated two-dimensional dusty plasma

NASA Astrophysics Data System (ADS)

Sheridan, T. E.

2016-09-01

Diffusion in a two-dimensional dusty plasma liquid (i.e., a Yukawa liquid) is studied experimentally. The dusty plasma liquid is heated stochastically by a surrounding three-dimensional toroidal dusty plasma gas which acts as a thermal reservoir. The measured dust velocity distribution functions are isotropic Maxwellians, giving a well-defined kinetic temperature. The mean-square displacement for dust particles is found to increase linearly with time, indicating normal diffusion. The measured diffusion coefficients increase approximately linearly with temperature. The effective collision rate is dominated by collective dust-dust interactions rather than neutral gas drag, and is comparable to the dusty-plasma frequency.

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

PubMed

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

2010-09-10

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

The molecular basis of the solution properties of hyaluronan investigated by confocal fluorescence recovery after photobleaching.

PubMed Central

Gribbon, P; Heng, B C; Hardingham, T E

1999-01-01

Hyaluronan (HA) is a highly hydrated polyanion, which is a network-forming and space-filling component in the extracellular matrix of animal tissues. Confocal fluorescence recovery after photobleaching (confocal-FRAP) was used to investigate intramolecular hydrogen bonding and electrostatic interactions in hyaluronan solutions. Self and tracer lateral diffusion coefficients within hyaluronan solutions were measured over a wide range of concentrations (c), with varying electrolyte and at neutral and alkaline pH. The free diffusion coefficient of fluoresceinamine-labeled HA of 500 kDa in PBS was 7.9 x 10(-8) cm(2) s(-1) and of 830 kDa HA was 5.6 x 10(-8) cm(2) s(-1). Reductions in self- and tracer-diffusion with c followed a stretched exponential model. Electrolyte-induced polyanion coil contraction and destiffening resulted in a 2.8-fold increase in self-diffusion between 0 and 100 mM NaCl. Disruption of hydrogen bonds by strong alkali (0.5 M NaOH) resulted in further larger increases in self- and tracer-diffusion coefficients, consistent with a more dynamic and permeable network. Concentrated hyaluronan solution properties were attributed to hydrodynamic and entanglement interactions between domains. There was no evidence of chain-chain associations. At physiological electrolyte concentration and pH, the greatest contribution to the intrinsic stiffness of hyaluronan appeared to be due to hydrogen bonds between adjacent saccharides. PMID:10512840

Influence of definition of impeller-vaneless diffuser boundary on physical validity of numerical simulations of viscid flow in the vaneless diffuser of a centrifugal compressor: A short review of case studies

NASA Astrophysics Data System (ADS)

Kabalyk, K.; Kryllowicz, W.

2017-09-01

The study aims to work out a set of recommendations for setting a proper distance between the trailing edge of impeller and the interface boundary, which on the one hand would not be too large to overpredict the impeller efficiency and not too short to introduce artificial wake-like flow structures at diffuser inlet on the other. Three individual two-element stages belonging to three different types known as medium- and low-flow coefficient stages are studied. Besides of the design flow coefficient, the focus is on the influence of impeller tip Mach number on the optimal location of the boundary.

Ionic conduction and self-diffusion near infinitesimal concentration in lithium salt-organic solvent electrolytes

NASA Astrophysics Data System (ADS)

Aihara, Yuichi; Sugimoto, Kyoko; Price, William S.; Hayamizu, Kikuko

2000-08-01

The Debye-Hückel-Onsager and Nernst-Einstein equations, which are based on two different conceptual approaches, constitute the most widely used equations for relating ionic conduction to ionic mobility. However, both of these classical (simple) equations are predictive of ionic conductivity only at very low salt concentrations. In the present work the ionic conductivity of four organic solvent-lithium salt-based electrolytes were measured. These experimental conductivity values were then contrasted with theoretical values calculated using the translational diffusion (also known as self-diffusion or intradiffusion) coefficients of all of the species present obtained using pulsed-gradient spin-echo (1H, 19F and 7Li) nuclear magnetic resonance self-diffusion measurements. The experimental results verified the applicability of both theoretical approaches at very low salt concentrations for these particular systems as well as helping to clarify the reasons for the divergence between theory and experiment. In particular, it was found that the correspondence between the Debye-Hückel-Onsager equation and experimental values could be improved by using the measured solvent self-diffusion values to correct for salt-induced changes in the solution viscosity. The concentration dependence of the self-diffusion coefficients is discussed in terms of the Jones-Dole equation.

Etude de la physico-chime d'un magnetoplasma de chlore pour la gravure sous-micrometrique

NASA Astrophysics Data System (ADS)

Pauna, Olivier Daniel

The aim of this thesis is to achieve a better understanding of physical and chemical phenomena occurring in a high-density plasma designed for sub-micron etching of thin films. The plasma is produced in chlorine by means of an electromagnetic surface wave and it can be confined by a uniform static magnetic field. The flexibility offered by the reactor in terms of operating conditions makes possible a parametric study of the influence of the magnetic confinement on the plasma characteristics. Thus, we have examined the plasma properties by means of several diagnostics techniques, including electrostatic probes, laser photodetachment of negative ions, ion acoustic wave propagation and optical emission spectroscopy. First, we investigated the influence of the operating conditions on the spatial properties of the plasma; this includes electric characteristics (electrons, positive and negative ions) as well as chemical characteristics (reactive neutrals). Second, we studied the impact of the reactor aspect ratio (i.e. reactor length/radius ratio) on both electrical and chemical characteristics. Together with these experimental studies, we have developed a bidimensional fluid model, by solving self-consistently the first two moments of Bolzmann equation and Poisson's equation. Using a semi-implicit scheme, it was possible to maintain a short computation time and to use this model to investigate a diffusion plasma in an electropositive gas. We were thus able to estimate the value of the diffusion coefficient in the direction perpendicular to the magnetic field. The results thus obtained are in good qualitative agreement with the diffusion coefficient proposed by Liebermann and Lichtenberg.

Diffusion via space discretization method to study the concentration dependence of self-diffusivity under confinement

NASA Astrophysics Data System (ADS)

Sant, Marco; Papadopoulos, George K.; Theodorou, Doros N.

2010-04-01

The concentration dependence of self-diffusivity is investigated by means of a novel method, extending our previously developed second-order Markov process model to periodic media. Introducing the concept of minimum-crossing surface, we obtain a unique decomposition of the self-diffusion coefficient into two parameters with specific physical meanings. Two case studies showing a maximum in self-diffusivity as a function of concentration are investigated, along with two cases where such a maximum cannot be present. Subsequently, the method is applied to the large cavity pore network of the ITQ-1 (Mobil tWenty tWo, MWW) zeolite for methane (displaying a maximum in self-diffusivity) and carbon dioxide (no maximum), explaining the diffusivity trend on the basis of the evolution of the model parameters as a function of concentration.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

PubMed

Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V

2014-08-21

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

Activation volumes of oxygen self-diffusion in fluorite structured oxides

DOE PAGES

Christopoulos, S-R G.; Kordatos, A.; Cooper, Michael William D.; ...

2016-10-27

In this study, fluorite structured oxides are used in numerous applications and as such it is necessary to determine their materials properties over a range of conditions. In the present study we employ molecular dynamics calculations to calculate the elastic and expansivity data, which are then used in a thermodynamic model (the cBΩ model) to calculate the activation volumes of oxygen self-diffusion coefficient in ThO 2, UO 2 and PuO 2 fluorite structured oxides over a wide temperature range. We present relations to calculate the activation volumes of oxygen self-diffusion coefficient in ThO 2, UO 2 and PuO 2 formore » a wide range of temperature (300–1700 K) and pressure (–7.5 to 7.5 GPa).« less

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding.

PubMed

Stadler, Andreas M; Demmel, Franz; Ollivier, Jacques; Seydel, Tilo

2016-08-03

Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions. Here, we report an experimental study on the conformational dynamics of different folded conformational states of apo- and holomyoglobin in solution. Global protein diffusion and internal molecular motions were probed by neutron time-of-flight and neutron backscattering spectroscopy on the picosecond and nanosecond time scales. Global protein diffusion was found to depend on the α-helical content of the protein suggesting that charges on the macromolecule increase the short-time diffusion of protein. With regard to the molten globules, a gel-like phase due to protein entanglement and interactions with neighbouring macromolecules was visible due to a reduction of the global diffusion coefficients on the nanosecond time scale. Diffusion coefficients, residence and relaxation times of internal protein dynamics and root mean square displacements of localised internal motions were determined for the investigated structural states. The difference in conformational entropy ΔSconf of the protein between the unfolded and the partially or fully folded conformations was extracted from the measured root mean square displacements. Using thermodynamic parameters from the literature and the experimentally determined ΔSconf values we could identify the entropic contribution of the hydration shell ΔShydr of the different folded states. Our results point out the relevance of conformational entropy of the protein and the hydration shell for stability and folding of myoglobin.

Time-resolved production and detection of reactive atoms

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

Grossman, L. W.; Hurst, G. S.

1977-09-01

Cesium iodide in the presence of a buffer gas was dissociated with a pulsed ultraviolet laser, which will be referred to as the source laser. This created a population of atoms at a well defined time and in a compact, well defined volume. A second pulsed laser, with a beam that completely surrounded that of the first, photoionized the cesium after a known time delay. This laser will be referred to as the detector laser. It was determined that for short time delays, all of the cesium atoms were easily ionized. When focused, the source laser generated an extremely intensemore » fluence. By accounting for the beam intensity profile it was shown that all of the molecules in the central portion of the beam can be dissociated and detected. Besides proving the feasibility of single-molecule detection, this enabled a determination of the absolute photodissociation cross section as a function of wavelength. Initial studies of the time decay of the cesium signal at low argon pressures indicated a non-exponential decay. This was consistent with a diffusion mechanism transporting cesium atoms out of the laser beam. Therefore, it was desired to conduct further experiments using a tightly focused source beam, passing along the axis of the detector beam. The theoretical behavior of this simple geometry accounting for diffusion and reaction is easily calculated. A diffusion coefficient can then be extracted by data fitting. If reactive decay is due to impurities constituting a fixed percentage of the buffer gas, then two-body reaction rates will scale linearly with pressure and three-body reaction rates will scale quadratically. Also, the diffusion coefficient will scale inversely with pressure. At low pressures it is conceivable that decay due to diffusion would be sufficiently rapid that all other processes can be neglected. Extraction of a diffusion coefficient would then be quite direct. Finally, study of the reaction of cesium and oxygen was undertaken.« less

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.

FAST TRACK COMMUNICATION: Quantum anomalies and linear response theory

NASA Astrophysics Data System (ADS)

Sela, Itamar; Aisenberg, James; Kottos, Tsampikos; Cohen, Doron

2010-08-01

The analysis of diffusive energy spreading in quantized chaotic driven systems leads to a universal paradigm for the emergence of a quantum anomaly. In the classical approximation, a driven chaotic system exhibits stochastic-like diffusion in energy space with a coefficient D that is proportional to the intensity ɛ2 of the driving. In the corresponding quantized problem the coherent transitions are characterized by a generalized Wigner time tɛ, and a self-generated (intrinsic) dephasing process leads to nonlinear dependence of D on ɛ2.

The Stokes-Einstein relation at moderate Schmidt number.

PubMed

Balboa Usabiaga, Florencio; Xie, Xiaoyi; Delgado-Buscalioni, Rafael; Donev, Aleksandar

2013-12-07

The Stokes-Einstein relation for the self-diffusion coefficient of a spherical particle suspended in an incompressible fluid is an asymptotic result in the limit of large Schmidt number, that is, when momentum diffuses much faster than the particle. When the Schmidt number is moderate, which happens in most particle methods for hydrodynamics, deviations from the Stokes-Einstein prediction are expected. We study these corrections computationally using a recently developed minimally resolved method for coupling particles to an incompressible fluctuating fluid in both two and three dimensions. We find that for moderate Schmidt numbers the diffusion coefficient is reduced relative to the Stokes-Einstein prediction by an amount inversely proportional to the Schmidt number in both two and three dimensions. We find, however, that the Einstein formula is obeyed at all Schmidt numbers, consistent with linear response theory. The mismatch arises because thermal fluctuations affect the drag coefficient for a particle due to the nonlinear nature of the fluid-particle coupling. The numerical data are in good agreement with an approximate self-consistent theory, which can be used to estimate finite-Schmidt number corrections in a variety of methods. Our results indicate that the corrections to the Stokes-Einstein formula come primarily from the fact that the particle itself diffuses together with the momentum. Our study separates effects coming from corrections to no-slip hydrodynamics from those of finite separation of time scales, allowing for a better understanding of widely observed deviations from the Stokes-Einstein prediction in particle methods such as molecular dynamics.

Relation of short-range and long-range lithium ion dynamics in glass-ceramics: Insights from 7Li NMR field-cycling and field-gradient studies

NASA Astrophysics Data System (ADS)

Haaks, Michael; Martin, Steve W.; Vogel, Michael

2017-09-01

We use various 7Li NMR methods to investigate lithium ion dynamics in 70Li 2S-30 P 2S5 glass and glass-ceramic obtained from this glass after heat treatment. We employ 7Li spin-lattice relaxometry, including field-cycling measurements, and line-shape analysis to investigate short-range ion jumps as well as 7Li field-gradient approaches to characterize long-range ion diffusion. The results show that ceramization substantially enhances the lithium ion mobility on all length scales. For the 70Li 2S-30 P 2S5 glass-ceramic, no evidence is found that bimodal dynamics result from different ion mobilities in glassy and crystalline regions of this sample. Rather, 7Li field-cycling relaxometry shows that dynamic susceptibilities in broad frequency and temperature ranges can be described by thermally activated jumps governed by a Gaussian distribution of activation energies g (Ea) with temperature-independent mean value Em=0.43 eV and standard deviation σ =0.07 eV . Moreover, use of this distribution allows us to rationalize 7Li line-shape results for the local ion jumps. In addition, this information about short-range ion dynamics further explains 7Li field-gradient results for long-range ion diffusion. In particular, we quantitatively show that, consistent with our experimental results, the temperature dependence of the self-diffusion coefficient D is not described by the mean activation energy Em of the local ion jumps, but by a significantly smaller apparent value whenever the distribution of correlation times G (logτ ) of the jump motion derives from an invariant distribution of activation energies and, hence, continuously broadens upon cooling. This effect occurs because the harmonic mean, which determines the results of diffusivity or also conductivity studies, continuously separates from the peak position of G (logτ ) when the width of this distribution increases.

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.

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.

Diffusing wave spectroscopy in Maxwellian fluids.

PubMed

Galvan-Miyoshi, J; Delgado, J; Castillo, R

2008-08-01

We present a critical assessment of the diffusing wave spectroscopy (DWS) technique for obtaining the characteristic lengths and for measuring the loss and storage moduli of a reasonable well-known wormlike micelle (WM) system. For this purpose, we tracked the Brownian motion of particles using DWS embedded in a Maxwellian fluid constituted by a wormlike micellar solution made of cetyltrimethylammonium bromide (CTAB), sodium salicylate (NaSal), and water. We found that the motion of particles was governed by the viscosity of the solvent at short times and by the stress relaxation mechanisms of the giant micelles at longer times. From the time evolution of the mean square displacement of particles, we could obtain for the WM solution the cage size where each particle is harmonically bound at short times, the long-time diffusion coefficient, and experimental values for the exponent that accounts for the broad spectrum of relaxation times at the plateau onset time found in the (deltar2(t)) vs. time curves. In addition, from the (deltar2(t)) vs. time curves, we obtained G'(omega) and G"(omega) for the WM solutions. All the DWS microreological information allowed us to estimate the characteristic lengths of the WM network. We compare our DWS microrheological results and characteristic lengths with those obtained with mechanical rheometers at different NaSal/CTAB concentration ratios and temperatures.

Self-Diffusion of Drops in a Dilute Sheared Emulsion

NASA Technical Reports Server (NTRS)

Loewenberg, Michael; Hinch, E. J.

1996-01-01

Self-diffusion coefficients that describe cross-flow migration of non-Brownian drops in a dilute sheared emulsion were obtained by trajectory calculations. A boundary integral formulation was used to describe pairwise interactions between deformable drops; interactions between undeformed drops were described with mobility functions for spherical drops. The results indicate that drops have large anisotropic self-diffusivities which depend strongly on the drop viscosity and modestly on the shear-rate. Pairwise interactions between drops in shear-flow do not appreciably promote drop breakup.

Tortuosity measurement and the effects of finite pulse widths on xenon gas diffusion NMR studies of porous media

NASA Technical Reports Server (NTRS)

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

2001-01-01

We have extended the utility of NMR as a technique to probe porous media structure over length scales of approximately 100-2000 microm by using the spin 1/2 noble gas 129Xe imbibed into the system's pore space. Such length scales are much greater than can be probed with NMR diffusion studies of water-saturated porous media. We utilized Pulsed Gradient Spin Echo NMR measurements of the time-dependent diffusion coefficient, D(t), of the xenon gas filling the pore space to study further the measurements of both the pore surface-area-to-volume ratio, S/V(p), and the tortuosity (pore connectivity) of the medium. In uniform-size glass bead packs, we observed D(t) decreasing with increasing t, reaching an observed asymptote of approximately 0.62-0.65D(0), that could be measured over diffusion distances extending over multiple bead diameters. Measurements of D(t)/D(0) at differing gas pressures showed this tortuosity limit was not affected by changing the characteristic diffusion length of the spins during the diffusion encoding gradient pulse. This was not the case at the short time limit, where D(t)/D(0) was noticeably affected by the gas pressure in the sample. Increasing the gas pressure, and hence reducing D(0) and the diffusion during the gradient pulse served to reduce the previously observed deviation of D(t)/D(0) from the S/V(p) relation. The Pade approximation is used to interpolate between the long and short time limits in D(t). While the short time D(t) points lay above the interpolation line in the case of small beads, due to diffusion during the gradient pulse on the order of the pore size, it was also noted that the experimental D(t) data fell below the Pade line in the case of large beads, most likely due to finite size effects.

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

PubMed

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

2015-03-09

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

Zero point energy leakage in condensed phase dynamics: An assessment of quantum simulation methods for liquid water

NASA Astrophysics Data System (ADS)

Habershon, Scott; Manolopoulos, David E.

2009-12-01

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Zero point energy leakage in condensed phase dynamics: an assessment of quantum simulation methods for liquid water.

PubMed

Habershon, Scott; Manolopoulos, David E

2009-12-28

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Brownian self-driven particles on the surface of a sphere

NASA Astrophysics Data System (ADS)

Apaza, Leonardo; Sandoval, Mario

2017-08-01

We present the dynamics of overdamped Brownian self-propelled particles moving on the surface of a sphere. The effect of self-propulsion on the diffusion of these particles is elucidated by determining their angular (azimuthal and polar) mean-square displacement. Short- and long-times analytical expressions for their angular mean-square displacement are offered. Finally, the particles' steady marginal angular probability density functions are also elucidated.

Oxygen concentration dependence of silicon oxide dynamical properties

NASA Astrophysics Data System (ADS)

Yajima, Yuji; Shiraishi, Kenji; Endoh, Tetsuo; Kageshima, Hiroyuki

2018-06-01

To understand oxidation in three-dimensional silicon, dynamic characteristics of a SiO x system with various stoichiometries were investigated. The calculated results show that the self-diffusion coefficient increases as oxygen density decreases, and the increase is large when the temperature is low. It also shows that the self-diffusion coefficient saturates, when the number of removed oxygen atoms is sufficiently large. Then, approximate analytical equations are derived from the calculated results, and the previously reported expression is confirmed in the extremely low-SiO-density range.

Single ion dynamics in molten sodium bromide

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

Alcaraz, O.; Trullas, J.; Demmel, F.

We present a study on the single ion dynamics in the molten alkali halide NaBr. Quasielastic neutron scattering was employed to extract the self-diffusion coefficient of the sodium ions at three temperatures. Molecular dynamics simulations using rigid and polarizable ion models have been performed in parallel to extract the sodium and bromide single dynamics and ionic conductivities. Two methods have been employed to derive the ion diffusion, calculating the mean squared displacements and the velocity autocorrelation functions, as well as analysing the increase of the line widths of the self-dynamic structure factors. The sodium diffusion coefficients show a remarkable goodmore » agreement between experiment and simulation utilising the polarisable potential.« less

Novel surface diffusion characteristics for a robust pentacene derivative on Au(1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Miller, Ryan A.; Larson, Amanda; Pohl, Karsten

2017-06-01

Molecular dynamics simulations have been performed in both the ab initio and classical mechanics frameworks of 5,6,7-trithiapentacene-13-one (TTPO) molecules on flat Au(1 1 1) surfaces. Results show new surface diffusion characteristics including a strong preference for the molecule to align its long axis parallel to the sixfold Au(1 1 1) symmetry directions and subsequently diffuse along these close-packed directions, and a calculated activation energy for diffusion of 0.142 eV, about four times larger than that for pure pentacene on Au. The temperature-dependent diffusion coefficients were calculated to help quantify the molecular mobility during the experimentally observed process of forming self-assembled monolayers on gold electrodes.

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-thermophoresis and thermal self-diffusion in liquids and gases.

PubMed

Brenner, Howard

2010-09-01

This paper demonstrates the existence of self-thermophoresis, a phenomenon whereby a virtual thermophoretic force arising from a temperature gradient in a quiescent single-component liquid or gas acts upon an individual molecule of that fluid in much the same manner as a "real" thermophoretic force acts upon a macroscopic, non-Brownian body immersed in that same fluid. In turn, self-thermophoresis acting in concert with Brownian self-diffusion gives rise to the phenomenon of thermal self-diffusion in single-component fluids. The latter furnishes quantitative explanations of both thermophoresis in pure fluids and thermal diffusion in binary mixtures (the latter composed of a dilute solution of a physicochemically inert solute whose molecules are large compared with those of the solvent continuum). Explicitly, the self-thermophoretic theory furnishes a simple expression for both the thermophoretic velocity U of a macroscopic body in a single-component fluid subjected to a temperature gradient ∇T , and the intimately related binary thermal diffusion coefficient D{T} for a two-component colloidal or macromolecular mixture. The predicted expressions U=-D{T}∇T≡-βD{S}∇T and D{T}=βD{S} (with β and D{S} the pure solvent's respective thermal expansion and isothermal self-diffusion coefficients) are each noted to accord reasonably well with experimental data for both liquids and gases. The likely source of systematic deviations of the predicted values of D{T} from these data is discussed. This appears to be the first successful thermodiffusion theory applicable to both liquids and gases, a not insignificant achievement considering that the respective thermal diffusivities and thermophoretic velocities of these two classes of fluids differ by as much as six orders of magnitude.

Molecular dynamics simulation of the diffusion of uranium species in clay pores.

PubMed

Liu, Xiao-yu; Wang, Lu-hua; Zheng, Zhong; Kang, Ming-liang; Li, Chun; Liu, Chun-li

2013-01-15

Molecular dynamics simulations were carried out to investigate the diffusive behavior of aqueous uranium species in montmorillonite pores. Three uranium species (UO(2)(2+), UO(2)CO(3), UO(2)(CO(3))(2)(2-)) were confirmed in both the adsorbed and diffuse layers. UO(2)(CO(3))(3)(4-) was neglected in the subsequent analysis due to its scare occurrence. The species-based diffusion coefficients in montmorillonite pores were then calculated, and compared with the water mobility and their diffusivity in aqueous solution/feldspar nanosized fractures. Three factors were considered that affected the diffusive behavior of the uranium species: the mobility of water, the self-diffusion coefficient of the aqueous species, and the electrostatic forces between the negatively charged surface and charged molecules. The mobility of U species in the adsorbed layer decreased in the following sequence: UO(2)(2+)>UO(2)CO(3)>UO(2)(CO(3))(2)(2-). In the diffuse layer, we obtained the highest diffusion coefficient for UO(2)(CO(3))(2)(2-) with the value of 5.48×10(-10) m(2) s(-1), which was faster than UO(2)(2+). For these two charged species, the influence of electrostatic forces on the diffusion of solutes in the diffuse layer is overwhelming, whereas the influence of self-diffusion and water mobility is minor. Our study demonstrated that the negatively charged uranyl carbonate complex must be addressed in the safety assessment of potential radioactive waste disposal systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Oxygen exchange at gas/oxide interfaces: how the apparent activation energy of the surface exchange coefficient depends on the kinetic regime.

PubMed

Fielitz, Peter; Borchardt, Günter

2016-08-10

In the dedicated literature the oxygen surface exchange coefficient KO and the equilibrium oxygen exchange rate [Fraktur R] are considered to be directly proportional to each other regardless of the experimental circumstances. Recent experimental observations, however, contradict the consequences of this assumption. Most surprising is the finding that the apparent activation energy of KO depends dramatically on the kinetic regime in which it has been determined, i.e. surface exchange controlled vs. mixed or diffusion controlled. This work demonstrates how the diffusion boundary condition at the gas/solid interface inevitably entails a correlation between the oxygen surface exchange coefficient KO and the oxygen self-diffusion coefficient DO in the bulk ("on top" of the correlation between KO and [Fraktur R] for the pure surface exchange regime). The model can thus quantitatively explain the range of apparent activation energies measured in the different regimes: in the surface exchange regime the apparent activation energy only contains the contribution of the equilibrium exchange rate, whereas in the mixed or in the diffusion controlled regime the contribution of the oxygen self-diffusivity has also to be taken into account, which may yield significantly higher apparent activation energies and simultaneously quantifies the correlation KO ∝ DO(1/2) observed for a large number of oxides in the mixed or diffusion controlled regime, respectively.

Position-dependent radiative transfer as a tool for studying Anderson localization: Delay time, time-reversal and coherent backscattering

NASA Astrophysics Data System (ADS)

van Tiggelen, B. A.; Skipetrov, S. E.; Page, J. H.

2017-05-01

Previous work has established that the localized regime of wave transport in open media is characterized by a position-dependent diffusion coefficient. In this work we study how the concept of position-dependent diffusion affects the delay time, the transverse confinement, the coherent backscattering, and the time reversal of waves. Definitions of energy transport velocity of localized waves are proposed. We start with a phenomenological model of radiative transfer and then present a novel perturbational approach based on the self-consistent theory of localization. The latter allows us to obtain results relevant for realistic experiments in disordered quasi-1D wave guides and 3D slabs.

Correlation and transport properties for mixtures at constant pressure and temperature

NASA Astrophysics Data System (ADS)

White, Alexander J.; Collins, Lee A.; Kress, Joel D.; Ticknor, Christopher; Clérouin, Jean; Arnault, Philippe; Desbiens, Nicolas

2017-06-01

Transport properties of mixtures of elements in the dense plasma regime play an important role in natural astrophysical and experimental systems, e.g., inertial confinement fusion. We present a series of orbital-free molecular dynamics simulations on dense plasma mixtures with comparison to a global pseudo ion in jellium model. Hydrogen is mixed with elements of increasingly high atomic number (lithium, carbon, aluminum, copper, and silver) at a fixed temperature of 100 eV and constant pressure set by pure hydrogen at 2 g/cm 3 , namely, 370 Mbars. We compute ionic transport coefficients, such as self-diffusion, mutual diffusion, and viscosity for various concentrations. Small concentrations of the heavy atoms significantly change the density of the plasma and decrease the transport coefficients. The structure of the mixture evidences a strong Coulomb coupling between heavy ions and the appearance of a broad correlation peak at short distances between hydrogen atoms. The concept of an effective one component plasma is used to quantify the overcorrelation of the light element induced by the admixture of a heavy element.

Correlation and transport properties for mixtures at constant pressure and temperature

DOE PAGES

White, Alexander J.; Collins, Lee A.; Kress, Joel D.; ...

2017-06-02

Transport properties of mixtures of elements in the dense plasma regime play an important role in natural astrophysical and experimental systems, e.g., inertial confinement fusion. In this paper, we present a series of orbital-free molecular dynamics simulations on dense plasma mixtures with comparison to a global pseudo ion in jellium model. Hydrogen is mixed with elements of increasingly high atomic number (lithium, carbon, aluminum, copper, and silver) at a fixed temperature of 100 eV and constant pressure set by pure hydrogen at 2g/cm 3, namely, 370 Mbars. We compute ionic transport coefficients, such as self-diffusion, mutual diffusion, and viscosity formore » various concentrations. Small concentrations of the heavy atoms significantly change the density of the plasma and decrease the transport coefficients. The structure of the mixture evidences a strong Coulomb coupling between heavy ions and the appearance of a broad correlation peak at short distances between hydrogen atoms. Finally, the concept of an effective one component plasma is used to quantify the overcorrelation of the light element induced by the admixture of a heavy element.« less

Correlation and transport properties for mixtures at constant pressure and temperature

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

White, Alexander J.; Collins, Lee A.; Kress, Joel D.

Transport properties of mixtures of elements in the dense plasma regime play an important role in natural astrophysical and experimental systems, e.g., inertial confinement fusion. In this paper, we present a series of orbital-free molecular dynamics simulations on dense plasma mixtures with comparison to a global pseudo ion in jellium model. Hydrogen is mixed with elements of increasingly high atomic number (lithium, carbon, aluminum, copper, and silver) at a fixed temperature of 100 eV and constant pressure set by pure hydrogen at 2g/cm 3, namely, 370 Mbars. We compute ionic transport coefficients, such as self-diffusion, mutual diffusion, and viscosity formore » various concentrations. Small concentrations of the heavy atoms significantly change the density of the plasma and decrease the transport coefficients. The structure of the mixture evidences a strong Coulomb coupling between heavy ions and the appearance of a broad correlation peak at short distances between hydrogen atoms. Finally, the concept of an effective one component plasma is used to quantify the overcorrelation of the light element induced by the admixture of a heavy element.« less

Brownian dynamics of confined rigid bodies

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

Delong, Steven; Balboa Usabiaga, Florencio; Donev, Aleksandar, E-mail: donev@courant.nyu.edu

2015-10-14

We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of the overdamped Langevin equations of motion, one based on the Fixman midpoint method and the othermore » based on a random finite difference approach, both of which ensure that the correct stochastic drift term is captured in a computationally efficient way. We study several examples of rigid colloidal particles diffusing near a no-slip boundary and demonstrate the importance of the choice of tracking point on the measured translational mean square displacement (MSD). We examine the average short-time as well as the long-time quasi-two-dimensional diffusion coefficient of a rigid particle sedimented near a bottom wall due to gravity. For several particle shapes, we find a choice of tracking point that makes the MSD essentially linear with time, allowing us to estimate the long-time diffusion coefficient efficiently using a Monte Carlo method. However, in general, such a special choice of tracking point does not exist, and numerical techniques for simulating long trajectories, such as the ones we introduce here, are necessary to study diffusion on long time scales.« less

Isotope fractionation by multicomponent diffusion (Invited)

NASA Astrophysics Data System (ADS)

Watkins, J. M.; Liang, Y.; Richter, F. M.; Ryerson, F. J.; DePaolo, D. J.

2013-12-01

Isotope fractionation by multicomponent diffusion The isotopic composition of mineral phases can be used to probe the temperatures and rates of mineral formation as well as the degree of post-mineralization alteration. The ability to interpret stable isotope variations is limited by our knowledge of three key parameters and their relative importance in determining the composition of a mineral grain and its surroundings: (1) thermodynamic (equilibrium) partitioning, (2) mass-dependent diffusivities, and (3) mass-dependent reaction rate coefficients. Understanding the mechanisms of diffusion and reaction in geological liquids, and how these mass transport processes discriminate between isotopes, represents an important problem that is receiving considerable attention in the geosciences. Our focus in this presentation will be isotope fractionation by chemical diffusion. Previous studies have documented that diffusive isotope effects vary depending on the cation as well as the liquid composition, but the ability to predict diffusive isotope effects from theory is limited; for example, it is unclear whether the magnitude of diffusive isotopic fractionations might also vary with the direction of diffusion in composition space. To test this hypothesis and to further guide the theoretical treatment of isotope diffusion, two chemical diffusion experiments and one self diffusion experiment were conducted at 1250°C and 0.7 GPa. In one experiment (A-B), CaO and Na2O counter-diffuse rapidly in the presence of a small SiO2 gradient. In the other experiment (D-E), CaO and SiO2 counter-diffuse more slowly in a small Na2O gradient. In both chemical diffusion experiments, Ca isotopes become fractionated by chemical diffusion but by different amounts, documenting for the first time that the magnitude of isotope fractionation by diffusion depends on the direction of diffusion in composition space. The magnitude of Ca isotope fractionation that develops is positively correlated with the rate of CaO diffusion; in A-B, the total variation is 2.5‰ whereas in D-E it is only 1.3‰. The diffusion of isotopes in a multicomponent system is modeled using a new expression for the isotope-specific diffusive flux that includes self diffusion terms in addition to the multicomponent chemical diffusion matrix. Kinetic theory predicts a mass dependence on isotopic mobility, i.e., self diffusivity, but it is unknown whether or how the mass dependence on self diffusivity translates into a mass dependence on chemical diffusion coefficients. The new experimental results allow us to assess several empirical expressions relating the self diffusivity and its mass dependence to the elements of the diffusion matrix and their mass dependence. Several plausible theoretical treatments can fit the data equally well. We are currently at the stage where experiments are guiding the theoretical treatment of the isotope fractionation by diffusion problem, underscoring the importance of experiments for aiding interpretations of isotopic variations in nature.

Self-trapping limited exciton diffusion in a monomeric perylene crystal as revealed by femtosecond transient absorption microscopy.

PubMed

Yago, Tomoaki; Tamaki, Yoshiaki; Furube, Akihiro; Katoh, Ryuzi

2008-08-14

Self-trapping and singlet-singlet annihilation of the free excitons in a monomeric (beta) perylene crystal were studied by using femtosecond transient absorption microscopy. The free exciton generated by the photo-excitation of the beta-perylene crystal relaxed to the self-trapped exciton with a rate constant of 7 x 10(10) s(-1). The singlet-singlet annihilation of the free exciton observed under the high excitation density conditions was competed with the self-trapping of the free exciton; we estimated the annihilation rate constant for the free exciton to be 1 x 10(-8) cm(3) s(-1) from the excitation density dependence of the free exciton decay. After self-trapping of the free exciton, no annihilation was observed in the 100 ps time range, suggesting that the diffusion coefficient was reduced drastically by self-trapping. The results show that the major factor limiting the exciton diffusion in the beta-perylene crystal is a relaxation of the free exciton to the self-trapped exciton, and not the lifetime of the exciton. Though the singlet-singlet annihilation rate constants and fluorescence lifetime of the beta-perylene crystal are similar to those of the anthracene crystal, the estimated exciton diffusion length (2 nm) in the beta-perylene crystal is much smaller than that (100 nm) in the anthracene crystal as a result of the exciton self-trapping.

Short Diffusion Time Diffusion-Weighted Imaging With Oscillating Gradient Preparation as an Early Magnetic Resonance Imaging Biomarker for Radiation Therapy Response Monitoring in Glioblastoma: A Preclinical Feasibility Study.

PubMed

Bongers, Andre; Hau, Eric; Shen, Han

2018-01-04

To investigate a novel alternative diffusion-weighted imaging (DWI) approach using oscillating gradients preparation (OGSE) to obtain much shorter effective diffusion times (Δ eff ) for tumor response monitoring by apparent diffusion coefficient (ADC) mapping in a glioblastoma mouse model. Twenty-four BALB/c nude mice inoculated with U87 glioblastoma cells were randomized into a control group and an irradiation group, which underwent a 15-day fractioned radiation therapy (RT) course with 2 Gy/d. Therapy response was assessed by mapping of ADCs at 6 time points using an in-house implementation of a cos-OGSE DWI sequence with Δ eff  = 1.25 ms and compared with a standard pulsed gradient DWI protocol (PGSE) with typical clinical diffusion time Δ eff  = 18 ms. Longitudinal ADC changes in tumor and contralateral white matter (WM) were statistically assessed using repeated-measures analysis of variance and post hoc (Sidak) testing. On short Δ eff OGSE maps tumor ADC was generally 30%-50% higher than in surrounding WM. Areas correlated well with histology. Tumor identification was generally more difficult on PGSE maps owing to nonsignificant WM/tumor contrast. During RT, OGSE maps also showed significant tumor ADC increase (approximately 15%) in response to radiation, consistently seen after 14-Gy RT dose. The clinical reference (PGSE) showed lower sensitivity to radiation changes, and no significant response across the radiation group and time course could be detected. Our short Δ eff DWI method using OGSE better reflected histologically defined tumor areas and enabled more consistent and earlier detection of microstructural radiation changes than conventional methods. Oscillating gradients preparation offers significant potential as a robust microstructural RT response biomarker, potentially helping to shift important therapy decisions to earlier stages in the RT time course. Copyright © 2018 Elsevier Inc. All rights reserved.

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.

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

PubMed

Lee, Song Hi; Rasaiah, Jayendran C

2013-09-28

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

Controlled release of functional proteins through designer self-assembling peptide nanofiber hydrogel scaffold

PubMed Central

Koutsopoulos, Sotirios; Unsworth, Larry D.; Nagai, Yusuke; Zhang, Shuguang

2009-01-01

The release kinetics for a variety of proteins of a wide range of molecular mass, hydrodynamic radii, and isoelectric points through a nanofiber hydrogel scaffold consisting of designer self-assembling peptides were studied by using single-molecule fluorescence correlation spectroscopy (FCS). In contrast to classical diffusion experiments, the single-molecule approach allowed for the direct determination of diffusion coefficients for lysozyme, trypsin inhibitor, BSA, and IgG both inside the hydrogel and after being released into the solution. The results of the FCS analyses and the calculated pristine in-gel diffusion coefficients were compared with the values obtained from the Stokes–Einstein equation, Fickian diffusion models, and the literature. The release kinetics suggested that protein diffusion through nanofiber hydrogels depended primarily on the size of the protein. Protein diffusivities decreased, with increasing hydrogel nanofiber density providing a means of controlling the release kinetics. Secondary and tertiary structure analyses and biological assays of the released proteins showed that encapsulation and release did not affect the protein conformation and functionality. Our results show that this biocompatible and injectable designer self-assembling peptide hydrogel system may be useful as a carrier for therapeutic proteins for sustained release applications. PMID:19273853

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...

Measurement of Soret and Fickian diffusion coefficients by orthogonal phase-shifting interferometry and its application to protein aqueous solutions

NASA Astrophysics Data System (ADS)

Torres, Juan F.; Komiya, Atsuki; Henry, Daniel; Maruyama, Shigenao

2013-08-01

We have developed a method to measure thermodiffusion and Fickian diffusion in transparent binary solutions. The measuring instrument consists of two orthogonally aligned phase-shifting interferometers coupled with a single rotating polarizer. This high-resolution interferometer, initially developed to measure isothermal diffusion coefficients in liquid systems [J. F. Torres, A. Komiya, E. Shoji, J. Okajima, and S. Maruyama, Opt. Lasers Eng. 50, 1287 (2012)], was modified to measure transient concentration profiles in binary solutions subject to a linear temperature gradient. A convectionless thermodiffusion field was created in a binary solution sample that is placed inside a Soret cell. This cell consists of a parallelepiped cavity with a horizontal cross-section area of 10 × 20 mm2, a variable height of 1-2 mm, and transparent lateral walls. The small height of the cell reduces the volume of the sample, shortens the measurement time, and increases the hydrodynamic stability of the system. An additional free diffusion experiment with the same optical apparatus provides the so-called contrast factors that relate the unwrapped phase and concentration gradients, i.e., the measurement technique is independent and robust. The Soret coefficient is determined from the concentration and temperature differences between the upper and lower boundaries measured by the interferometer and thermocouples, respectively. The Fickian diffusion coefficient is obtained by fitting a numerical solution to the experimental concentration profile. The method is validated through the measurement of thermodiffusion in the well-known liquid pairs of ethanol-water (ethanol 39.12 wt.%) and isobutylbenzene-dodecane (50.0 wt.%). The obtained coefficients agree with the literature values within 5.0%. Finally, the developed technique is applied to visualize biomolecular thermophoresis. Two protein aqueous solutions at 3 mg/ml were used as samples: aprotinin (6.5 kDa)-water and lysozyme (14.3 kDa)-water. It was found that the former protein molecules are thermophilic and the latter thermophobic. In contrast to previously reported methods, this technique is suitable for both short time and negative Soret coefficient measurements.

Fluctuation-enhanced electric conductivity in electrolyte solutions.

PubMed

Péraud, Jean-Philippe; Nonaka, Andrew J; Bell, John B; Donev, Aleksandar; Garcia, Alejandro L

2017-10-10

We analyze the effects of an externally applied electric field on thermal fluctuations for a binary electrolyte fluid. We show that the fluctuating Poisson-Nernst-Planck (PNP) equations for charged multispecies diffusion coupled with the fluctuating fluid momentum equation result in enhanced charge transport via a mechanism distinct from the well-known enhancement of mass transport that accompanies giant fluctuations. Although the mass and charge transport occurs by advection by thermal velocity fluctuations, it can macroscopically be represented as electrodiffusion with renormalized electric conductivity and a nonzero cation-anion diffusion coefficient. Specifically, we predict a nonzero cation-anion Maxwell-Stefan coefficient proportional to the square root of the salt concentration, a prediction that agrees quantitatively with experimental measurements. The renormalized or effective macroscopic equations are different from the starting PNP equations, which contain no cross-diffusion terms, even for rather dilute binary electrolytes. At the same time, for infinitely dilute solutions the renormalized electric conductivity and renormalized diffusion coefficients are consistent and the classical PNP equations with renormalized coefficients are recovered, demonstrating the self-consistency of the fluctuating hydrodynamics equations. Our calculations show that the fluctuating hydrodynamics approach recovers the electrophoretic and relaxation corrections obtained by Debye-Huckel-Onsager theory, while elucidating the physical origins of these corrections and generalizing straightforwardly to more complex multispecies electrolytes. Finally, we show that strong applied electric fields result in anisotropically enhanced "giant" velocity fluctuations and reduced fluctuations of salt concentration.

Fluctuation-enhanced electric conductivity in electrolyte solutions

PubMed Central

Péraud, Jean-Philippe; Nonaka, Andrew J.; Bell, John B.; Donev, Aleksandar; Garcia, Alejandro L.

2017-01-01

We analyze the effects of an externally applied electric field on thermal fluctuations for a binary electrolyte fluid. We show that the fluctuating Poisson–Nernst–Planck (PNP) equations for charged multispecies diffusion coupled with the fluctuating fluid momentum equation result in enhanced charge transport via a mechanism distinct from the well-known enhancement of mass transport that accompanies giant fluctuations. Although the mass and charge transport occurs by advection by thermal velocity fluctuations, it can macroscopically be represented as electrodiffusion with renormalized electric conductivity and a nonzero cation–anion diffusion coefficient. Specifically, we predict a nonzero cation–anion Maxwell–Stefan coefficient proportional to the square root of the salt concentration, a prediction that agrees quantitatively with experimental measurements. The renormalized or effective macroscopic equations are different from the starting PNP equations, which contain no cross-diffusion terms, even for rather dilute binary electrolytes. At the same time, for infinitely dilute solutions the renormalized electric conductivity and renormalized diffusion coefficients are consistent and the classical PNP equations with renormalized coefficients are recovered, demonstrating the self-consistency of the fluctuating hydrodynamics equations. Our calculations show that the fluctuating hydrodynamics approach recovers the electrophoretic and relaxation corrections obtained by Debye–Huckel–Onsager theory, while elucidating the physical origins of these corrections and generalizing straightforwardly to more complex multispecies electrolytes. Finally, we show that strong applied electric fields result in anisotropically enhanced “giant” velocity fluctuations and reduced fluctuations of salt concentration. PMID:28973890

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

Results for diffusion-weighted imaging with a fourth-channel gradient insert.

PubMed

Feldman, Rebecca E; Scholl, Timothy J; Alford, Jamu K; Handler, William B; Harris, Chad T; Chronik, Blaine A

2011-12-01

Diffusion-weighted imaging suffers from motion artifacts and relatively low signal quality due to the long echo times required to permit the diffusion encoding. We investigated the inclusion of a noncylindrical fourth gradient coil, dedicated entirely to diffusion encoding, into the imaging system. Standard three-axis whole body gradients were used during image acquisition, but we designed and constructed an insert coil to perform diffusion encodings. We imaged three phantoms on a 3-T system with a range of diffusion coefficients. Using the insert gradient, we were able to encode b values of greater than 1300 s/mm(2) with an echo time of just 83 ms. Images obtained using the insert gradient had higher signal to noise ratios than those obtained using the whole body gradient: at 500 s/mm(2) there was a 18% improvement in signal to noise ratio, at 1000 s/mm(2) there was a 39% improvement in signal to noise ratio, and at 1350 s/mm(2) there was a 56% improvement in signal to noise ratio. Using the insert gradient, we were capable of doing diffusion encoding at high b values by using relatively short echo times. Copyright © 2011 Wiley Periodicals, Inc.

Self-diffusivity and interdiffusivity of molten aluminum-copper alloys under pressure, derived from molecular dynamics.

PubMed

Rudd, Robert E; Cabot, William H; Caspersen, Kyle J; Greenough, Jeffrey A; Richards, David F; Streitz, Frederick H; Miller, Paul L

2012-03-01

We use molecular dynamics (MD) to simulate diffusion in molten aluminum-copper (AlCu) alloys. The self-diffusivities and Maxwell-Stefan diffusivities are calculated for AlCu mixtures using the Green-Kubo formulas at temperatures from 1000 to 4000 K and pressures from 0 to 25 GPa, along with additional points at higher temperatures and pressures. The diffusivities are corrected for finite-size effects. The Maxwell-Stefan diffusivity is compared to the diffusivity calculated from the self-diffusivities using a generalization of the Darken equation. We find that the effects of cross-correlation are small. Using the calculated self-diffusivities, we have assessed whether dilute hard-sphere and dilute Lennard-Jones models apply to the molten mixture. Neither of the two dilute gas diffusivities describes the diffusivity in molten Al and Cu. We report generalized analytic models for the self-diffusivities and interdiffusivity (mutual diffusivity) that fit the MD results well. The MD-derived transport coefficients are in good agreement with the available experimental data. We also report MD calculations of the viscosity and an analytic fit to those results. The ionic thermal conductivity is discussed briefly.

Self-diffusivity and interdiffusivity of molten aluminum-copper alloys under pressure, derived from molecular dynamics

NASA Astrophysics Data System (ADS)

Rudd, Robert E.; Cabot, William H.; Caspersen, Kyle J.; Greenough, Jeffrey A.; Richards, David F.; Streitz, Frederick H.; Miller, Paul L.

2012-03-01

We use molecular dynamics (MD) to simulate diffusion in molten aluminum-copper (AlCu) alloys. The self-diffusivities and Maxwell-Stefan diffusivities are calculated for AlCu mixtures using the Green-Kubo formulas at temperatures from 1000 to 4000 K and pressures from 0 to 25 GPa, along with additional points at higher temperatures and pressures. The diffusivities are corrected for finite-size effects. The Maxwell-Stefan diffusivity is compared to the diffusivity calculated from the self-diffusivities using a generalization of the Darken equation. We find that the effects of cross-correlation are small. Using the calculated self-diffusivities, we have assessed whether dilute hard-sphere and dilute Lennard-Jones models apply to the molten mixture. Neither of the two dilute gas diffusivities describes the diffusivity in molten Al and Cu. We report generalized analytic models for the self-diffusivities and interdiffusivity (mutual diffusivity) that fit the MD results well. The MD-derived transport coefficients are in good agreement with the available experimental data. We also report MD calculations of the viscosity and an analytic fit to those results. The ionic thermal conductivity is discussed briefly.

Time-Dependent Influence of Cell Membrane Permeability on MR Diffusion Measurements

PubMed Central

Li, Hua; Jiang, Xiaoyu; Xie, Jingping; McIntyre, J. Oliver; Gore, John C.; Xu, Junzhong

2015-01-01

Purpose To investigate the influence of cell membrane permeability on diffusion measurements over a broad range of diffusion times. Methods Human myelogenous leukemia K562 cells were cultured and treated with saponin to selectively alter cell membrane permeability, resulting in a broad physiologically relevant range from 0.011 μm/ms to 0.044 μm/ms. Apparent diffusion coefficient (ADC) values were acquired with the effective diffusion time (Δeff) ranging from 0.42 to 3000 ms. Cosine-modulated oscillating gradient spin echo (OGSE) measurements were performed to achieve short Δeff from 0.42 to 5 ms, while stimulated echo acquisitions (STEAM) were used to achieve long Δeff from 11 to 2999 ms. Computer simulations were also performed to support the experimental results. Results Both computer simulations and experiments in vitro showed that the influence of membrane permeability on diffusion MR measurements is highly dependent on the choice of diffusion time, and it is negligible only when the diffusion time is at least one order of magnitude smaller than the intracellular exchange lifetime. Conclusion The influence of cell membrane permeability on the measured ADCs is negligible in OGSE measurements at moderately high frequencies. By contrast, cell membrane permeability has a significant influence on ADC and quantitative diffusion measurements at low frequencies such as those sampled using conventional pulsed gradient methods. PMID:26096552

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

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.

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.

Collective diffusion in carbon nanotubes: Crossover between one dimension and three dimensions

NASA Astrophysics Data System (ADS)

Chen, Pei-Rong; Xu, Zhi-Cheng; Gu, Yu; Zhong, Wei-Rong

2016-08-01

Using non-equilibrium molecular dynamics and Monte Carlo methods, we study the collective diffusion of helium in carbon nanotubes. The results show that the collective diffusion coefficient (CDC) increases with the dimension of the channel. The collective diffusion coefficient has a linear relationship with the temperature and the concentration. There exist a ballistic transport in short carbon nanotubes and a diffusive transport in long carbon nanotubes. Fick’s law has an invalid region in the nanoscale channel. Project supported by the National Natural Science Foundation of China (Grant Nos. 11004082 and 11291240477), the Natural Science Foundation of Guangdong Province, China (Grant No. 2014A030313367), and the Fundamental Research Funds for the Central Universities, Jinan University (Grant No. 11614341).

Empirical correlations between the arrhenius' parameters of impurities' diffusion coefficients in CdTe crystals

DOE PAGES

Shcherbak, L.; Kopach, O.; Fochuk, P.; ...

2015-01-21

Understanding of self- and dopant-diffusion in semiconductor devices is essential to our being able to assure the formation of well-defined doped regions. In this paper, we compare obtained in the literature up to date the Arrhenius’ parameters (D=D 0exp(–ΔE a/kT)) of point-defect diffusion coefficients and the I-VII groups impurities in CdTe crystals and films. We found that in the diffusion process there was a linear dependence between the pre-exponential factor, D 0, and the activation energy, ΔE a, of different species: This was evident in the self-diffusivity and isovalent impurity Hg diffusivity as well as for the dominant IIIA andmore » IVA groups impurities and Chlorine, except for the fast diffusing elements (e.g., Cu and Ag), chalcogens O, S, and Se, halogens I and Br as well as the transit impurities Mn, Co, Fe. As a result, reasons of the lack of correspondence of the data to compensative dependence are discussed.« less

First-principles investigation of thermodynamic and kinetic properties in titanium-hydrogen system and B2-nickel-alminum compound: Phase stability, point defect complexes and diffusion

NASA Astrophysics Data System (ADS)

Xu, Qingchuan

The purpose of this thesis is to show the technique of predicting thermodynamic and kinetic properties from first-principles using density functional theory (DFT) calculations, cluster expansion methods and Monte Carlo simulations instead of experiments. Two material systems are selected as examples: one is an interstitial system (Ti-H system) and another is a substitutional compound (B2-NiAl alloy). For Ti-H system, this thesis investigated hydride stability, exploring the role of configurational degrees of freedom, zero-point vibrational energy and coherency strains. The tetragonal gamma-TiH phase was predicted to be unstable relative to hcp alpha-Ti and fcc based delta-TiH2. Zero point vibrational energy makes the gamma phase even less stable. The coherency strains between hydride precipitates and alpha-Ti matrix stabilize gamma-TiH relative to alpha-Ti and delta-TiH2. We also found that hydrogen prefers octahedral sites at low hydrogen concentration and tetrahedral sites at high concentration. For B2-NiAl, this thesis investigated the point defects and various diffusion mechanisms. A low barrier collective hop was discovered that could mediate Al diffusion through the anti-structural-bridge (ASB) mechanism. We also found an alternative hop sequence for the migration of a triple defect and a six-jump-cycle than that proposed previously. Going beyond the mean field approximation, we found that the inclusion of interactions among point defects is crucial to predict the concentration of defect complexes. Accounting for interactions among defects and incorporating all diffusion mechanisms proposed for B2-NiAl in Monte Carlo simulation, we calculated tracer diffusion coefficients. For the first time, the relative importance of various diffusion mechanisms is revealed. The ASB hop is the dominant mechanism for Ni in Ni-rich alloy and for Al diffusion in Al-rich alloys. Other mechanisms also play a role to various extents. We also calculated the self and interdiffusion coefficients for B2-NiAl. We found in Al-rich alloys that the thermodynamic factor of Al is much greater than that of Ni while in Ni-rich alloys they are very similar. This difference in thermodynamic factors results in a much higher self-diffusion coefficient of Al compared to that of Ni in Al-rich alloys and also causes two different interdiffusion coefficients.

Scalar Resonant Relaxation of Stars around a Massive Black Hole

NASA Astrophysics Data System (ADS)

Bar-Or, Ben; Fouvry, Jean-Baptiste

2018-06-01

In nuclear star clusters, the potential is governed by the central massive black hole (MBH), so that stars move on nearly Keplerian orbits and the total potential is almost stationary in time. Yet, the deviations of the potential from the Keplerian one, due to the enclosed stellar mass and general relativity, will cause the stellar orbits to precess. Moreover, as a result of the finite number of stars, small deviations of the potential from spherical symmetry induce residual torques that can change the stars’ angular momentum faster than the standard two-body relaxation. The combination of these two effects drives a stochastic evolution of orbital angular momentum, a process named “resonant relaxation” (RR). Owing to recent developments in the description of the relaxation of self-gravitating systems, we can now fully describe scalar resonant relaxation (relaxation of the magnitude of the angular momentum) as a diffusion process. In this framework, the potential fluctuations due to the complex orbital motion of the stars are described by a random correlated noise with statistical properties that are fully characterized by the stars’ mean field motion. On long timescales, the cluster can be regarded as a diffusive system with diffusion coefficients that depend explicitly on the mean field stellar distribution through the properties of the noise. We show here, for the first time, how the diffusion coefficients of scalar RR, for a spherically symmetric system, can be fully calculated from first principles, without any free parameters. We also provide an open source code that evaluates these diffusion coefficients numerically.

Li diffusion and the effect of local structure on Li mobility in Li2O-SiO2 glasses.

PubMed

Bauer, Ute; Welsch, Anna-Maria; Behrens, Harald; Rahn, Johanna; Schmidt, Harald; Horn, Ingo

2013-12-05

Aimed to improve the understanding of lithium migration mechanisms in ion conductors, this study focuses on Li dynamics in binary Li silicate glasses. Isotope exchange experiments and conductivity measurements were carried out to determine self-diffusion coefficients and activation energies for Li migration in Li2Si3O7 and Li2Si6O13 glasses. Samples of identical composition but different isotope content were combined for diffusion experiments in couples or triples. Diffusion profiles developed between 511 and 664 K were analyzed by femtosecond laser ablation combined with multiple collector inductively coupled plasma mass spectrometry (fs LA-MC-ICP-MS) and secondary ion mass spectrometry (SIMS). Analyses of diffusion profiles and comparison of diffusion data reveal that the isotope effect of lithium diffusion in silicate glasses is rather small, consistent with classical diffusion behavior. Ionic conductivity of glasses was measured between 312 and 675 K. The experimentally obtained self-diffusion coefficient, D(IE), and ionic diffusion coefficient, D(σ), derived from specific DC conductivity provided information about correlation effects during Li diffusion. The D(IE)/D(σ) is higher for the trisilicate (0.27 ± 0.05) than that for the hexasilicate (0.17 ± 0.02), implying that increasing silica content reduces the efficiency of Li jumps in terms of long-range movement. This trend can be rationalized by structural concepts based on nuclear magnetic resonance (NMR) and Raman spectroscopy as well as molecular dynamic simulations, that is, lithium is percolating in low-dimensional, alkali-rich regions separated by a silica-rich matrix.

Oxygen self-diffusion in ThO 2 under pressure: Connecting point defect parameters with bulk properties

DOE PAGES

Cooper, Michael William D.; Fitzpatrick, M. E.; Tsoukalas, L. H.; ...

2016-06-06

ThO 2 is a candidate material for use in nuclear fuel applications and as such it is important to investigate its materials properties over a range of temperatures and pressures. In the present study molecular dynamics calculations are used to calculate elastic and expansivity data. These are used in the framework of a thermodynamic model, the cBΩ model, to calculate the oxygen self-diffusion coefficient in ThO 2 over a range of pressures (–10–10 GPa) and temperatures (300–1900 K). As a result, increasing the hydrostatic pressure leads to a significant reduction in oxygen self-diffusion. Conversely, negative hydrostatic pressure significantly enhances oxygenmore » self-diffusion.« less

Test-retest reliability and repeatability of renal diffusion tensor MRI in healthy subjects.

PubMed

Cutajar, Marica; Clayden, Jonathan D; Clark, Christopher A; Gordon, Isky

2011-12-01

This study assessed test-retest reliability and repeatability of diffusion tensor imaging (DTI) in the kidneys. Seven healthy volunteers (age range, 19-31 years), were imaged three consecutive times on the same day (short-term reliability) and the same imaging protocol was repeated after a month (long-term reliability). Diffusion-weighted magnetic resonance imaging scans in the coronal-oblique projection of the kidney were acquired on a 1.5 T scanner using a multi-section echo-planar sequence; six contiguous slices each 5 mm thick, diffusion sensitisation along 20 non-collinear directions, TR=730 ms, TE=73 ms and 2 b-values (0 and 400 s mm(-2)). Volunteers were asked to hold their breath throughout each data acquisition (approx. 20 s). The apparent diffusion coefficient (ADC) and fractional anisotropy (FA) values were obtained from maps generated using dedicated software MIStar (Apollo Medical Imaging, Melbourne, Australia). Statistical analyses of both short- and long-term repeats were carried out from which the within-subject coefficient of variation (wsCV) was calculated. The wsCV obtained for both the ADC and FA values were less than 10% in all the analyses carried out. In addition, paired (repeated measures) t-test was used to measure the variation between the diffusion parameters collected from the two scanning sessions a month apart. It showed no significant difference and the wsCV obtained after comparing the first and second scans were found to be smaller than 15% for both ADC and FA. Renal DTI produces reliable and repeatable results which make longitudinal investigation of patients viable. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Thermophysical properties of liquid Ni around the melting temperature from molecular dynamics simulation

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

Rozas, R. E.; Department of Physics, University of Bío-Bío, Av. Collao 1202, P.O. Box 5C, Concepción; Demiraǧ, A. D.

Thermophysical properties of liquid nickel (Ni) around the melting temperature are investigated by means of classical molecular dynamics (MD) simulation, using three different embedded atom method potentials to model the interactions between the Ni atoms. Melting temperature, enthalpy, static structure factor, self-diffusion coefficient, shear viscosity, and thermal diffusivity are compared to recent experimental results. Using ab initio MD simulation, we also determine the static structure factor and the mean-squared displacement at the experimental melting point. For most of the properties, excellent agreement is found between experiment and simulation, provided the comparison relative to the corresponding melting temperature. We discuss themore » validity of the Hansen-Verlet criterion for the static structure factor as well as the Stokes-Einstein relation between self-diffusion coefficient and shear viscosity. The thermal diffusivity is extracted from the autocorrelation function of a wavenumber-dependent temperature fluctuation variable.« less

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

Construction of three-dimensional DNA hydrogels from linear building blocks.

PubMed

Nöll, Tanja; Schönherr, Holger; Wesner, Daniel; Schopferer, Michael; Paululat, Thomas; Nöll, Gilbert

2014-08-04

A three-dimensional DNA hydrogel was generated by self-assembly of short linear double-stranded DNA (dsDNA) building blocks equipped with sticky ends. The resulting DNA hydrogel is thermoresponsive and the length of the supramolecular dsDNA structures varies with temperature. The average diffusion coefficients of the supramolecular dsDNA structures formed by self-assembly were determined by diffusion-ordered NMR spectroscopy (DOSY NMR) for temperatures higher than 60 °C. Temperature-dependent rheological measurements revealed a gel point of 42±1 °C. Below this temperature, the resulting material behaved as a true gel of high viscosity with values for the storage modulus G' being significantly larger than that for the loss modulus G''. Frequency-dependent rheological measurements at 20 °C revealed a mesh size (ξ) of 15 nm. AFM analysis of the diluted hydrogel in the dry state showed densely packed structures of entangled chains, which are also expected to contain multiple interlocked rings and catenanes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oscillating and pulsed gradient diffusion magnetic resonance microscopy over an extended b-value range: implications for the characterization of tissue microstructure.

PubMed

Portnoy, S; Flint, J J; Blackband, S J; Stanisz, G J

2013-04-01

Oscillating gradient spin-echo (OGSE) pulse sequences have been proposed for acquiring diffusion data with very short diffusion times, which probe tissue structure at the subcellular scale. OGSE sequences are an alternative to pulsed gradient spin echo measurements, which typically probe longer diffusion times due to gradient limitations. In this investigation, a high-strength (6600 G/cm) gradient designed for small-sample microscopy was used to acquire OGSE and pulsed gradient spin echo data in a rat hippocampal specimen at microscopic resolution. Measurements covered a broad range of diffusion times (TDeff = 1.2-15.0 ms), frequencies (ω = 67-1000 Hz), and b-values (b = 0-3.2 ms/μm2). Variations in apparent diffusion coefficient with frequency and diffusion time provided microstructural information at a scale much smaller than the imaging resolution. For a more direct comparison of the techniques, OGSE and pulsed gradient spin echo data were acquired with similar effective diffusion times. Measurements with similar TDeff were consistent at low b-value (b < 1 ms/μm(2) ), but diverged at higher b-values. Experimental observations suggest that the effective diffusion time can be helpful in the interpretation of low b-value OGSE data. However, caution is required at higher b, where enhanced sensitivity to restriction and exchange render the effective diffusion time an unsuitable representation. Oscillating and pulsed gradient diffusion techniques offer unique, complementary information. In combination, the two methods provide a powerful tool for characterizing complex diffusion within biological tissues. Copyright © 2012 Wiley Periodicals, Inc.

Active colloidal propulsion over a crystalline surface

NASA Astrophysics Data System (ADS)

Choudhury, Udit; Straube, Arthur V.; Fischer, Peer; Gibbs, John G.; Höfling, Felix

2017-12-01

We study both experimentally and theoretically the dynamics of chemically self-propelled Janus colloids moving atop a two-dimensional crystalline surface. The surface is a hexagonally close-packed monolayer of colloidal particles of the same size as the mobile one. The dynamics of the self-propelled colloid reflects the competition between hindered diffusion due to the periodic surface and enhanced diffusion due to active motion. Which contribution dominates depends on the propulsion strength, which can be systematically tuned by changing the concentration of a chemical fuel. The mean-square displacements (MSDs) obtained from the experiment exhibit enhanced diffusion at long lag times. Our experimental data are consistent with a Langevin model for the effectively two-dimensional translational motion of an active Brownian particle in a periodic potential, combining the confining effects of gravity and the crystalline surface with the free rotational diffusion of the colloid. Approximate analytical predictions are made for the MSD describing the crossover from free Brownian motion at short times to active diffusion at long times. The results are in semi-quantitative agreement with numerical results of a refined Langevin model that treats translational and rotational degrees of freedom on the same footing.

Thermodynamics, Diffusion, and Structure of Mg2SiO4 forsterite grain boundaries from atomistic modeling

NASA Astrophysics Data System (ADS)

Adjaoud, O.; Marquardt, K.; Jahn, S.

2011-12-01

Most materials are not single crystals but consist of crystalline grains of various sizes, misorientated with respect to each other and joint by grain boundaries. The latter influence many of the material properties. For instance, grain boundaries are short circuits for diffusion and thus they strongly influence transport properties of materials such as electrical conductivity, or mineral growth rates, creep, or phase transform. Olivine is a major component of the Earth's upper mantle and therefore it is of considerable importance to study its physical and thermodynamic polycrystalline properties. In the present study, we have used molecular dynamics simulations to model thermodynamics, self-diffusion and structure of a series of [100] symmetric tilt grain boundaries in forsterite. The interactions between the atoms are modeled by an advanced ionic interaction potential (Jahn and Madden, 2007). The parameters of the potential are fitted to ab initio results. The model was optimized for the Ca-Mg-Al-Si-O system and shows good transferability in a wide range of pressures, temperatures, and compositions. Thermodynamics and structure were simulated at ambient conditions, and self-diffusion coefficients were determined at ambient pressure and temperatures of 1250, 1500, 1750, and 2000 K. We find that the energy and excess free volume of the grain boundaries in forsterite depend significantly on the misorientation angle of the grain boundary. One of our modeled structures is compared with an high-resolution transmission electron micrograph (HRTEM) (Heinemann et al., 2005). We relate our findings to previous studies of grain boundaries in ionic materials and in metals. For small misorientation angles (up to 22.1°), grain boundary structures consist of an array of c-edge dislocations as suggested by Heinemann et al. (2005) and their energies can be readily fit with the Read-Shockley dislocation model for grain boundaries. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Similar to energies and excess free volumes, the self-diffusion coefficients of Mg and O depend significantly on the misorientation angle of the grain boundaries and they are well fitted with Arrhenius law. We compare our results to MgO grain boundary diffusion in forsterite derived from reaction rim growth experiments (Gardés and Heinrich, 2010).

Brownian Motion of Asymmetric Boomerang Colloidal Particles

NASA Astrophysics Data System (ADS)

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan; Sun, Kai; Wei, Qi-Huo

2014-03-01

We used video microscopy and single particle tracking to study the diffusion and local behaviors of asymmetric boomerang particles in a quasi-two dimensional geometry. The motion is biased towards the center of hydrodynamic stress (CoH) and the mean square displacements of the particles are linear at short and long times with different diffusion coefficients and in the crossover regime it is sub-diffusive. Our model based on Langevin theory shows that these behaviors arise from the non-coincidence of the CoH with the center of the body. Since asymmetric boomerangs represent a class of rigid bodies of more generals shape, therefore our findings are generic and true for any non-skewed particle in two dimensions. Both experimental and theoretical results will be discussed.

Improved classical united-atom force field for imidazolium-based ionic liquids: tetrafluoroborate, hexafluorophosphate, methylsulfate, trifluoromethylsulfonate, acetate, trifluoroacetate, and bis(trifluoromethylsulfonyl)amide.

PubMed

Zhong, Xiujuan; Liu, Zhiping; Cao, Dapeng

2011-08-25

A cost-effective, classical united-atom (UA) force field for ionic liquids (ILs) was proposed, which can be used in simulations of ILs composed by 1-alkyl-3-methyl-imidazolium cations ([C(n)mim](+)) and seven kinds of anions, including tetrafluoroborate ([BF(4)](-)), hexafluorophosphate ([PF(6)](-)), methylsulfate ([CH(3)SO(4)](-)), trifluoromethylsulfonate ([CF(3)SO(3)](-)), acetate ([CH(3)CO(2)](-)), trifluoroacetate ([CF(3)CO(2)](-)), and bis(trifluoromethylsulfonyl)amide ([NTf(2)](-)). The same strategy in our previous work (J. Phys. Chem. B 2010, 114, 4572) was used to parametrize the force field, in which the effective atom partial charges are fitted by the electrostatic potential surface (ESP) of ion pair dimers to account for the overall effects of polarization in ILs. The total charges (absolute values) on the cation/anion are in the range of 0.64-0.75, which are rescaled to 0.8 for all kinds of ions by a compromise between transferability and accuracy. Extensive molecular dynamics (MD) simulations were performed over a wide range of temperatures to validate the force field, especially on the enthalpies of vaporization (ΔH(vap)) and transport properties, including the self-diffusion coefficient and shear viscosity. The liquid densities were predicted very well for all of the ILs studied in this work with typical deviations of less than 1%. The simulated ΔH(vap) at 298 and 500 K are also in good agreement with the measured values by different experimental methods, with a slight overestimation of about 5 kJ/mol. The influence of ΔC(p) (the difference between the molar heat capacity at constant pressure of the gas and that of liquid) on the calculation of ΔH(vap) is also discussed. The transport coefficients were estimated by the equilibrium MD method using 20-60 ns trajectories to improve the sampling. The proposed force field gives a good description of the self-diffusion coefficients and shear viscosities, which is comparable to the recently developed polarizable force field. Although slightly lower dynamics is found in simulations by our force field, the order of magnitude of the self-diffusion coefficient and viscosity are reproduced for all the ILs very well over a wide temperature range. The largest underestimation of the self-diffusion coefficient is about one-third of the experimental values, while the largest overestimation of the viscosity is about two times the experimental values. © 2011 American Chemical Society

Numerical and analytical assessment of radon diffusion in various media and potential of charcoal as radon detector

NASA Astrophysics Data System (ADS)

Rybalkin, Andrey

Numerical assessments of radon diffusion together with analytical estimates for short-time and long-time exposure were the first objective of this thesis with the goal to demonstrate how radon propagates in various media. Theoretical predictions were compared to numerical simulations, and obtained values of total radon activities inside each material match quite well with the analytical estimates. These estimates, for activated and nonactivated charcoal, were then used to evaluate the possibility of designing a charcoal system to be used as a radon detector. Another objective was to use nonactivated charcoal samples and measure the level of radon accumulation, and use these data to estimate radon diffusion and adsorption coefficients. The analytical approach was developed to estimate these values. Radon adsorption coefficient in nonactivated charcoal was found to be from 0.2 to 0.4 m3/kg. Radon diffusion coefficient for nonactivated charcoal is in the range of 1.2×10-11 to 5.1×10-10 m2/s in comparison to activated charcoal with adsorption coefficient of 4 m3/kg and diffusion coefficient of 1.43×10-9 m2/s. The third objective was to use GEANT4 numerical code to simulate decay of 238U series and 222Rn in an arbitrary soil sample. Based on that model, the goal was to provide a guideline for merging GEANT4 radioactive decay modeling with the diffusion of radon in a soil sample. It is known that radon can be used as an earthquake predictor by measuring its concentration in groundwater, or if possible, along the faults. Numerical simulations of radon migration by diffusion only were made to estimate how fast and how far radon can move along the fault strands. Among the known cases of successful correlations between radon concentration anomalies and earthquake are the 1966 Tashkent and 1976 Songpan-Pingwu earthquakes. Thus, an idea of radon monitoring along the Wasatch Fault, using system of activated/nonactivated charcoals together with solid state radon detectors is suggested in the thesis. Also, the use of neutron activation analysis for soil samples, collected along and away from Wasatch Fault, and looking for the trace elements can result in correlation with earthquakes, occurred in the past. This approach can be used for earthquake prediction in future.

Warthin tumor of the parotid gland: diagnostic value of MR imaging with histopathologic correlation.

PubMed

Ikeda, Mitsuaki; Motoori, Ken; Hanazawa, Toyoyuki; Nagai, Yuichiro; Yamamoto, Seiji; Ueda, Takuya; Funatsu, Hiroyuki; Ito, Hisao

2004-08-01

The purpose of our study was to describe the MR imaging appearance of Warthin tumors multiple MR imaging techniques and to interpret the difference in appearance from that of malignant parotid tumors. T1-weighted, T2-weighted, short inversion time inversion recovery, diffusion-weighted, and contrast-enhanced dynamic MR images of 19 Warthin tumors and 17 malignant parotid tumors were reviewed. MR imaging results were compared with those of pathologic analysis. Epithelial stromata and lymphoid tissue with slitlike small cysts in Warthin tumors showed early enhancement and a high washout rate (> or =30%) on dynamic contrast-enhanced images, and accumulations of complicated cysts showed early enhancement and a low washout ratio (< 30%). The areas containing complicated cysts showed high signal intensity on T1-weighted images, whereas some foci in those areas showed low signal intensity on short tau inversion recovery images. The mean minimum signal intensity ratios (SIRmin) of Warthin tumor on short tau inversion recovery (0.29 +/- 0.22 SD) (P < .01) and T2-weighted images (0.28 +/- 0.09) (P < .05) were significantly lower than those of malignant parotid tumors (0.53 +/- 0.19, 0.48 +/- 0.19). The average washout ratio of Warthin tumors (44.0 +/- 20.4%) was higher than that of malignant parotid tumors (11.9 +/- 11.6%). The mean apparent diffusion coefficient of Warthin tumors (0.96 +/- 0.13 x 10(-3)mm2/s) was significantly lower (P < .01) than that of malignant tumors (1.19 +/- 0.19 x 10(-3)mm2/s). Detecting hypointense areas of short tau inversion recovery and T2-weighted images or low apparent diffusion coefficient values on diffusion-weighted images was useful for predicting whether salivary gland tumors were Warthin tumors. The findings of the dynamic contrast-enhanced study also were useful.

Measurement of ageing effect on chloride diffusion coefficients in cementitious matrices

NASA Astrophysics Data System (ADS)

Andrade, C.; Castellote, M.; d'Andrea, R.

2011-05-01

Most of the low-level nuclear waste disposal facilities are based in engineered multi barrier systems where reinforced concrete is one of the basic materials. The calculation of the time until steel reinforcement depassivation is a need due to the demand of prediction of the service life of concrete structures in radioactive repositories. In doing that, one of the main steps is the transport of chloride ions towards the reinforcement, as one of the most aggressive agents for the rebars in concrete is chloride ions. Ageing of concrete related to chloride penetration leads to significant decrease of the "apparent diffusion" coefficient with time. If this effect is not considered, considerable bias can be introduced when predicting service life of reinforced concrete of repositories. Several effects have been addressed on their influence on the ageing of concrete, including the evolution with time of the concrete pore refinement, the binding of chlorides to the cement phases and to the changes of chloride "surface concentration". These effects have been studied in specimens made with different mixes trying to represent a wide range of mineral addition proportions. The analysis of their evolution with time has shown that the resistivity alone or the joint consideration of resistivity and binding capacity ( Cb/ Cf), are appropriate parameters to appraise the diffusivity ageing. For practical reasons, an accelerated procedure is proposed in order to calculate ageing for short periods of time.

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.

Predicting the Kinetics of Ice Recrystallization in Aqueous Sugar Solutions

PubMed Central

2018-01-01

The quality of stored frozen products such as foods and biomaterials generally degrades in time due to the growth of large ice crystals by recrystallization. While there is ample experimental evidence that recrystallization within such products (or model systems thereof) is often dominated by diffusion-limited Ostwald ripening, the application of Ostwald-ripening theories to predict measured recrystallization rates has only met with limited success. For a model system of polycrystalline ice within an aqueous solution of sugars, we here show recrystallization rates can be predicted on the basis of Ostwald ripening theory, provided (1) the theory accounts for the fact the solution can be nonideal, nondilute and of different density than the crystals, (2) the effect of ice-phase volume fraction on the diffusional flux of water between crystals is accurately described, and (3) all relevant material properties (involving binary Fick diffusion coefficients, the thermodynamic factor of the solution, and the surface energy of ice) are carefully estimated. To enable calculation of material properties, we derive an alternative formulation of Ostwald ripening in terms of the Maxwell–Stefan instead of the Fick approach to diffusion. First, this leads to a cancellation of the thermodynamic factor (a measure for the nonideality of a solution), which is a notoriously difficult property to obtain. Second, we show that Maxwell–Stefan diffusion coefficients can to a reasonable approximation be related to self-diffusion coefficients, which are relatively easy to measure or predict in comparison to Fick diffusion coefficients. Our approach is validated for a binary system of water and sucrose, for which we show predicted recrystallization rates of ice compare well to experimental results, with relative deviations of at most a factor of 2. PMID:29651228

Predicting the Kinetics of Ice Recrystallization in Aqueous Sugar Solutions.

PubMed

van Westen, Thijs; Groot, Robert D

2018-04-04

The quality of stored frozen products such as foods and biomaterials generally degrades in time due to the growth of large ice crystals by recrystallization. While there is ample experimental evidence that recrystallization within such products (or model systems thereof) is often dominated by diffusion-limited Ostwald ripening, the application of Ostwald-ripening theories to predict measured recrystallization rates has only met with limited success. For a model system of polycrystalline ice within an aqueous solution of sugars, we here show recrystallization rates can be predicted on the basis of Ostwald ripening theory, provided (1) the theory accounts for the fact the solution can be nonideal, nondilute and of different density than the crystals, (2) the effect of ice-phase volume fraction on the diffusional flux of water between crystals is accurately described, and (3) all relevant material properties (involving binary Fick diffusion coefficients, the thermodynamic factor of the solution, and the surface energy of ice) are carefully estimated. To enable calculation of material properties, we derive an alternative formulation of Ostwald ripening in terms of the Maxwell-Stefan instead of the Fick approach to diffusion. First, this leads to a cancellation of the thermodynamic factor (a measure for the nonideality of a solution), which is a notoriously difficult property to obtain. Second, we show that Maxwell-Stefan diffusion coefficients can to a reasonable approximation be related to self-diffusion coefficients, which are relatively easy to measure or predict in comparison to Fick diffusion coefficients. Our approach is validated for a binary system of water and sucrose, for which we show predicted recrystallization rates of ice compare well to experimental results, with relative deviations of at most a factor of 2.

Precise measurement of the self-diffusion coefficient for poly(ethylene glycol) in aqueous solution using uniform oligomers

NASA Astrophysics Data System (ADS)

Shimada, Kayori; Kato, Haruhisa; Saito, Takeshi; Matsuyama, Shigetomo; Kinugasa, Shinichi

2005-06-01

Uniform poly(ethylene glycol) (PEG) oligomers, with a degree of polymerization n =1-40, were separated by preparative supercritical fluid chromatography from commercial monodispersed samples. Diffusion coefficients, D, for separated uniform PEG oligomers were measured in dilute solutions of deuterium oxide (D2O) at 30 ° C, using pulsed-field gradient nuclear magnetic resonance. The measured D for each molecular weight was extrapolated to infinite dilution. Diffusion coefficients obtained at infinite dilution follow the scaling behavior of Zimm-type diffusion, even in the lower molecular weight range. Molecular-dynamics simulations for PEG in H2O also showed this scaling behavior, and reproduced close hydrodynamic interactions between PEG and water. These findings suggest that diffusion of PEG in water is dominated by hydrodynamic interaction over a wide molecular weight range, including at low molecular weights around 1000.

Effect of Structure on Transport Properties (Viscosity, Ionic Conductivity, and Self-Diffusion Coefficient) of Aprotic Heterocyclic Anion (AHA) Room-Temperature Ionic Liquids. 1. Variation of Anionic Species.

PubMed

Sun, Liyuan; Morales-Collazo, Oscar; Xia, Han; Brennecke, Joan F

2015-12-03

A series of room temperature ionic liquids (RTILs) based on 1-ethyl-3-methylimidazolium ([emim](+)) with different aprotic heterocyclic anions (AHAs) were synthesized and characterized as potential electrolyte candidates for lithium ion batteries. The density and transport properties of these ILs were measured over the temperature range between 283.15 and 343.15 K at ambient pressure. The temperature dependence of the transport properties (viscosity, ionic conductivity, self-diffusion coefficient, and molar conductivity) is fit well by the Vogel-Fulcher-Tamman (VFT) equation. The best-fit VFT parameters, as well as linear fits to the density, are reported. The ionicity of these ILs was quantified by the ratio of the molar conductivity obtained from the ionic conductivity and molar concentration to that calculated from the self-diffusion coefficients using the Nernst-Einstein equation. The results of this study, which is based on ILs composed of both a planar cation and planar anions, show that many of the [emim][AHA] ILs exhibit very good conductivity for their viscosities and provide insight into the design of ILs with enhanced dynamics that may be suitable for electrolyte applications.

Probe pressure effects on human skin diffuse reflectance and fluorescence spectroscopy measurements

PubMed Central

Lim, Liang; Nichols, Brandon; Rajaram, Narasimhan; Tunnell, James W.

2011-01-01

Diffuse reflectance and fluorescence spectroscopy are popular research techniques for noninvasive disease diagnostics. Most systems include an optical fiber probe that transmits and collects optical spectra in contact with the suspected lesion. The purpose of this study is to investigate probe pressure effects on human skin spectroscopic measurements. We conduct an in-vivo experiment on human skin tissue to study the short-term (<2 s) and long-term (>30 s) effects of probe pressure on diffuse reflectance and fluorescence measurements. Short-term light probe pressure (P0 < 9 mN∕mm2) effects are within 0 ± 10% on all physiological properties extracted from diffuse reflectance and fluorescence measurements, and less than 0 ± 5% for diagnostically significant physiological properties. Absorption decreases with site-specific variations due to blood being compressed out of the sampled volume. Reduced scattering coefficient variation is site specific. Intrinsic fluorescence shows a large standard error, although no specific pressure-related trend is observed. Differences in tissue structure and morphology contribute to site-specific probe pressure effects. Therefore, the effects of pressure can be minimized when the pressure is small and applied for a short amount of time; however, long-term and large pressures induce significant distortions in measured spectra. PMID:21280899

Excess entropy scaling for the segmental and global dynamics of polyethylene melts.

PubMed

Voyiatzis, Evangelos; Müller-Plathe, Florian; Böhm, Michael C

2014-11-28

The range of validity of the Rosenfeld and Dzugutov excess entropy scaling laws is analyzed for unentangled linear polyethylene chains. We consider two segmental dynamical quantities, i.e. the bond and the torsional relaxation times, and two global ones, i.e. the chain diffusion coefficient and the viscosity. The excess entropy is approximated by either a series expansion of the entropy in terms of the pair correlation function or by an equation of state for polymers developed in the context of the self associating fluid theory. For the whole range of temperatures and chain lengths considered, the two estimates of the excess entropy are linearly correlated. The scaled bond and torsional relaxation times fall into a master curve irrespective of the chain length and the employed scaling scheme. Both quantities depend non-linearly on the excess entropy. For a fixed chain length, the reduced diffusion coefficient and viscosity scale linearly with the excess entropy. An empirical reduction to a chain length-independent master curve is accessible for both dynamic quantities. The Dzugutov scheme predicts an increased value of the scaled diffusion coefficient with increasing chain length which contrasts physical expectations. The origin of this trend can be traced back to the density dependence of the scaling factors. This finding has not been observed previously for Lennard-Jones chain systems (Macromolecules, 2013, 46, 8710-8723). Thus, it limits the applicability of the Dzugutov approach to polymers. In connection with diffusion coefficients and viscosities, the Rosenfeld scaling law appears to be of higher quality than the Dzugutov approach. An empirical excess entropy scaling is also proposed which leads to a chain length-independent correlation. It is expected to be valid for polymers in the Rouse regime.

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

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

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

PubMed

Dutt, Arun K

2005-09-22

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

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.

Current understanding of point defects and diffusion processes in silicon

NASA Technical Reports Server (NTRS)

Tan, T. Y.; Goesele, U.

1985-01-01

The effects of oxidation of Si which established that vacancies (V) and Si self interstitials (I) coexist in Si at high temperatures under thermal equilibrium and oxidizing conditions are discussed. Some essential points associated with Au diffusion in Si are then discussed. Analysis of Au diffusion results allowed a determination of the I component and an estimate of the V component of the Si self diffusion coefficient. A discussion of theories on high concentration P diffusion into Si is then presented. Although presently there still is no theory that is completely satisfactory, significant progresses are recently made in treating some essential aspects of this subject.

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.

Self-diffusion studies by intra- and inter-molecular spin-lattice relaxometry using field-cycling: Liquids, plastic crystals, porous media, and polymer segments.

PubMed

Kimmich, Rainer; Fatkullin, Nail

2017-08-01

Field-cycling NMR relaxometry is a well-established technique for probing molecular dynamics in a frequency range from typically a few kHz up to several tens of MHz. For the interpretation of relaxometry data, it is quite often assumed that the spin-lattice relaxation process is of an intra-molecular nature so that rotational fluctuations dominate. However, dipolar interactions as the main type of couplings between protons and other dipolar species without quadrupole moments can imply appreciable inter-molecular contributions. These fluctuate due to translational displacements and to a lesser degree also by rotational reorientations in the short-range limit. The analysis of the inter-molecular proton spin-lattice relaxation rate thus permits one to evaluate self-diffusion variables such as the diffusion coefficient or the mean square displacement on a time scale from nanoseconds to several hundreds of microseconds. Numerous applications to solvents, plastic crystals and polymers will be reviewed. The technique is of particular interest for polymer dynamics since inter-molecular spin-lattice relaxation diffusometry bridges the time scales of quasi-elastic neutron scattering and field-gradient NMR diffusometry. This is just the range where model-specific intra-coil mechanisms are assumed to occur. They are expected to reveal themselves by characteristic power laws for the time-dependence of the mean-square segment displacement. These can be favorably tested on this basis. Results reported in the literature will be compared with theoretical predictions. On the other hand, there is a second way for translational diffusion phenomena to affect the spin-lattice relaxation dispersion. If rotational diffusion of molecules is restricted, translational diffusion properties can be deduced even from molecular reorientation dynamics detected by intra-molecular spin-lattice relaxation. This sort of scenario will be relevant for adsorbates on surfaces or polymer segments under entanglement and chain connectivity constraints. Under such conditions, reorientations will be correlated with translational displacements leading to the so-called RMTD relaxation process (reorientation mediated by translational displacements). Applications to porous glasses, protein solutions, lipid bilayers, and clays will be discussed. Finally, we will address the intriguing fact that the various time limits of the segment mean-square displacement of polymers in some cases perfectly reproduce predictions of the tube/reptation model whereas the reorientation dynamics suggests strongly deviating power laws. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation.

PubMed

Sharma, Anirban; Ghorai, Pradip Kr

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

Effect of water on structure and dynamics of [BMIM][PF{sub 6}] ionic liquid: An all-atom molecular dynamics simulation investigation

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

Sharma, Anirban; Ghorai, Pradip Kr., E-mail: pradip@iiserkol.ac.in

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF{sub 6}]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure ILmore » but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.« less

Fluctuation-enhanced electric conductivity in electrolyte solutions

DOE PAGES

Péraud, Jean-Philippe; Nonaka, Andrew J.; Bell, John B.; ...

2017-09-26

In this work, we analyze the effects of an externally applied electric field on thermal fluctuations for a binary electrolyte fluid. We show that the fluctuating Poisson–Nernst–Planck (PNP) equations for charged multispecies diffusion coupled with the fluctuating fluid momentum equation result in enhanced charge transport via a mechanism distinct from the well-known enhancement of mass transport that accompanies giant fluctuations. Although the mass and charge transport occurs by advection by thermal velocity fluctuations, it can macroscopically be represented as electrodiffusion with renormalized electric conductivity and a nonzero cation–anion diffusion coefficient. Specifically, we predict a nonzero cation–anion Maxwell– Stefan coefficient proportionalmore » to the square root of the salt concentration, a prediction that agrees quantitatively with experimental measurements. The renormalized or effective macroscopic equations are different from the starting PNP equations, which contain no cross-diffusion terms, even for rather dilute binary electrolytes. At the same time, for infinitely dilute solutions the renormalized electric conductivity and renormalized diffusion coefficients are consistent and the classical PNP equations with renormalized coefficients are recovered, demonstrating the self-consistency of the fluctuating hydrodynamics equations. Our calculations show that the fluctuating hydrodynamics approach recovers the electrophoretic and relaxation corrections obtained by Debye–Huckel–Onsager theory, while elucidating the physical origins of these corrections and generalizing straightforwardly to more complex multispecies electrolytes. Lastly, we show that strong applied electric fields result in anisotropically enhanced “giant” velocity fluctuations and reduced fluctuations of salt concentration.« less

Fluctuation-enhanced electric conductivity in electrolyte solutions

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

Péraud, Jean-Philippe; Nonaka, Andrew J.; Bell, John B.

In this work, we analyze the effects of an externally applied electric field on thermal fluctuations for a binary electrolyte fluid. We show that the fluctuating Poisson–Nernst–Planck (PNP) equations for charged multispecies diffusion coupled with the fluctuating fluid momentum equation result in enhanced charge transport via a mechanism distinct from the well-known enhancement of mass transport that accompanies giant fluctuations. Although the mass and charge transport occurs by advection by thermal velocity fluctuations, it can macroscopically be represented as electrodiffusion with renormalized electric conductivity and a nonzero cation–anion diffusion coefficient. Specifically, we predict a nonzero cation–anion Maxwell– Stefan coefficient proportionalmore » to the square root of the salt concentration, a prediction that agrees quantitatively with experimental measurements. The renormalized or effective macroscopic equations are different from the starting PNP equations, which contain no cross-diffusion terms, even for rather dilute binary electrolytes. At the same time, for infinitely dilute solutions the renormalized electric conductivity and renormalized diffusion coefficients are consistent and the classical PNP equations with renormalized coefficients are recovered, demonstrating the self-consistency of the fluctuating hydrodynamics equations. Our calculations show that the fluctuating hydrodynamics approach recovers the electrophoretic and relaxation corrections obtained by Debye–Huckel–Onsager theory, while elucidating the physical origins of these corrections and generalizing straightforwardly to more complex multispecies electrolytes. Lastly, we show that strong applied electric fields result in anisotropically enhanced “giant” velocity fluctuations and reduced fluctuations of salt concentration.« less

A spin echo sequence with a single-sided bipolar diffusion gradient pulse to obtain snapshot diffusion weighted images in moving media

NASA Astrophysics Data System (ADS)

Freidlin, R. Z.; Kakareka, J. W.; Pohida, T. J.; Komlosh, M. E.; Basser, P. J.

2012-08-01

In vivo MRI data can be corrupted by motion. Motion artifacts are particularly troublesome in Diffusion Weighted MRI (DWI), since the MR signal attenuation due to Brownian motion can be much less than the signal loss due to dephasing from other types of complex tissue motion, which can significantly degrade the estimation of self-diffusion coefficients, diffusion tensors, etc. This paper describes a snapshot DWI sequence, which utilizes a novel single-sided bipolar diffusion sensitizing gradient pulse within a spin echo sequence. The proposed method shortens the diffusion time by applying a single refocused bipolar diffusion gradient on one side of a refocusing RF pulse, instead of a set of diffusion sensitizing gradients, separated by a refocusing RF pulse, while reducing the impact of magnetic field inhomogeneity by using a spin echo sequence. A novel MRI phantom that can exhibit a range of complex motions was designed to demonstrate the robustness of the proposed DWI sequence.

Accurate measurement of dispersion data through short and narrow tubes used in very high-pressure liquid chromatography.

PubMed

Gritti, Fabrice; McDonald, Thomas; Gilar, Martin

2015-09-04

An original method is proposed for the accurate and reproducible measurement of the time-based dispersion properties of short L< 50cm and narrow rc< 50μm tubes at mobile phase flow rates typically used in very high-pressure liquid chromatography (vHPLC). Such tubes are used to minimize sample dispersion in vHPLC; however, their dispersion characteristics cannot be accurately measured at such flow rates due to system dispersion contribution of vHPLC injector and detector. It is shown that using longer and wider tubes (>10μL) enables a reliable measurement of the dispersion data. We confirmed that the dimensionless plot of the reduced dispersion coefficient versus the reduced linear velocity (Peclet number) depends on the aspect ratio, L/rc, of the tube, and unexpectedly also on the diffusion coefficient of the analyte. This dimensionless plot could be easily obtained for a large volume tube, which has the same aspect ratio as that of the short and narrow tube, and for the same diffusion coefficient. The dispersion data for the small volume tube are then directly extrapolated from this plot. For instance, it is found that the maximum volume variances of 75μm×30.5cm and 100μm×30.5cm prototype finger-tightened connecting tubes are 0.10 and 0.30μL(2), respectively, with an accuracy of a few percent and a precision smaller than seven percent. Copyright © 2015 Elsevier B.V. All rights reserved.

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

USGS Publications Warehouse

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

2015-01-01

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

Augmentation of oxygen transport by various hemoglobins as determined by pulsed field gradient NMR.

PubMed

Budhiraja, Vikas; Hellums, J David; Post, Jan F M

2002-11-01

Diffusion of oxyhemoglobin has been shown to augment the oxygen transport inside the red blood cells. Measurement of hemoglobin diffusion coefficients by pulsed-field gradient (PFG) nuclear magnetic resonance (NMR) technique can be used for estimating this augmentation effect. Self-diffusion coefficients of polymerized and unpolymerized bovine hemoglobin (Hb) and several other proteins were measured using this technique. The Hb diffusion coefficient was used to determine the effective permeability of oxygen and augmentation of oxygen transport through samples of Hb solutions due to diffusion of oxyhemoglobin. The values compared well with our previous diffusion cell measurements of effective diffusivity and augmentation. Our NMR studies show that even at low concentrations the augmentation of oxygen transport due to diffusion can be significant. The PFG NMR technique can thus provide an accurate and easy method for measuring augmentation of oxygen transport, especially in dilute samples of Hb. The results on polyhemoglobin and high-molecular-weight hemoglobin are of both basic interest and practical value in assessing the promise and performance of hemoglobin-based blood substitutes.

Quasilinear diffusion coefficients in a finite Larmor radius expansion for ion cyclotron heated plasmas

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

Lee, Jungpyo; Wright, John; Bertelli, Nicola

In this study, a reduced model of quasilinear velocity diffusion by a small Larmor radius approximation is derived to couple the Maxwell’s equations and the Fokker Planck equation self-consistently for the ion cyclotron range of frequency waves in a tokamak. The reduced model ensures the important properties of the full model by Kennel-Engelmann diffusion, such as diffusion directions, wave polarizations, and H-theorem. The kinetic energy change (Wdot ) is used to derive the reduced model diffusion coefficients for the fundamental damping (n = 1) and the second harmonic damping (n = 2) to the lowest order of the finite Larmormore » radius expansion. The quasilinear diffusion coefficients are implemented in a coupled code (TORIC-CQL3D) with the equivalent reduced model of the dielectric tensor. We also present the simulations of the ITER minority heating scenario, in which the reduced model is verified within the allowable errors from the full model results.« less

Quasilinear diffusion coefficients in a finite Larmor radius expansion for ion cyclotron heated plasmas

DOE PAGES

Lee, Jungpyo; Wright, John; Bertelli, Nicola; ...

2017-04-24

In this study, a reduced model of quasilinear velocity diffusion by a small Larmor radius approximation is derived to couple the Maxwell’s equations and the Fokker Planck equation self-consistently for the ion cyclotron range of frequency waves in a tokamak. The reduced model ensures the important properties of the full model by Kennel-Engelmann diffusion, such as diffusion directions, wave polarizations, and H-theorem. The kinetic energy change (Wdot ) is used to derive the reduced model diffusion coefficients for the fundamental damping (n = 1) and the second harmonic damping (n = 2) to the lowest order of the finite Larmormore » radius expansion. The quasilinear diffusion coefficients are implemented in a coupled code (TORIC-CQL3D) with the equivalent reduced model of the dielectric tensor. We also present the simulations of the ITER minority heating scenario, in which the reduced model is verified within the allowable errors from the full model results.« less

Molecular Dynamics Simulations of Grain Boundary and Bulk Diffusion in Metals.

NASA Astrophysics Data System (ADS)

Plimpton, Steven James

Diffusion is a microscopic mass transport mechanism that underlies many important macroscopic phenomena affecting the structural, electrical, and mechanical properties of metals. This thesis presents results from atomistic simulation studies of diffusion both in bulk and in the fast diffusion paths known as grain boundaries. Using the principles of molecular dynamics single boundaries are studied and their structure and dynamic properties characterized. In particular, tilt boundary bicrystal and bulk models of fcc Al and bcc alpha-Fe are simulated. Diffusion coefficients and activation energies for atomic motion are calculated for both models and compared to experimental data. The influence of the interatomic pair potential on the diffusion is studied in detail. A universal relation between the melting temperature that a pair potential induces in a simulated bulk model and the potential energy barrier height for atomic hopping is derived and used to correlate results for a wide variety of pair potentials. Using these techniques grain boundary and bulk diffusion coefficients for any fcc material can be estimated from simple static calculations without the need to perform more time-consuming dynamic simulations. The influences of two other factors on grain boundary diffusion are also studied because of the interest of the microelectronics industry in the diffusion related reliability problem known as electromigration. The first factor, known to affect the self diffusion rate of Al, is the presence of Cu impurity atoms in Al tilt boundaries. The bicrystal model for Al is seeded randomly with Cu atoms and a simple hybrid Morse potential used to model the Al-Cu interaction. While some effect due to the Cu is noted, it is concluded that pair potentials are likely an inadequate approximation for the alloy system. The second factor studied is the effect of the boundary orientation angle on the diffusion rate. Symmetric bcc Fe boundaries are relaxed to find optimal structures and their diffusion coefficients calculated. Good agreement is found with the dislocation pipe model for tilt boundary diffusion.

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.

Numerical simulation of multi-dimensional NMR response in tight sandstone

NASA Astrophysics Data System (ADS)

Guo, Jiangfeng; Xie, Ranhong; Zou, Youlong; Ding, Yejiao

2016-06-01

Conventional logging methods have limitations in the evaluation of tight sandstone reservoirs. The multi-dimensional nuclear magnetic resonance (NMR) logging method has the advantage that it can simultaneously measure transverse relaxation time (T 2), longitudinal relaxation time (T 1) and diffusion coefficient (D). In this paper, we simulate NMR measurements of tight sandstone with different wettability and saturations by the random walk method and obtain the magnetization decays of Carr-Purcell-Meiboom-Gill pulse sequences with different wait times (TW) and echo spacings (TE) under a magnetic field gradient, resulting in D-T 2-T 1 maps by the multiple echo trains joint inversion method. We also study the effects of wettability, saturation, signal-to-noise ratio (SNR) of data and restricted diffusion on the D-T 2-T 1 maps in tight sandstone. The results show that with decreasing wetting fluid saturation, the surface relaxation rate of the wetting fluid gradually increases and the restricted diffusion phenomenon becomes more and more obvious, which leads to the wetting fluid signal moving along the direction of short relaxation and the direction of the diffusion coefficient decreasing in D-T 2-T 1 maps. Meanwhile, the non-wetting fluid position in D-T 2-T 1 maps does not change with saturation variation. With decreasing SNR, the ability to identify water and oil signals based on NMR maps gradually decreases. The wetting fluid D-T 1 and D-T 2 correlations in NMR diffusion-relaxation maps of tight sandstone are obtained through expanding the wetting fluid restricted diffusion models, and are further applied to recognize the wetting fluid in simulated D-T 2 maps and D-T 1 maps.

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.

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.

NMR and molecular dynamics study of the size, shape, and composition of reverse micelles in a cetyltrimethylammonium bromide (CTAB)/n-hexane/pentanol/water microemulsion.

PubMed

Mills, Amanda J; Wilkie, John; Britton, Melanie M

2014-09-11

The size, shape, and composition of reverse micelles (RMs) in a cetyltrimethylammonium bromide (CTAB)/pentanol/n-hexane/water microemulsion were investigated using pulsed gradient stimulated echo (PGSTE) nuclear magnetic resonance (NMR) measurements and molecular modeling. PGSTE data were collected at observation times (Δ) of 10, 40, and 450 ms. At long observation times, CTAB and pentanol exhibited single diffusion coefficients. However, at short (Δ ≤ 40 ms) observation times both CTAB and pentanol exhibited slow and fast diffusion coefficients. These NMR data indicate that both CTAB and pentanol molecules reside in different environments within the microemulsion and that there is exchange between regions on the millisecond time scale. Molecular dynamic simulations of the CTAB RM, in a solvent box containing n-hexane and pentanol, produced an ellipsoid shaped RM. Using structural parameters from these simulations and the Stokes-Einstein relation, the structure factor and dimensions of the reverse micelle were determined. Analysis of the composition of the interphase also showed that there was a variation in the ratio of surfactant to cosurfactant molecules depending on the curvature of the interphase.

Needlelike motion of prolate ellipsoids in the sea of spheres

NASA Astrophysics Data System (ADS)

Vasanthi, R.; Ravichandran, S.; Bagchi, Biman

2001-05-01

Molecular dynamics simulations of translational motion of isolated prolate ellipsoids in the sea of spheres have been carried out for several different values of the aspect ratio (κ), obtained by changing either the length or the diameter of the ellipsoids, at several different solvent densities. The interaction among the spheres is given by the Lennard-Jones pair potential while that between spheres and ellipsoids is given by a modified Gay-Berne potential. Both the mean-square displacements of the center of mass of the ellipsoids and their orientational time correlation function have been calculated. It is found that at short to intermediate times, the motion of ellipsoids is anisotropic and primarily needlelike—the molecules prefer to move parallel to their long axis. The ratio of these two diffusion constants (D∥ and D⊥) approaches κ, suggesting a decoupling of D∥ from the length of the ellipsoid. The diffusion becomes isotropic in the long time with the total diffusion coefficient given by D∥+2D⊥. The crossover from the anisotropic to the isotropic diffusion is surprisingly sharp and clear in most cases.

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.

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.

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.

Distribution and Dynamic Properties of Xenon Dissolved in the Ionic Smectic Phase of [C16mim][NO3]: MD Simulation and Theoretical Model.

PubMed

Frezzato, Diego; Saielli, Giacomo

2016-03-10

We have investigated the structural and dynamic properties of Xe dissolved in the ionic liquid crystal (ILC) phase of 1-hexadecyl-3-methylimidazolium nitrate using classical molecular dynamics (MD) simulations. Xe is found to be preferentially dissolved within the hydrophobic environment of the alkyl chains rather than in the ionic layers of the smectic phase. The structural parameters and the estimated local diffusion coefficients concerning the short-time motion of Xe are used to parametrize a theoretical model based on the Smoluchowski equation for the macroscopic dynamics across the smectic layers, a feature which cannot be directly obtained from the relatively short MD simulations. This protocol represents an efficient combination of computational and theoretical tools to obtain information on slow processes concerning the permeability and diffusivity of the xenon in smectic ILCs.

PSO-Assisted Development of New Transferable Coarse-Grained Water Models.

PubMed

Bejagam, Karteek K; Singh, Samrendra; An, Yaxin; Berry, Carter; Deshmukh, Sanket A

2018-02-15

We have employed two-to-one mapping scheme to develop three coarse-grained (CG) water models, namely, 1-, 2-, and 3-site CG models. Here, for the first time, particle swarm optimization (PSO) and gradient descent methods were coupled to optimize the force-field parameters of the CG models to reproduce the density, self-diffusion coefficient, and dielectric constant of real water at 300 K. The CG MD simulations of these new models conducted with various timesteps, for different system sizes, and at a range of different temperatures are able to predict the density, self-diffusion coefficient, dielectric constant, surface tension, heat of vaporization, hydration free energy, and isothermal compressibility of real water with excellent accuracy. The 1-site model is ∼3 and ∼4.5 times computationally more efficient than 2- and 3-site models, respectively. To utilize the speed of 1-site model and electrostatic interactions offered by 2- and 3-site models, CG MD simulations of 1:1 combination of 1- and 2-/3-site models were performed at 300 K. These mixture simulations could also predict the properties of real water with good accuracy. Two new CG models of benzene, consisting of beads with and without partial charges, were developed. All three water models showed good capacity to solvate these benzene models.

Percutaneous absorption of sunscreen agents from liquid paraffin: self-association of octyl salicylate and effects on skin flux.

PubMed

Jiang, R; Roberts, M S; Prankerd, R J; Benson, H A

1997-07-01

This study provides an investigation of the availability of octyl salicylate (OS), a common sunscreen agent, from liquid paraffin and the effect of OS on skin permeability. A model membrane system to isolate the vehicle effect from membrane permeability has been developed. Partitioning of OS between liquid paraffin and aqueous receptor phases was conducted. Partition coefficients increased with increase in OS concentration. A range of OS concentrations in liquid paraffin was diffused across human epidermis and synthetic membranes into 4% bovine serum albumin in phosphate-buffered saline and 50% ethanol. Absorption profiles of OS obtained from silicone and low-density polyethylene (LDPE) membranes were similar to each other but higher than for the high-density polyethylene [HDPE (3 times)] membrane and human epidermis (15 times). The steady state fluxes and apparent permeability coefficients (Kp') obtained from the diffusion studies showed the same trends with all membranes, except for the HDPE membrane which showed greater increase in flux and Kp' at concentrations above 30%. IR spectra showed that several bands of OS were shifted with concentrations, and the molecular models further suggested that the main contribution to the self-association is from non-1,4 van der Waals interactions.

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

NASA Astrophysics Data System (ADS)

Pilinski, M.; Crowley, G.

2014-12-01

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

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

NASA Astrophysics Data System (ADS)

Pilinski, M. D.; Crowley, G.

2015-04-01

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

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.

Kinetic model for the short-term dissolution of a rhyolitic glass

USGS Publications Warehouse

White, A.F.; Claassen, H.C.

1980-01-01

Aqueous dissolution experiments with the vitric phase of a rhyolitic tuff were performed at 25??C and constant pH in the range 4.5-7.5. Results suggest interchange of aqueous hydrogen ions for cations situated both on the surface and within the glass. At time intervals from 24 to 900 hr., dissolution kinetics are controlled by ion transport to and from sites within the glass. Experimental data indicate that parabolic diffusion rate of a chemical species from the solid is a nonlinear function of its aqueous concentration. A numerical solution to Fick's second law is presented for diffusion of sodium, which relates it's aqueous concentration to it's concentration on glass surface, by a Freundlich adsorption isotherm. The pH influence on sodium diffusion in the model can be accounted for by use of a pH-dependent diffusion coefficient and a pH-independent adsorption isotherm. ?? 1980.

Three-Dimensional Tracking of Interfacial Hopping Diffusion

NASA Astrophysics Data System (ADS)

Wang, Dapeng; Wu, Haichao; Schwartz, Daniel K.

2017-12-01

Theoretical predictions have suggested that molecular motion at interfaces—which influences processes including heterogeneous catalysis, (bio)chemical sensing, lubrication and adhesion, and nanomaterial self-assembly—may be dominated by hypothetical "hops" through the adjacent liquid phase, where a diffusing molecule readsorbs after a given hop according to a probabilistic "sticking coefficient." Here, we use three-dimensional (3D) single-molecule tracking to explicitly visualize this process for human serum albumin at solid-liquid interfaces that exert varying electrostatic interactions on the biomacromolecule. Following desorption from the interface, a molecule experiences multiple unproductive surface encounters before readsorption. An average of approximately seven surface collisions is required for the repulsive surfaces, decreasing to approximately two and a half for surfaces that are more attractive. The hops themselves are also influenced by long-range interactions, with increased electrostatic repulsion causing hops of longer duration and distance. These findings explicitly demonstrate that interfacial diffusion is dominated by biased 3D Brownian motion involving bulk-surface coupling and that it can be controlled by influencing short- and long-range adsorbate-surface interactions.

Universal time-dependent dispersion properties for diffusion in a one-dimensional critically tilted potential

NASA Astrophysics Data System (ADS)

Guérin, T.; Dean, D. S.

2017-01-01

We consider the time-dependent dispersion properties of overdamped tracer particles diffusing in a one-dimensional periodic potential under the influence of an additional constant tilting force F . The system is studied in the region where the force is close to the critical value Fc at which the barriers separating neighboring potential wells disappear. We show that, when F crosses the critical value, the shape of the mean-square displacement (MSD) curves is strongly modified. We identify a diffusive regime at intermediate-time scales with an effective diffusion coefficient which is much larger than the late-time diffusion coefficient for F >Fc , whereas for F

Arrhenius analysis of anisotropic surface self-diffusion on the prismatic facet of ice.

PubMed

Gladich, Ivan; Pfalzgraff, William; Maršálek, Ondřej; Jungwirth, Pavel; Roeselová, Martina; Neshyba, Steven

2011-11-28

We present an Arrhenius analysis of self-diffusion on the prismatic surface of ice calculated from molecular dynamics simulations. The six-site water model of Nada and van der Eerden was used in combination with a structure-based criterion for determining the number of liquid-like molecules in the quasi-liquid layer. Simulated temperatures range from 230 K-287 K, the latter being just below the melting temperature of the model, 289 K. Calculated surface diffusion coefficients agree with available experimental data to within quoted precision. Our results indicate a positive Arrhenius curvature, implying a change in the mechanism of self-diffusion from low to high temperature, with a concomitant increase in energy of activation from 29.1 kJ mol(-1) at low temperature to 53.8 kJ mol(-1) close to the melting point. In addition, we find that the surface self-diffusion is anisotropic at lower temperatures, transitioning to isotropic in the temperature range of 240-250 K. We also present a framework for self-diffusion in the quasi-liquid layer on ice that aims to explain these observations.

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

NASA Astrophysics Data System (ADS)

Yang, Jing; Youssef, Mostafa; Yildiz, Bilge

2018-01-01

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

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.

Transport coefficients of Lennard-Jones fluids: A molecular-dynamics and effective-hard-sphere treatment

NASA Astrophysics Data System (ADS)

Heyes, David M.

1988-04-01

This study evaluates the shear viscosity, self-diffusion coefficient, and thermal conductivity of the Lennard-Jones (LJ) fluid over essentially the entire fluid range by molecular-dynamics (MD) computer simulation. The Green-Kubo (GK) method is mainly used. In addition, for shear viscosity, homogeneous shear nonequilibrium MD (NEMD) is also employed and compared with experimental data on argon along isotherms. Reasonable agreement between GK, NEMD, and experiment is found. Hard-sphere MD modified Chapman-Enskog expressions for these transport coefficients are tested with use of a temperature-dependent effective hard-sphere diameter. Excellent agreement is found for shear viscosity. The thermal conductivity and, more so, self-diffusion coefficient is less successful in this respect. This behavior is attributed to the attractive part to the LJ potential and its soft repulsive core. Expressions for the constant-volume and -pressure activation energies for these transport coefficients are derived solely in terms of the thermodynamic properties of the LJ fluid. Also similar expressions for the activation volumes are given, which should have a wider range of applications than just for the LJ system.

Computation of shear-induced collective-diffusivity in emulsions

NASA Astrophysics Data System (ADS)

Malipeddi, Abhilash Reddy; Sarkar, Kausik

2017-11-01

The shear-induced collective-diffusivity of drops in an emulsion is calculated through simulation. A front-tracking finite difference method is used to integrate the Navier-Stokes equations. When a cloud of drops is subjected to shear flow, after a certain time, the width of the cloud increases with the 1/3 power of time. This scaling of drop-cloud-width with time is characteristic of (sub-)diffusion that arises from irreversible two-drop interactions. The collective diffusivity is calculated from this relationship. A feature of the procedure adopted here is the modest computational requirement, wherein, a few drops ( 70) in shear for short time ( 70 strain) is found to be sufficient to get a good estimate. As far as we know, collective-diffusivity has not been calculated for drops through simulation till now. The computed values match with experimental measurements reported in the literature. The diffusivity in emulsions is calculated for a range of Capillary (Ca) and Reynolds (Re) numbers. It is found to be a unimodal function of Ca , similar to self-diffusivity. A sub-linear increase of the diffusivity with Re is seen for Re < 5 . This work has been limited to a viscosity matched case.

Stokes-Einstein relation in liquid iron-nickel alloy up to 300 GPa

NASA Astrophysics Data System (ADS)

Cao, Q.-L.; Wang, P.-P.

2017-05-01

Molecular dynamic simulations were applied to investigate the Stokes-Einstein relation (SER) and the Rosenfeld entropy scaling law (ESL) in liquid Fe0.9Ni0.1 over a sufficiently broad range of temperatures (0.70 < T/Tm < 1.85 Tm is melting temperature) and pressures (from 50 GPa to 300 GPa). Our results suggest that the SER and ESL hold well in the normal liquid region and break down in the supercooled region under high-pressure conditions, and the deviation becomes larger with decreasing temperature. In other words, the SER can be used to calculate the viscosity of liquid Earth's outer core from the self-diffusion coefficients of iron/nickel and the ESL can be used to predict the viscosity and diffusion coefficients of liquid Earth's outer core form its structural properties. In addition, the pressure dependence of effective diameters cannot be ignored in the course of using the SER. Moreover, ESL provides a useful, structure-based probe for the validity of SER, while the ratio of the self-diffusion coefficients of the components cannot be used as a probe for the validity of SER.

Relation between heat of vaporization, ion transport, molar volume, and cation-anion binding energy for ionic liquids.

PubMed

Borodin, Oleg

2009-09-10

A number of correlations between heat of vaporization (H(vap)), cation-anion binding energy (E(+/-)), molar volume (V(m)), self-diffusion coefficient (D), and ionic conductivity for 29 ionic liquids have been investigated using molecular dynamics (MD) simulations that employed accurate and validated many-body polarizable force fields. A significant correlation between D and H(vap) has been found, while the best correlation was found for -log(DV(m)) vs H(vap) + 0.28E(+/-). A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids. A deviation of some ILs from the reported master curve is explained based upon ion packing and proposed diffusion pathways. No general correlations were found between the ion diffusion coefficient and molecular volume or the diffusion coefficient and cation/anion binding energy.

Dynamical properties and transport coefficients of one-dimensional Lennard-Jones fluids: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Bazhenov, Alexiev M.; Heyes, David M.

1990-01-01

The thermodynamics, structure, and transport coefficients, as defined by the Green-Kubo integrals, of the one-dimensional Lennard-Jones fluid are evaluated for a wide range of state points by molecular dynamics computer simulation. These calculations are performed for the first time for thermal conductivity and the viscosity. We observe a transition from hard-rod behavior at low number density to harmonic-spring fluid behavior in the close-packed limit. The self-diffusion coefficient decays with increasing density to a finite limiting value. The thermal conductivity increases with density, tending to ∞ in the close-packed limit. The viscosity in contrast maximizes at intermediate density, tending to zero in the zero density and close-packed limits.

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.

Modeling uptake of hydrophobic organic contaminants into polyethylene passive samplers.

PubMed

Thompson, Jay M; Hsieh, Ching-Hong; Luthy, Richard G

2015-02-17

Single-phase passive samplers are gaining acceptance as a method to measure hydrophobic organic contaminant (HOC) concentration in water. Although the relationship between the HOC concentration in water and passive sampler is linear at equilibrium, mass transfer models are needed for nonequilibrium conditions. We report measurements of organochlorine pesticide diffusion and partition coefficients with respect to polyethylene (PE), and present a Fickian approach to modeling HOC uptake by PE in aqueous systems. The model is an analytic solution to Fick's second law applied through an aqueous diffusive boundary layer and a polyethylene layer. Comparisons of the model with existing methods indicate agreement at appropriate boundary conditions. Laboratory release experiments on the organochlorine pesticides DDT, DDE, DDD, and chlordane in well-mixed slurries support the model's applicability to aqueous systems. In general, the advantage of the model is its application in the cases of well-agitated systems, low values of polyethylene-water partioning coefficients, thick polyethylene relative to the boundary layer thickness, and/or short exposure times. Another significant advantage is the ability to estimate, or at least bound, the needed exposure time to reach a desired CPE without empirical model inputs. A further finding of this work is that polyethylene diffusivity does not vary by transport direction through the sampler thickness.

Overview of SIMS-Based Experimental Studies of Tracer Diffusion in Solids and Application to Mg Self-Diffusion

DOE PAGES

Kulkarni, Nagraj S.; Bruce Warmack, Robert J.; Radhakrishnan, Bala; ...

2014-09-23

Tracer diffusivities provide the most fundamental information on diffusion in materials and are the foundation of robust diffusion databases. Compared to traditional radiotracer techniques that utilize radioactive isotopes, the secondary ion mass spectrometry (SIMS) based thin-film technique for tracer diffusion is based on the use of enriched stable isotopes that can be accurately profiled using SIMS. Experimental procedures & techniques that are utilized for the measurement of tracer diffusion coefficients are presented for pure magnesium, which presents some unique challenges due to the ease of oxidation. The development of a modified Shewmon-Rhines diffusion capsule for annealing Mg and an ultra-highmore » vacuum (UHV) system for sputter deposition of Mg isotopes are discussed. Optimized conditions for accurate SIMS depth profiling in polycrystalline Mg are provided. An automated procedure for the correction of heat-up and cool-down times during tracer diffusion annealing is discussed. The non-linear fitting of a SIMS depth profile data using the thin film Gaussian solution to obtain the tracer diffusivity along with the background tracer concentration and tracer film thickness is discussed. An Arrhenius fit of the Mg self-diffusion data obtained using the low-temperature SIMS measurements from this study and the high-temperature radiotracer measurements of Shewmon and Rhines (1954) was found to be a good representation of both types of diffusion data that cover a broad range of temperatures between 250 - 627° C (523 900 K).« 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.

Determination of crystal residence timescales in magma reservoirs by diffusion modeling of dendritic phosphorus zoning patterns in olivine

NASA Astrophysics Data System (ADS)

Chakraborty, S.; Potrafke, A.

2016-12-01

Deciphering the early stages of crystallization and the chronological evolution of phenocrysts in magma reservoirs is one of the main goals in volcanology. Established approaches that model the concentration evolution of fast diffusing elements like Fe/Mg carry limited information on timescales once the concentration gradients are homogenized. Elements that diffuse more slowly, such as P and Al, become useful in these cases. We present a novel modeling tool that combines high-resolution EMP mapping of slow diffusing phosphorus in olivine with 2D kinetic modeling of the diffusive relaxation of initial chemical zoning pattern of P as well as Fe/Mg. The modeling approach offers a new possibility for determining crystal residence times in magma reservoirs. P diffusion coefficients from the experimental determination of [1] and Fe/Mg diffusion coefficients from [2] were used. The method yields a time-bracket between the minimum time required to homogenize the zoning of fast-diffusing Fe/Mg and the maximum time period for which details of chemical zoning of slow-diffusing P may be retained. To illustrate the approach we have studied the compositional zoning patterns of 7 olivine crystals from Piton de la Fournaise volcano, La Réunion. All crystals show a narrow range of forsterite contents (=Fo82-84) with fully homogenized Fe/Mg distribution, whereas P-mapping reveals oscillatory to dendritic zoning patterns [3]. P concentrations scatter in the range of 0.4 wt-% to below detection limit. Revealed phosphorus zoning patterns were considered to display the initial crystal architecture, whereas Fe and Mg zoning has been wiped out due to faster diffusion. For La Réunion magmas at 1453 K, timescales between few days to weeks were determined to be the time brackets for growth and residence of the olivine crystals in the magmas. These short residence times combined with knowledge of very fast developing dendritic crystals that have recently been revealed worldwide [e.g. 3] indicate that dendritic crystal growth in such rapidly evolving dynamic environments should be considered as a widespread feature of olivine growth and evolution of many basaltic volcanic systems. [1] Watson et al., 2015, Am Min, 100, pp. 2053-2065 [2] Dohmen et al., 2007, Phys Chem Miner, 34(6), pp. 389-407 [3] Welsch et al., 2014, Geology, 42, pp. 867-870

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.

Self-diffusion of magnesium in spinel and in equilibrium melts - Constraints on flash heating of silicates

NASA Technical Reports Server (NTRS)

Sheng, Y. J.; Wasserburg, G. J.; Hutcheon, I. D.

1992-01-01

An isotopic tracer is used to measure Mg self-diffusion in spinel and coexisting melt at bulk chemical equilibrium. The diffusion coefficients were calculated from the measured isotope profiles using a model that includes the complementary diffusion of Mg-24, Mg-25, and Mg-26 in both phases with the constraint that the Mg content of each phase is constant. The activation energy and preexponential factor for Mg self-diffusion in spinel are, respectively, 384 +/- 7 kJ and 74.6 +/- 1.1 sq cm/s. These data indicate Mg diffusion in spinel is much slower than previous estimates. The activation energy for Mg self-diffusion in coexisting melt is 343 +/- 25 kJ and the preexponential factor is 7791.9 +/- 1.3 sq cm/s. These results are used to evaluate cooling rates of plagioclase-olivine inclusions (POIs) in the Allende meteorite. Given a maximum melting temperature for POIs of about 1500 C, these results show that a 1-micron radius spinel would equilibrate isotopically with a melt within about 60 min.

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.

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.

Interpreting high time resolution galactic cosmic ray observations in a diffusive context

NASA Astrophysics Data System (ADS)

Jordan, A.; Spence, H. E.; Blake, J. B.; Shaul, D. A.

2009-12-01

We interpret galactic cosmic ray (GCR) variations near Earth within a diffusive context. The variations occur on time-/size-scales ranging from Forbush decreases (Fds), to substructure embedded within Fds, to smaller amplitude and shorter duration variations during relatively benign interplanetary conditions. We use high time resolution GCR observations from the High Sensitivity Telescope (HIST) on Polar and from the Spectrometer for INTEGRAL (SPI) and also use solar wind plasma and magnetic field observations from ACE and/or Wind. To calculate the coefficient of diffusion, we combine these datasets with a simple convection-diffusion model for relativistic charged particles in a magnetic field. We find reasonable agreement between our and previous estimates of the coefficient. We also show whether changes in the coefficient of diffusion are sufficient to explain the above GCR variations.

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.

Ballistic and diffusive dynamics in a two-dimensional ideal gas of macroscopic chaotic Faraday waves.

PubMed

Welch, Kyle J; Hastings-Hauss, Isaac; Parthasarathy, Raghuveer; Corwin, Eric I

2014-04-01

We have constructed a macroscopic driven system of chaotic Faraday waves whose statistical mechanics, we find, are surprisingly simple, mimicking those of a thermal gas. We use real-time tracking of a single floating probe, energy equipartition, and the Stokes-Einstein relation to define and measure a pseudotemperature and diffusion constant and then self-consistently determine a coefficient of viscous friction for a test particle in this pseudothermal gas. Because of its simplicity, this system can serve as a model for direct experimental investigation of nonequilibrium statistical mechanics, much as the ideal gas epitomizes equilibrium statistical mechanics.

Negative self-referential processing is associated with genetic variation in the serotonin transporter-linked polymorphic region (5-HTTLPR): Evidence from two independent studies.

PubMed

Dainer-Best, Justin; Disner, Seth G; McGeary, John E; Hamilton, Bethany J; Beevers, Christopher G

2018-01-01

The current research examined whether carriers of the short 5-HTTLPR allele (in SLC6A4), who have been shown to selectively attend to negative information, exhibit a bias towards negative self-referent processing. The self-referent encoding task (SRET) was used to measure self-referential processing of positive and negative adjectives. Ratcliff's diffusion model isolated and extracted decision-making components from SRET responses and reaction times. Across the initial (N = 183) and replication (N = 137) studies, results indicated that short 5-HTTLPR allele carriers more easily categorized negative adjectives as self-referential (i.e., higher drift rate). Further, drift rate was associated with recall of negative self-referential stimuli. Findings across both studies provide further evidence that genetic variation may contribute to the etiology of negatively biased processing of self-referent information. Large scale studies examining the genetic contributions to negative self-referent processing may be warranted.

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

PubMed

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

2015-01-01

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

TU-F-CAMPUS-I-01: Head and Neck Squamous Cell Carcinoma: Short-Term Repeatability of Apparent Diffusion Coefficient and Intravoxel Incoherent Motion Parameters at 3.0T

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

Ding, Y; Fuller, C; Mohamed, A

2015-06-15

Purpose: Many published studies have recently demonstrated the potential value of intravoxel incoherent motion (IVIM) analysis for disease evaluation. However, few have questioned its measurement repeatability/reproducibility when applied. The purpose of this study was to determine the short-term measurement repeatability of apparent diffusion coefficient ADC, true diffusion coefficient D, pseudodiffusion coefficient D* and perfusion fraction f, in head and neck squamous cell carcinoma (HNSCC) primary tumors and metastatic nodes. Methods: Ten patients with known HNSCC were examined twice using echo-planar DW-MRI with 12 b values (0 to 800 s/mm2) 1hour to 24 hours apart before radiation treatment. All patients weremore » scanned with the customized radiation treatment immobilization devices to reduce motion artifacts and to improve image registration in repeat scans. Regions of interests were drawn in primary tumor and metastases node in each patient (Fig. 1). ADC and IVIM parameters D, D* and f were calculated by least squares data fitting. Short-term test–retest repeatability of ADC and IVIM parameters were assessed by measuring Bland–Altman limits of agreements (BA-LA). Results: Sixteen HNSCC lesions were assessed in 10 patients. Repeatability of perfusion-sensitive parameters, D* and f, in HNSCC lesions was poor (BA-LA: -144% to 88% and −57% to 96% for D* and f, respectively); a lesser extent was observed for the diffusion-sensitive parameters of ADC and D (BA-LA: −34% to 39% and −37% to 40%, for ADC and D, respectively) (Fig. 2). Conclusion: Poor repeatability of D*/f and good repeatability for ADC/D were observed in HNSCC primary tumors and metastatic nodes. Efforts should be made to improve the measurement repeatability of perfusion-sensitive IVIM parameters.« less

Stochastic nature of series of waiting times.

PubMed

Anvari, Mehrnaz; Aghamohammadi, Cina; Dashti-Naserabadi, H; Salehi, E; Behjat, E; Qorbani, M; Nezhad, M Khazaei; Zirak, M; Hadjihosseini, Ali; Peinke, Joachim; Tabar, M Reza Rahimi

2013-06-01

Although fluctuations in the waiting time series have been studied for a long time, some important issues such as its long-range memory and its stochastic features in the presence of nonstationarity have so far remained unstudied. Here we find that the "waiting times" series for a given increment level have long-range correlations with Hurst exponents belonging to the interval 1/2

Universal time-dependent dispersion properties for diffusion in a one-dimensional critically tilted potential.

PubMed

Guérin, T; Dean, D S

2017-01-01

We consider the time-dependent dispersion properties of overdamped tracer particles diffusing in a one-dimensional periodic potential under the influence of an additional constant tilting force F. The system is studied in the region where the force is close to the critical value F_{c} at which the barriers separating neighboring potential wells disappear. We show that, when F crosses the critical value, the shape of the mean-square displacement (MSD) curves is strongly modified. We identify a diffusive regime at intermediate-time scales with an effective diffusion coefficient which is much larger than the late-time diffusion coefficient for F>F_{c}, whereas for F

Effect of intravenous gadolinium-DTPA on diffusion-weighted imaging of brain tumors: a short temporal interval assessment.

PubMed

Li, Xiang; Qu, Jin-Rong; Luo, Jun-Peng; Li, Jing; Zhang, Hong-Kai; Shao, Nan-Nan; Kwok, Keith; Zhang, Shou-Ning; Li, Yan-le; Liu, Cui-Cui; Zee, Chi-Shing; Li, Hai-Liang

2014-09-01

To determine the effect of intravenous administration of gadolinium (Gd) contrast medium (Gd-DTPA) on diffusion-weighted imaging (DWI) for the evaluation of normal brain parenchyma vs. brain tumor following a short temporal interval. Forty-four DWI studies using b values of 0 and 1000 s/mm(2) were performed before, immediately after, 1 min after, 3 min after, and 5 min after the administration of Gd-DTPA on 62 separate lesions including 15 meningioma, 17 glioma and 30 metastatic lesions. The signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and apparent diffusion coefficient (ADC) values of the brain tumor lesions and normal brain tissues were measured on pre- and postcontrast images. Statistical analysis using paired t-test between precontrast and postcontrast data were obtained on three brain tumors and normal brain tissue. The SNR and CNR of brain tumors and the SNR of normal brain tissue showed no statistical differences between pre- and postcontrast (P > 0.05). The ADC values on the three cases of brain tumors demonstrated significant initial increase on the immediate time point (P < 0.01) and decrease on following the 1 min time point (P < 0.01) after contrast. Significant decrease of ADC value was still found at 3min and 5min time point in the meningioma group (P < 0.01) with gradual normalization over time. The ADC values of normal brain tissues demonstrated significant initial elevation on the immediately postcontrast DWI sequence (P < 0.01). Contrast medium can cause a slight but statistically significant change on the ADC value within a short temporal interval after the contrast administration. The effect is both time and lesion-type dependent. © 2013 Wiley Periodicals, Inc.

Effects of Refractive Index and Diffuse or Specular Boundaries on a Radiating Isothermal Layer

NASA Technical Reports Server (NTRS)

Siegel, R.; Spuckler, C. M.

1994-01-01

Equilibrium temperatures of an absorbing-emitting layer were obtained for exposure to incident radiation and with the layer boundaries either specular or diffuse. For high refractive indices the surface condition can influence the radiative heat balance if the layer optical thickness is small. Hence for a spectrally varying absorption coefficient the layer temperature is affected if there is significant radiative energy in the spectral range with a small absorption coefficient. Similar behavior was obtained for transient radiative cooling of a layer where the results are affected by the initial temperature and hence the fraction of energy radiated in the short wavelength region where the absorption coefficient is small. The results are a layer without internal scattering. If internal scattering is significant, the radiation reaching the internal surface of a boundary is diffused and the effect of the two different surface conditions would become small.

Magnetic resonance imaging and relaxometry to study water transport mechanisms in a commercially available gastrointestinal therapeutic system (GITS) tablet.

PubMed

Broadbent, Amber L; Fell, Rob J; Codd, Sarah L; Lightley, Kim A; Konagurthu, Sanjay; Koehler-King, Dory G; Seymour, Joseph D

2010-09-15

The hydration of 4 mg Cardura XL (Pfizer), a commercially available gastrointestinal therapeutic system (GITS) tablet, was investigated using magnetic resonance imaging (MRI). A short echo time (T(e)=2.81 ms) technique for MRI of the hydration of a GITS tablet was implemented. From the MR images, signal intensity profiles were generated and interpreted in the context of diffusive and osmotic transport mechanisms. A distinct transition from diffusive to osmotic transport was measured at a timescale relevant to the measured drug release time. Diffusion and osmotic rate coefficients for water in the drug and polymer sweller layers of the tablet were quantified. Spin-lattice T(1) and spin-spin T(2) relaxation times of the water signal from within the tablet were measured as a function of hydration time in order to incorporate the effects of relaxation into interpretation of signal intensity and provide unique information on the distribution of water in different physical and chemical environments within the tablet. Copyright 2010 Elsevier B.V. All rights reserved.

Enhanced ionic liquid mobility induced by confinement in 1D CNT membranes

NASA Astrophysics Data System (ADS)

Berrod, Q.; Ferdeghini, F.; Judeinstein, P.; Genevaz, N.; Ramos, R.; Fournier, A.; Dijon, J.; Ollivier, J.; Rols, S.; Yu, D.; Mole, R. A.; Zanotti, J.-M.

2016-04-01

Water confined within carbon nanotubes (CNT) exhibits tremendous enhanced transport properties. Here, we extend this result to ionic liquids (IL) confined in vertically aligned CNT membranes. Under confinement, the IL self-diffusion coefficient is increased by a factor 3 compared to its bulk reference. This could lead to high power battery separators.Water confined within carbon nanotubes (CNT) exhibits tremendous enhanced transport properties. Here, we extend this result to ionic liquids (IL) confined in vertically aligned CNT membranes. Under confinement, the IL self-diffusion coefficient is increased by a factor 3 compared to its bulk reference. This could lead to high power battery separators. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01445c

Sensitivity study on durability variables of marine concrete structures

NASA Astrophysics Data System (ADS)

Zhou, Xin'gang; Li, Kefei

2013-06-01

In order to study the influence of parameters on durability of marine concrete structures, the parameter's sensitivity analysis was studied in this paper. With the Fick's 2nd law of diffusion and the deterministic sensitivity analysis method (DSA), the sensitivity factors of apparent surface chloride content, apparent chloride diffusion coefficient and its time dependent attenuation factor were analyzed. The results of the analysis show that the impact of design variables on concrete durability was different. The values of sensitivity factor of chloride diffusion coefficient and its time dependent attenuation factor were higher than others. Relative less error in chloride diffusion coefficient and its time dependent attenuation coefficient induces a bigger error in concrete durability design and life prediction. According to probability sensitivity analysis (PSA), the influence of mean value and variance of concrete durability design variables on the durability failure probability was studied. The results of the study provide quantitative measures of the importance of concrete durability design and life prediction variables. It was concluded that the chloride diffusion coefficient and its time dependent attenuation factor have more influence on the reliability of marine concrete structural durability. In durability design and life prediction of marine concrete structures, it was very important to reduce the measure and statistic error of durability design variables.

Stochastic nature of series of waiting times

NASA Astrophysics Data System (ADS)

Anvari, Mehrnaz; Aghamohammadi, Cina; Dashti-Naserabadi, H.; Salehi, E.; Behjat, E.; Qorbani, M.; Khazaei Nezhad, M.; Zirak, M.; Hadjihosseini, Ali; Peinke, Joachim; Tabar, M. Reza Rahimi

2013-06-01

Although fluctuations in the waiting time series have been studied for a long time, some important issues such as its long-range memory and its stochastic features in the presence of nonstationarity have so far remained unstudied. Here we find that the “waiting times” series for a given increment level have long-range correlations with Hurst exponents belonging to the interval 1/2

Kinetic mechanism of the thermal-induced self-organization of Au/Si nanodroplets on Si(100): Size and roughness evolution

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

Ruffino, F.; Canino, A.; Grimaldi, M. G.

Very thin Au layer was deposited on Si(100) using the sputtering technique. By annealing at 873 K Au/Si nanodroplets were formed and their self-organization was induced changing the annealing time. The evolution of droplet size distribution, center-to-center distance distribution, and droplet density as a function of the annealing time at 873 K was investigated by Rutherford backscattering spectrometry, atomic force microscopy (AFM), and scanning electron microscopy. As a consequence of such study, the droplet clustering is shown to be a ripening process of hemispherical three-dimensional structures limited by the Au surface diffusion. The application of the ripening theory allowed usmore » to calculate the surface diffusion coefficient and all other parameters needed to describe the entire process. Furthermore, the AFM measurements allowed us to study the roughness evolution of the sputtered Au thin film and compare the experimental data with the dynamic scaling theories of growing interfaces.« less

Brownian dynamics and dynamic Monte Carlo simulations of isotropic and liquid crystal phases of anisotropic colloidal particles: a comparative study.

PubMed

Patti, Alessandro; Cuetos, Alejandro

2012-07-01

We report on the diffusion of purely repulsive and freely rotating colloidal rods in the isotropic, nematic, and smectic liquid crystal phases to probe the agreement between Brownian and Monte Carlo dynamics under the most general conditions. By properly rescaling the Monte Carlo time step, being related to any elementary move via the corresponding self-diffusion coefficient, with the acceptance rate of simultaneous trial displacements and rotations, we demonstrate the existence of a unique Monte Carlo time scale that allows for a direct comparison between Monte Carlo and Brownian dynamics simulations. To estimate the validity of our theoretical approach, we compare the mean square displacement of rods, their orientational autocorrelation function, and the self-intermediate scattering function, as obtained from Brownian dynamics and Monte Carlo simulations. The agreement between the results of these two approaches, even under the condition of heterogeneous dynamics generally observed in liquid crystalline phases, is excellent.

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

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

PubMed

Gupta, Rahul

2018-02-01

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

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.

Self-diffusion of protons in H{sub 2}O ice VII at high pressures: Anomaly around 10 GPa

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

Noguchi, Naoki, E-mail: noguchi-n@okayama-u.ac.jp; Okuchi, Takuo

2016-06-21

The self-diffusion of ice VII in the pressure range of 5.5–17 GPa and temperature range of 400–425 K was studied using micro Raman spectroscopy and a diamond anvil cell. The diffusion was monitored by observing the distribution of isotope tracers: D{sub 2}O and H{sub 2}{sup 18}O. The diffusion coefficient of hydrogen reached a maximum value around 10 GPa. It was two orders of magnitude greater at 10 GPa than at 6 GPa. Hydrogen diffusion was much faster than oxygen diffusion, which indicates that protonic diffusion is the dominant mechanism for the diffusion of hydrogen in ice VII. This mechanism ismore » in remarkable contrast to the self-diffusion in ice I{sub h} that is dominated by an interstitial mechanism for the whole water molecule. An anomaly around 10 GPa in ice VII indicates that the rate-determining process for the proton diffusion changes from the diffusion of ionic defects to the diffusion of rotational defects, which was suggested by proton conductivity measurements and molecular dynamics simulations.« less

Surface mass diffusion over an extended temperature range on Pt(111)

NASA Astrophysics Data System (ADS)

Rajappan, M.; Swiech, W.; Ondrejcek, M.; Flynn, C. P.

2007-06-01

Surface mass diffusion is investigated on Pt(111) at temperatures in the range 710-1220 K. This greatly extends the range over which diffusion is known from step fluctuation spectroscopy (SFS). In the present research, a beam of Pt- self-ions is employed to create a suitable structure on step edges. The surface mass diffusion coefficients then follow from the decay of Fourier components observed by low-energy electron microscopy (LEEM) at selected annealing temperatures. The results agree with SFS values where they overlap, and continue smoothly to low temperature. This makes it unlikely that diffusion along step edges plays a major role in step edge relaxation through the temperature range studied. The surface mass diffusion coefficient for the range 710-1520 K deduced from the present work, together with previous SFS data, is Ds = 4 × 10-3 exp(-1.47 eV/kBT) cm2 s-1.

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).

A Molecular Dynamics Simulation of the Molten Ternary System (Li, K, Cs)Cl

NASA Astrophysics Data System (ADS)

Matsumiya, Masahiko; Takagi, Ryuzo

2000-12-01

The self-exchange velocity (SEV) of neighboring unlike ions, has been evaluated by molecular dynamics simulations of molten CsCl, (Li, K)C1 and (Li, K, Cs)Cl at 673 K. From the increase of the SEV's in the same order as the internal mobilities it is conjectured that there is a strong correlation between these two properties. The pair correlation functions, and the self-diffusion coefficients and the SEV's of Li+, K+, and Cs+ with reference to Cl- have also been calculated. The results allow to conclude that the self-exchange velocity of the cations become vCs < vK < vLi at xCs =0.1 and vLi < vK < vCs at xCs > 0.4. The sequence of the self-diffusion coefficients agrees with that of the SEV's. The results enable to conclude that it is possible to enrich Cs at up to xCs ~ 0.3 - 0.4 in the molten LiCl-KCl eutectic system.

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

Mutual diffusion of binary liquid mixtures containing methanol, ethanol, acetone, benzene, cyclohexane, toluene, and carbon tetrachloride

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

Guevara-Carrion, Gabriela; Janzen, Tatjana; Muñoz-Muñoz, Y. Mauricio

Mutual diffusion coefficients of all 20 binary liquid mixtures that can be formed out of methanol, ethanol, acetone, benzene, cyclohexane, toluene, and carbon tetrachloride without a miscibility gap are studied at ambient conditions of temperature and pressure in the entire composition range. The considered mixtures show a varying mixing behavior from almost ideal to strongly non-ideal. Predictive molecular dynamics simulations employing the Green-Kubo formalism are carried out. Radial distribution functions are analyzed to gain an understanding of the liquid structure influencing the diffusion processes. It is shown that cluster formation in mixtures containing one alcoholic component has a significant impactmore » on the diffusion process. The estimation of the thermodynamic factor from experimental vapor-liquid equilibrium data is investigated, considering three excess Gibbs energy models, i.e., Wilson, NRTL, and UNIQUAC. It is found that the Wilson model yields the thermodynamic factor that best suits the simulation results for the prediction of the Fick diffusion coefficient. Four semi-empirical methods for the prediction of the self-diffusion coefficients and nine predictive equations for the Fick diffusion coefficient are assessed and it is found that methods based on local composition models are more reliable. Finally, the shear viscosity and thermal conductivity are predicted and in most cases favorably compared with experimental literature values.« less

Measurement setup for the simultaneous determination of diffusivity and Seebeck coefficient in a multi-anvil apparatus

NASA Astrophysics Data System (ADS)

Jacobsen, M. K.; Liu, W.; Li, B.

2012-09-01

In this paper, a high pressure setup is presented for performing simultaneous measurements of Seebeck coefficient and thermal diffusivity in multianvil apparatus for the purpose of enhancing the study of transport phenomena. Procedures for the derivation of Seebeck coefficient and thermal diffusivity/conductivity, as well as their associated sources of errors, are presented in detail, using results obtained on the filled skutterudite, Ce0.8Fe3CoSb12, up to 12 GPa at ambient temperature. Together with recent resistivity and sound velocity measurements in the same apparatus, these developments not only provide the necessary data for a self-consistent and complete characterization of the figure of merit of thermoelectric materials under pressure, but also serve as an important tool for furthering our knowledge of the dynamics and interplay between these transport phenomena.

Measurement setup for the simultaneous determination of diffusivity and Seebeck coefficient in a multi-anvil apparatus.

PubMed

Jacobsen, M K; Liu, W; Li, B

2012-09-01

In this paper, a high pressure setup is presented for performing simultaneous measurements of Seebeck coefficient and thermal diffusivity in multianvil apparatus for the purpose of enhancing the study of transport phenomena. Procedures for the derivation of Seebeck coefficient and thermal diffusivity/conductivity, as well as their associated sources of errors, are presented in detail, using results obtained on the filled skutterudite, Ce(0.8)Fe(3)CoSb(12,) up to 12 GPa at ambient temperature. Together with recent resistivity and sound velocity measurements in the same apparatus, these developments not only provide the necessary data for a self-consistent and complete characterization of the figure of merit of thermoelectric materials under pressure, but also serve as an important tool for furthering our knowledge of the dynamics and interplay between these transport phenomena.

Calculation of Transport Coefficients in Dense Plasma Mixtures

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

Hydrodynamics of confined colloidal fluids in two dimensions

NASA Astrophysics Data System (ADS)

Sané, Jimaan; Padding, Johan T.; Louis, Ard A.

2009-05-01

We apply a hybrid molecular dynamics and mesoscopic simulation technique to study the dynamics of two-dimensional colloidal disks in confined geometries. We calculate the velocity autocorrelation functions and observe the predicted t-1 long-time hydrodynamic tail that characterizes unconfined fluids, as well as more complex oscillating behavior and negative tails for strongly confined geometries. Because the t-1 tail of the velocity autocorrelation function is cut off for longer times in finite systems, the related diffusion coefficient does not diverge but instead depends logarithmically on the overall size of the system. The Langevin equation gives a poor approximation to the velocity autocorrelation function at both short and long times.

Anomalous subdiffusion in fluorescence photobleaching recovery: a Monte Carlo study.

PubMed Central

Saxton, M J

2001-01-01

Anomalous subdiffusion is hindered diffusion in which the mean-square displacement of a diffusing particle is proportional to some power of time less than one. Anomalous subdiffusion has been observed for a variety of lipids and proteins in the plasma membranes of a variety of cells. Fluorescence photobleaching recovery experiments with anomalous subdiffusion are simulated to see how to analyze the data. It is useful to fit the recovery curve with both the usual recovery equation and the anomalous one, and to judge the goodness of fit on log-log plots. The simulations show that the simplest approximate treatment of anomalous subdiffusion usually gives good results. Three models of anomalous subdiffusion are considered: obstruction, fractional Brownian motion, and the continuous-time random walk. The models differ significantly in their behavior at short times and in their noise level. For obstructed diffusion the approach to the percolation threshold is marked by a large increase in noise, a broadening of the distribution of diffusion coefficients and anomalous subdiffusion exponents, and the expected abrupt decrease in the mobile fraction. The extreme fluctuations in the recovery curves at and near the percolation threshold result from extreme fluctuations in the geometry of the percolation cluster. PMID:11566793

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

Study of the measurement for the diffusion coefficient by digital holographic interferometry.

PubMed

Zhang, Shi; He, Maogang; Zhang, Ying; Peng, Sanguo; He, Xinxin

2015-11-01

In the measurement of the diffusion coefficient by digital holographic interferometry, the conformity between the experiment and the ideal physical model is lacking analysis. Two data processing methods are put forward to overcome this problem. By these methods, it is found that there is obvious asymmetry in the experiment and the asymmetry is becoming smaller with time. Besides, the initial time for diffusion cannot be treated as a constant throughout the whole experiment. This means that there is a difference between the experiment and the physical model. With these methods, the diffusion coefficient of KCl in water at 0.33  mol/L and 25°C is measured. When the asymmetry is ignored, the result is 1.839×10(-9)  m2/s, which is in good agreement with the data in the literature. Because the asymmetry is becoming smaller with time, the experimental data in the latter time period conforms to the ideal physical model. With this idea, a more accurate diffusion coefficient is 2.003×10(-9)  m2/s, which is about 10% larger than the data in the literature.

Self-Healing of Unentangled Polymer Networks with Reversible Bonds

PubMed Central

Stukalin, Evgeny B.; Cai, Li-Heng; Kumar, N. Arun; Leibler, Ludwik; Rubinstein, Michael

2013-01-01

Self-healing polymeric materials are systems that after damage can revert to their original state with full or partial recovery of mechanical strength. Using scaling theory we study a simple model of autonomic self-healing of unentangled polymer networks. In this model one of the two end monomers of each polymer chain is fixed in space mimicking dangling chains attachment to a polymer network, while the sticky monomer at the other end of each chain can form pairwise reversible bond with the sticky end of another chain. We study the reaction kinetics of reversible bonds in this simple model and analyze the different stages in the self-repair process. The formation of bridges and the recovery of the material strength across the fractured interface during the healing period occur appreciably faster after shorter waiting time, during which the fractured surfaces are kept apart. We observe the slowest formation of bridges for self-adhesion after bringing into contact two bare surfaces with equilibrium (very low) density of open stickers in comparison with self-healing. The primary role of anomalous diffusion in material self-repair for short waiting times is established, while at long waiting times the recovery of bonds across fractured interface is due to hopping diffusion of stickers between different bonded partners. Acceleration in bridge formation for self-healing compared to self-adhesion is due to excess non-equilibrium concentration of open stickers. Full recovery of reversible bonds across fractured interface (formation of bridges) occurs after appreciably longer time than the equilibration time of the concentration of reversible bonds in the bulk. PMID:24347684

Time-dependent Models for Blazar Emission with the Second-order Fermi Acceleration

NASA Astrophysics Data System (ADS)

Asano, Katsuaki; Takahara, Fumio; Kusunose, Masaaki; Toma, Kenji; Kakuwa, Jun

2014-01-01

The second-order Fermi acceleration (Fermi-II) driven by turbulence may be responsible for the electron acceleration in blazar jets. We test this model with time-dependent simulations. The hard electron spectrum predicted by the Fermi-II process agrees with the hard photon spectrum of 1ES 1101-232. For other blazars that show softer spectra, the Fermi-II model requires radial evolution of the electron injection rate and/or diffusion coefficient in the outflow. Such evolutions can yield a curved electron spectrum, which can reproduce the synchrotron spectrum of Mrk 421 from the radio to the X-ray regime. The photon spectrum in the GeV energy range of Mrk 421 is hard to fit with a synchrotron self-Compton model. However, if we introduce an external radio photon field with a luminosity of 4.9 × 1038 erg s-1, GeV photons are successfully produced via inverse Compton scattering. The temporal variability of the diffusion coefficient or injection rate causes flare emission. The observed synchronicity of X-ray and TeV flares implies a decrease of the magnetic field in the flaring source region.

High Temperature Degradation Mechanisms in Polymer Matrix Composites

NASA Technical Reports Server (NTRS)

Cunningham, Ronan A.

1996-01-01

Polymer matrix composites are increasingly used in demanding structural applications in which they may be exposed to harsh environments. The durability of such materials is a major concern, potentially limiting both the integrity of the structures and their useful lifetimes. The goal of the current investigation is to develop a mechanism-based model of the chemical degradation which occurs, such that given the external chemical environment and temperatures throughout the laminate, laminate geometry, and ply and/or constituent material properties, we can calculate the concentration of diffusing substances and extent of chemical degradation as functions of time and position throughout the laminate. This objective is met through the development and use of analytical models, coupled to an analysis-driven experimental program which offers both quantitative and qualitative information on the degradation mechanism. Preliminary analyses using a coupled diffusion/reaction model are used to gain insight into the physics of the degradation mechanisms and to identify crucial material parameters. An experimental program is defined based on the results of the preliminary analysis which allows the determination of the necessary material coefficients. Thermogravimetric analyses are carried out in nitrogen, air, and oxygen to provide quantitative information on thermal and oxidative reactions. Powdered samples are used to eliminate diffusion effects. Tests in both inert and oxidative environments allow the separation of thermal and oxidative contributions to specimen mass loss. The concentration dependency of the oxidative reactions is determined from the tests in pure oxygen. Short term isothermal tests at different temperatures are carried out on neat resin and unidirectional macroscopic specimens to identify diffusion effects. Mass loss, specimen shrinkage, the formation of degraded surface layers and surface cracking are recorded as functions of exposure time. Geometry effects in the neat resin, and anisotropic diffusion effects in the composites, are identified through the use of specimens with different aspect ratios. The data is used with the model to determine reaction coefficients and effective diffusion coefficients. The empirical and analytical correlations confirm the preliminary model results which suggest that mass loss at lower temperatures is dominated by oxidative reactions and that these reaction are limited by diffusion of oxygen from the surface. The mechanism-based model is able to successfully capture the basic physics of the degradation phenomena under a wide range of test conditions. The analysis-based test design is successful in separating out oxidative, thermal, and diffusion effects to allow the determination of material coefficients. This success confirms the basic picture of the process; however, a more complete understanding of some aspects of the physics are required before truly predictive capability can be achieved.

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

Reversible geminate recombination of hydrogen-bonded water molecule pair

NASA Astrophysics Data System (ADS)

Markovitch, Omer; Agmon, Noam

2008-08-01

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

Computer simulations of adsorption and diffusion for binary mixtures of methane and hydrogen in titanosilicates.

PubMed

Mitchell, Martha C; Gallo, Marco; Nenoff, Tina M

2004-07-22

Equilibrium molecular dynamics (MD) simulations of equimolar mixtures of hydrogen and methane were performed in three different titanosilicates: naturally occurring zorite and two synthetic titanosilicates, ETS-4 and ETS-10. In addition, single-component MD simulations and adsorption isotherms generated using grand canonical Monte Carlo simulations were performed to support the mixture simulations. The goal of this study was to determine the best membrane material to carry out hydrogen/methane separations. ETS-10 has a three-dimensional pore network. ETS-4 and zorite have two-dimensional pore networks. The simulations carried out in this study show that the increased porosity of ETS-10 results in self-diffusion coefficients for both hydrogen and methane that are higher in ETS-10 than in either ETS-4 or zorite. Methane only showed appreciable displacement in ETS-10. The ability of the methane molecules to move in all three directions in ETS-10 was demonstrated by the high degree of isotropy shown in the values of the x, y, and z components of the self-diffusion coefficient for methane in ETS-10. From our simulations we conclude that ETS-10 would be better suited for fast industrial separations of hydrogen and methane. However, the separation would not result in a pure hydrogen stream. In contrast, ETS-4 and zorite would act as true molecular sieves for separations of hydrogen and methane, as the methane would not move through membranes made of these materials. This was indicated by the near-zero self-diffusion coefficient of methane in ETS-4 and zorite.

Computer simulations of adsorption and diffusion for binary mixtures of methane and hydrogen in titanosilicates

NASA Astrophysics Data System (ADS)

Mitchell, Martha C.; Gallo, Marco; Nenoff, Tina M.

2004-07-01

Equilibrium molecular dynamics (MD) simulations of equimolar mixtures of hydrogen and methane were performed in three different titanosilicates: naturally occurring zorite and two synthetic titanosilicates, ETS-4 and ETS-10. In addition, single-component MD simulations and adsorption isotherms generated using grand canonical Monte Carlo simulations were performed to support the mixture simulations. The goal of this study was to determine the best membrane material to carry out hydrogen/methane separations. ETS-10 has a three-dimensional pore network. ETS-4 and zorite have two-dimensional pore networks. The simulations carried out in this study show that the increased porosity of ETS-10 results in self-diffusion coefficients for both hydrogen and methane that are higher in ETS-10 than in either ETS-4 or zorite. Methane only showed appreciable displacement in ETS-10. The ability of the methane molecules to move in all three directions in ETS-10 was demonstrated by the high degree of isotropy shown in the values of the x, y, and z components of the self-diffusion coefficient for methane in ETS-10. From our simulations we conclude that ETS-10 would be better suited for fast industrial separations of hydrogen and methane. However, the separation would not result in a pure hydrogen stream. In contrast, ETS-4 and zorite would act as true molecular sieves for separations of hydrogen and methane, as the methane would not move through membranes made of these materials. This was indicated by the near-zero self-diffusion coefficient of methane in ETS-4 and zorite.

Dynamics in dense hard-sphere colloidal suspensions

NASA Astrophysics Data System (ADS)

Orsi, Davide; Fluerasu, Andrei; Moussaïd, Abdellatif; Zontone, Federico; Cristofolini, Luigi; Madsen, Anders

2012-01-01

The dynamic behavior of a hard-sphere colloidal suspension was studied by x-ray photon correlation spectroscopy and small-angle x-ray scattering over a wide range of particle volume fractions. The short-time mobility of the particles was found to be smaller than that of free particles even at relatively low concentrations, showing the importance of indirect hydrodynamic interactions. Hydrodynamic functions were derived from the data, and for moderate particle volume fractions (Φ≤ 0.40) there is good agreement with earlier many-body theory calculations by Beenakker and Mazur [Physica A0378-437110.1016/0378-4371(84)90206-1 120, 349 (1984)]. Important discrepancies appear at higher concentrations, above Φ≈ 0.40, where the hydrodynamic effects are overestimated by the Beenakker-Mazur theory, but predicted accurately by an accelerated Stokesian dynamics algorithm developed by Banchio and Brady [J. Chem. Phys.0021-960610.1063/1.1571819 118, 10323 (2003)]. For the relaxation rates, good agreement was also found between the experimental data and a scaling form predicted by the mode coupling theory. In the high concentration range, with the fluid suspensions approaching the glass transition, the long-time diffusion coefficient was compared with the short-time collective diffusion coefficient to verify a scaling relation previously proposed by Segrè and Pusey [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.77.771 77, 771 (1996)]. We discuss our results in view of previous experimental attempts to validate this scaling law [L. Lurio , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.84.785 84, 785 (2000)].

Describing Temperature-Dependent Self-Diffusion Coefficients and Fluidity of 1- and 3-Alcohols with the Compensated Arrhenius Formalism.

PubMed

Fleshman, Allison M; Forsythe, Grant E; Petrowsky, Matt; Frech, Roger

2016-09-22

The location of the hydroxyl group in monohydroxy alcohols greatly affects the temperature dependence of the liquid structure due to hydrogen bonding. Temperature-dependent self-diffusion coefficients, fluidity (the inverse of viscosity), dielectric constant, and density have been measured for several 1-alcohols and 3-alcohols with varying alkyl chain lengths. The data are modeled using the compensated Arrhenius formalism (CAF). The CAF follows a modified transition state theory using an Arrhenius-like expression to describe the transport property, which consists of a Boltzmann factor containing an energy of activation, Ea, and an exponential prefactor containing the temperature-dependent solution dielectric constant, εs(T). Both 1- and 3-alcohols show the Ea of diffusion coefficients (approximately 43 kJ mol(-1)) is higher than the Ea of fluidity (approximately 35 kJ mol(-1)). The temperature dependence of the exponential prefactor in these associated liquids is explained using the dielectric constant and the Kirkwood-Frölich correlation factor, gk. It is argued that the dielectric constant must be used to account for the additional temperature dependence due to variations in the liquid structure (e.g., hydrogen bonding) for the CAF to accurately model the transport property.

Self-attracting walk on heterogeneous networks

NASA Astrophysics Data System (ADS)

Kim, Kanghun; Kyoung, Jaegu; Lee, D.-S.

2016-05-01

Understanding human mobility in cyberspace becomes increasingly important in this information era. While human mobility, memory-dependent and subdiffusive, is well understood in Euclidean space, it remains elusive in random heterogeneous networks like the World Wide Web. Here we study the diffusion characteristics of self-attracting walks, in which a walker is more likely to move to the locations visited previously than to unvisited ones, on scale-free networks. Under strong attraction, the number of distinct visited nodes grows linearly in time with larger coefficients in more heterogeneous networks. More interestingly, crossovers to sublinear growths occur in strongly heterogeneous networks. To understand these phenomena, we investigate the characteristic volumes and topology of the cluster of visited nodes and find that the reinforced attraction to hubs results in expediting exploration first but delaying later, as characterized by the scaling exponents that we derive. Our findings and analysis method can be useful for understanding various diffusion processes mediated by human.

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.

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.

Effect of component substitution on the atomic dynamics in glass-forming binary metallic melts

NASA Astrophysics Data System (ADS)

Nowak, B.; Holland-Moritz, D.; Yang, F.; Voigtmann, Th.; Evenson, Z.; Hansen, T. C.; Meyer, A.

2017-08-01

We investigate the substitution of early transition metals (Zr, Hf, and Nb) in Ni-based binary glass-forming metallic melts and the impact on structural and dynamical properties by using a combination of neutron scattering, electrostatic levitation (ESL), and isotopic substitution. The self-diffusion coefficients measured by quasielastic neutron scattering (QENS) identify a sluggish diffusion as well as an increased activation energy by almost a factor of 2 for Hf35Ni65 compared to Zr36Ni64 . This finding can be explained by the locally higher packing density of Hf atoms in Hf35Ni65 compared to Zr atoms in Zr36Ni64 , which has been derived from interatomic distances by analyzing the measured partial structure factors. Furthermore, QENS measurements of liquid Hf35Ni65 prepared with 60Ni , which has a vanishing incoherent scattering cross section, have demonstrated that self-diffusion of Hf is slowed down compared to the concentration weighted self-diffusion of Hf and Ni. This implies a dynamical decoupling between larger Hf and smaller Ni atoms, which can be related to a saturation effect of unequal atomic nearest-neighbor pairs, that was observed recently for Ni-rich compositions in Zr-Ni metallic melts. In order to establish a structure-dynamics relation, measured partial structure factors have been used as an input for mode-coupling theory (MCT) of the glass transition to calculate self-diffusion coefficients for the different atomic components. Remarkably, MCT can reproduce the increased activation energy for Hf35Ni65 as well as the dynamical decoupling between Hf and Ni atoms.

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

PubMed Central

Gupta, Rahul

2018-01-01

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

Application of Molecular Dynamics Simulations in Molecular Property Prediction II: Diffusion Coefficient

PubMed Central

Wang, Junmei; Hou, Tingjun

2011-01-01

In this work, we have evaluated how well the General AMBER force field (GAFF) performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, 5 organic compounds in aqueous solutions, 4 proteins in aqueous solutions, and 9 organic compounds in non-aqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned error (AUE) and the root-mean-square error (RMSE) are 0.137 and 0.171 ×10−5 cm−2s−1, respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for 8 organic solvents with experimental data (R2 = 0.784), 4 proteins in aqueous solutions (R2 = 0.996) and 9 organic compounds in non-aqueous solutions (R2 = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide (DMSO) and cyclohexane have been studied. The major MD settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement (MSD) collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. PMID:21953689

An empirical relation between the limiting ionic molar conductivities and self-diffusion coefficients of pure solvents

NASA Astrophysics Data System (ADS)

Matsuyama, Hisashi; Motoyoshi, Kota

2018-05-01

The limiting ionic molar conductivity (λ∞) of an electrolyte solution depends on the self-diffusion coefficient (Ds) of the pure solvent when the temperature (T) changes. To study the Ds-dependence of λ∞, we proposed a new empirical relation λ∞ ∝(Ds / T) t , with a parameter t. The relation is applied to the λ∞ and Ds of alkali, tetra-alkyl ammonium, and halogen ions in water or methanol. All ions except for tetra-alkyl ammonium ions in water exhibit excellent linear relationships in their λ∞ ∝(Ds / T) t plots, with t in the range from 0.88 to 1.26. This is the first report showing an affirmative linear correlation between λ∞ and Ds.

Static and transport properties of alkyltrimethylammonium cation-based room-temperature ionic liquids.

PubMed

Seki, Shiro; Tsuzuki, Seiji; Hayamizu, Kikuko; Serizawa, Nobuyuki; Ono, Shimpei; Takei, Katsuhito; Doi, Hiroyuki; Umebayashi, Yasuhiro

2014-05-01

We have measured physicochemical properties of five alkyltrimethylammonium cation-based room-temperature ionic liquids and compared them with those obtained from computational methods. We have found that static properties (density and refractive index) and transport properties (ionic conductivity, self-diffusion coefficient, and viscosity) of these ionic liquids show close relations with the length of the alkyl chain. In particular, static properties obtained by experimental methods exhibit a trend complementary to that by computational methods (refractive index ∝ [polarizability/molar volume]). Moreover, the self-diffusion coefficient obtained by molecular dynamics (MD) simulation was consistent with the data obtained by the pulsed-gradient spin-echo nuclear magnetic resonance technique, which suggests that computational methods can be supplemental tools to predict physicochemical properties of room-temperature ionic liquids.

Dilution effects on combined magnetic and electric dipole interactions: A study of ferromagnetic cobalt nanoparticles with tuneable interactions

NASA Astrophysics Data System (ADS)

Hod, M.; Dobroserdova, A.; Samin, S.; Dobbrow, C.; Schmidt, A. M.; Gottlieb, M.; Kantorovich, S.

2017-08-01

Improved understanding of complex interactions between nanoparticles will facilitate the control over the ensuing self-assembled structures. In this work, we consider the dynamic changes occurring upon dilution in the self-assembly of a system of ferromagnetic cobalt nanoparticles that combine magnetic, electric, and steric interactions. The systems examined here vary in the strength of the magnetic dipole interactions and the amount of point charges per particle. Scattering techniques are employed for the characterization of the self-assembly aggregates, and zeta-potential measurements are employed for the estimation of surface charges. Our experiments show that for particles with relatively small initial number of surface electric dipoles, an increase in particle concentration results in an increase in diffusion coefficients; whereas for particles with relatively high number of surface dipoles, no effect is observed upon concentration changes. We attribute these changes to a shift in the adsorption/desorption equilibrium of the tri-n-octylphosphine oxide (TOPO) molecules on the particle surface. We put forward an explanation, based on the combination of two theoretical models. One predicts that the growing concentration of electric dipoles, stemming from the addition of tri-n-octylphosphine oxide (TOPO) as co-surfactant during particle synthesis, on the surface of the particles results in the overall repulsive interaction. Secondly, using density functional theory, we explain that the observed behaviour of the diffusion coefficient can be treated as a result of the concentration dependent nanoparticle self-assembly: additional repulsion leads to the reduction in self-assembled aggregate size despite the shorter average interparticle distances, and as such provides the growth of the diffusion coefficient.

Dilution effects on combined magnetic and electric dipole interactions: A study of ferromagnetic cobalt nanoparticles with tuneable interactions.

PubMed

Hod, M; Dobroserdova, A; Samin, S; Dobbrow, C; Schmidt, A M; Gottlieb, M; Kantorovich, S

2017-08-28

Improved understanding of complex interactions between nanoparticles will facilitate the control over the ensuing self-assembled structures. In this work, we consider the dynamic changes occurring upon dilution in the self-assembly of a system of ferromagnetic cobalt nanoparticles that combine magnetic, electric, and steric interactions. The systems examined here vary in the strength of the magnetic dipole interactions and the amount of point charges per particle. Scattering techniques are employed for the characterization of the self-assembly aggregates, and zeta-potential measurements are employed for the estimation of surface charges. Our experiments show that for particles with relatively small initial number of surface electric dipoles, an increase in particle concentration results in an increase in diffusion coefficients; whereas for particles with relatively high number of surface dipoles, no effect is observed upon concentration changes. We attribute these changes to a shift in the adsorption/desorption equilibrium of the tri-n-octylphosphine oxide (TOPO) molecules on the particle surface. We put forward an explanation, based on the combination of two theoretical models. One predicts that the growing concentration of electric dipoles, stemming from the addition of tri-n-octylphosphine oxide (TOPO) as co-surfactant during particle synthesis, on the surface of the particles results in the overall repulsive interaction. Secondly, using density functional theory, we explain that the observed behaviour of the diffusion coefficient can be treated as a result of the concentration dependent nanoparticle self-assembly: additional repulsion leads to the reduction in self-assembled aggregate size despite the shorter average interparticle distances, and as such provides the growth of the diffusion coefficient.

An investigation of turbulent transport in the extreme lower atmosphere

NASA Technical Reports Server (NTRS)

Koper, C. A., Jr.; Sadeh, W. Z.

1975-01-01

A model in which the Lagrangian autocorrelation is expressed by a domain integral over a set of usual Eulerian autocorrelations acquired concurrently at all points within a turbulence box is proposed along with a method for ascertaining the statistical stationarity of turbulent velocity by creating an equivalent ensemble to investigate the flow in the extreme lower atmosphere. Simultaneous measurements of turbulent velocity on a turbulence line along the wake axis were carried out utilizing a longitudinal array of five hot-wire anemometers remotely operated. The stationarity test revealed that the turbulent velocity is approximated as a realization of a weakly self-stationary random process. Based on the Lagrangian autocorrelation it is found that: (1) large diffusion time predominated; (2) ratios of Lagrangian to Eulerian time and spatial scales were smaller than unity; and, (3) short and long diffusion time scales and diffusion spatial scales were constrained within their Eulerian counterparts.

FRACTIONAL PEARSON DIFFUSIONS.

PubMed

Leonenko, Nikolai N; Meerschaert, Mark M; Sikorskii, Alla

2013-07-15

Pearson diffusions are governed by diffusion equations with polynomial coefficients. Fractional Pearson diffusions are governed by the corresponding time-fractional diffusion equation. They are useful for modeling sub-diffusive phenomena, caused by particle sticking and trapping. This paper provides explicit strong solutions for fractional Pearson diffusions, using spectral methods. It also presents stochastic solutions, using a non-Markovian inverse stable time change.

Microscopic theory for dynamics in entangled polymer nanocomposites

NASA Astrophysics Data System (ADS)

Yamamoto, Umi

New microscopic theories for describing dynamics in polymer nanocomposites are developed and applied. The problem is addressed from two distinct perspectives and using two different theoretical approaches. The first half of this dissertation studies the long-time and intermediate-time dynamics of nanoparticles in entangled and unentangled polymer melts for dilute particle concentrations. Using a combination of mode-coupling, Brownian motion, and polymer physics ideas, the nanoparticle long-time diffusion coefficients is formulated in terms of multiple length-scales, packing microstructures, and spatially-resolved polymer density fluctuation dynamics. The key motional mechanism is described via the parallel relaxation of the force exerted on the particle controlled by collective polymer constraint-release and the particle self-motion. A sharp but smooth crossover from the hydrodynamic to the non-hydrodynamic regime is predicted based on the Stokes-Einstein violation ratio as a function of all the system variables. Quantitative predictions are made for the recovery of the Stokes-Einstein law, and the diffusivity in the crossover regime agrees surprisingly well with large-scale molecular dynamics simulations for all particle sizes and chain lengths studied. The approach is also extended to address intermediate-time anomalous transport of a single nanoparticle and two-particle relative diffusion. The second half of this dissertation focuses on developing a novel dynamical theory for a liquid of infinitely-thin rods in the presence of hard spherical obstacles, aiming at a technical and conceptual extension of the existing paradigm for entangled polymer dynamics. As a fundamental theoretical development, the two-component generalization of a first-principles dynamic meanfield approach is presented. The theory enforces inter-needle topological uncrossability and needlesphere impenetrability in a unified manner, leading to a generalized theory of entanglements that includes the sphere excluded volume effect. Coupled self-consistent equations for the generalized diffusion tensors are constructed, and the expressions for the transverse localization lengths and the long-time diffusion coefficients are derived. In the static sphere limit, we find the effective tube diameter is generally reduced as a function of a single confinement parameter that quantifies the number of particles penetrating into the pure-polymer tube. A preliminary extension to treat flexible chain melts has also been achieved, and shown to agree reasonably well with simulations. The anisotropic needle diffusion constants are rich functions of the length-scale ratios, needle concentration and particle volume fraction. We show that the steric blocking of the longitudinal motion causes a literal and simultaneous localization of the two diffusion channels, and entangled needles can diffuse via a modified reptation dynamics over a window of polymer concentration but the compression of the tube and the blocking of the reptation motion must be accounted for. Generalization to treat mobile spheres is also possible and fully formulated.

Charge Effect on the Formation of Polyoxometalate-Based Supramolecular Polygons Driven by Metal Coordination.

PubMed

Piot, Madeleine; Hupin, Sébastien; Lavanant, Hélène; Afonso, Carlos; Bouteiller, Laurent; Proust, Anna; Izzet, Guillaume

2017-07-17

The metal-driven self-assembly of a Keggin-based hybrid bearing two remote pyridine units was investigated. The resulting supramolecular species were identified by combination of 2D diffusion NMR spectroscopy (DOSY) and electrospray ionization mass spectrometry (ESI-MS) as a mixture of molecular triangles and squares. This behavior is different from that of the structural analogue Dawson-based hybrid displaying a higher charge, which only led to the formation of molecular triangles. This study highlights the decisive effect of the charge of the POMs in their self-assembly processes that disfavors the formation of large assemblies. An isothermal titration calorimetry (ITC) experiment confirmed the stronger binding in the case of the Keggin hybrids. A correlation between the diffusion coefficient D and the molecular mass M of the POM-based building block and its coordination oligomers was also observed. We show that the diffusion coefficient of these compounds is mainly determined by their occupied volume rather than by their shape.

Thermal homogeneity of plastication processes in single-screw extruders

NASA Astrophysics Data System (ADS)

Bu, L. X.; Agbessi, Y.; Béreaux, Y.; Charmeau, J.-Y.

2018-05-01

Single-screw plastication, used in extrusion and in injection moulding, is a major way of processing commodity thermoplastics. During the plastication phase, the polymeric material is melted by the combined effects of shear-induced self-heating (viscous dissipation) and heat conduction coming from the barrel. In injection moulding, a high level of reliability is usually achieved that makes this process ideally suited to mass market production. Nonetheless, process fluctuations still appear that make moulded part quality control an everyday issue. In this work, we used a combined modelling of plastication, throughput calculation and laminar dispersion, to investigate if, and how, thermal fluctuations could propagate along the screw length and affect the melt homogeneity at the end of the metering section. To do this, we used plastication models to relate changes in processing parameters to changes in the plastication length. Moreover, a simple model of throughput calculation is used to relate the screw geometry, the polymer rheology and the processing parameters to get a good estimate of the mass flow rate. Hence, we found that the typical residence time in a single screw is around one tenth of the thermal diffusion time scale. This residence time is too short for the dispersion coefficient to reach a steady state, but too long to be able to neglect radial thermal diffusion and resort to a purely convective solution. Therefore, a full diffusion/convection problem has to be solved with a base flow described by the classic pressure and drag velocity field. Preliminary results already show the major importance of the processing parameters in the breakthrough curve of an arbitrary temperature fluctuation at the end of the metering section of injection moulding screw. When the flow back-pressure is high, the temperature fluctuation is spread more evenly with time, whereas a pressure drop in the flow will results in a breakthrough curve which presents a larger peak of fluctuation.

String-like collective motion and diffusion in the interfacial region of ice

NASA Astrophysics Data System (ADS)

Wang, Xinyi; Tong, Xuhang; Zhang, Hao; Douglas, Jack F.

2017-11-01

We investigate collective molecular motion and the self-diffusion coefficient Ds of water molecules in the mobile interfacial layer of the secondary prismatic plane (11 2 ¯ 0 ) of hexagonal ice by molecular dynamics simulation based on the TIP4P/2005 water potential and a metrology of collective motion drawn from the field of glass-forming liquids. The width ξ of the mobile interfacial layer varies from a monolayer to a few nm as the temperature is increased towards the melting temperature Tm, in accordance with recent simulations and many experimental studies, although different experimental methods have differed in their precise estimates of the thickness of this layer. We also find that the dynamics within this mobile interfacial ice layer is "dynamically heterogeneous" in a fashion that has many features in common with glass-forming liquids and the interfacial dynamics of crystalline Ni over the same reduced temperature range, 2/3 < T/Tm < 1. In addition to exhibiting non-Gaussian diffusive transport, decoupling between mass diffusion and the structural relaxation time, and stretched exponential relaxation, we find string-like collective molecular exchange motion in the interfacial zone within the ice interfacial layer and colored noise fluctuations in the mean square molecular atomic displacement 〈u2〉 after a "caging time" of 1 ps, i.e., the Debye-Waller factor. However, while the heterogeneous dynamics of ice is clearly similar in many ways to molecular and colloidal glass-forming materials, we find distinct trends between the diffusion coefficient activation energy Ea for diffusion Ds and the interfacial width ξ from the scale of collective string-like motion L than those found in glass-forming liquids.

Plasma Diffusion in Self-Consistent Fluctuations

NASA Technical Reports Server (NTRS)

Smets, R.; Belmont, G.; Aunai, N.

2012-01-01

The problem of particle diffusion in position space, as a consequence ofeleclromagnetic fluctuations is addressed. Numerical results obtained with a self-consistent hybrid code are presented, and a method to calculate diffusion coefficient in the direction perpendicular to the mean magnetic field is proposed. The diffusion is estimated for two different types of fluctuations. The first type (resuiting from an agyrotropic in itiai setting)is stationary, wide band white noise, and associated to Gaussian probability distribution function for the magnetic fluctuations. The second type (result ing from a Kelvin-Helmholtz instability) is non-stationary, with a power-law spectrum, and a non-Gaussian probabi lity distribution function. The results of the study allow revisiting the question of loading particles of solar wind origin in the Earth magnetosphere.

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.

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.

Time-dependent diffusion MRI in cancer: tissue modeling and applications

NASA Astrophysics Data System (ADS)

Reynaud, Olivier

2017-11-01

In diffusion weighted imaging (DWI), the apparent diffusion coefficient has been recognized as a useful and sensitive surrogate for cell density, paving the way for non-invasive tumor staging, and characterization of treatment efficacy in cancer. However, microstructural parameters, such as cell size, density and/or compartmental diffusivities affect diffusion in various fashions, making of conventional DWI a sensitive but non-specific probe into changes happening at cellular level. Alternatively, tissue complexity can be probed and quantified using the time dependence of diffusion metrics, sometimes also referred to as temporal diffusion spectroscopy when only using oscillating diffusion gradients. Time-dependent diffusion (TDD) is emerging as a strong candidate for specific and non-invasive tumor characterization. Despite the lack of a general analytical solution for all diffusion times / frequencies, TDD can be probed in various regimes where systems simplify in order to extract relevant information about tissue microstructure. The fundamentals of TDD are first reviewed (a) in the short time regime, disentangling structural and diffusive tissue properties, and (b) near the tortuosity limit, assuming weakly heterogeneous media near infinitely long diffusion times. Focusing on cell bodies (as opposed to neuronal tracts), a simple but realistic model for intracellular diffusion can offer precious insight on diffusion inside biological systems, at all times. Based on this approach, the main three geometrical models implemented so far (IMPULSED, POMACE, VERDICT) are reviewed. Their suitability to quantify cell size, intra- and extracellular spaces (ICS and ECS) and diffusivities are assessed. The proper modeling of tissue membrane permeability – hardly a newcomer in the field, but lacking applications - and its impact on microstructural estimates are also considered. After discussing general issues with tissue modeling and microstructural parameter estimation (i.e. fitting), potential solutions are detailed. The in vivo applications of this new, non-invasive, specific approach in cancer are reviewed, ranging from the characterization of gliomas in rodent brains and observation of time-dependence in breast tissue lesions and prostate cancer, to the recent preclinical evaluation of new treatments efficacy. It is expected that clinical applications of TDD will strongly benefit the community in terms of non-invasive cancer screening.

Anomalous diffusion of poly(ethylene oxide) in agarose gels.

PubMed

Brenner, Tom; Matsukawa, Shingo

2016-11-01

We report on the effect of probe size and diffusion time of poly(ethylene) oxide in agarose gels. Time-dependence of the diffusion coefficient, reflecting anomalous diffusion, was observed for poly(ethylene) oxide chains with hydrodynamic radii exceeding about 20nm at an agarose concentration of 2%. The main conclusion is that the pore distribution includes pores that are only several nm across, in agreement with scattering reports in the literature. Interpretation of the diffusion coefficient dependence on the probe size based on a model of entangled rigid rods yielded a rod length of 72nm. Copyright © 2016. Published by Elsevier B.V.

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

Perturbative studies of toroidal momentum transport in KSTAR H-mode and the effect of ion temperature perturbation

NASA Astrophysics Data System (ADS)

Yang, S. M.; Na, Yong-Su; Na, D. H.; Park, J.-K.; Shi, Y. J.; Ko, W. H.; Lee, S. G.; Hahm, T. S.

2018-06-01

Perturbative experiments have been carried out using tangential neutral beam injection (NBI) and non-resonant magnetic perturbation (NRMP) to analyze the momentum transport properties in KSTAR H-modes. Diffusive and non-diffusive terms of momentum transport are evaluated from the transient analysis. Although the operating conditions and methodologies applied in the two cases are similar, the momentum transport properties obtained show clear differences. The estimated momentum diffusivity and pinch obtained in the NBI modulation experiments is larger than that in the NRMP modulation experiments. We found that this discrepancy could be a result of uncertainties in the assumption for the analysis. By introducing time varying momentum transport coefficients depending on the temperature gradient, the linearized equation shows that if the temperature perturbation exists, the evolution of toroidal rotation perturbation could be faster than the transport rate of mean quantity, since the evolution of toroidal rotation perturbation is related to , a momentum diffusivity from perturbative analysis. This could explain the estimated higher momentum diffusivity using time independent transport coefficients in NBI experiments with higher ion temperature perturbation compared to that in NRMP modulation experiments. The differences in the momentum transport coefficient with NRMP and NBI are much reduced by considering time varying momentum transport coefficients in the time dependent transport simulation.

Soliton solutions, stability analysis and conservation laws for the brusselator reaction diffusion model with time- and constant-dependent coefficients

NASA Astrophysics Data System (ADS)

Inc, Mustafa; Yusuf, Abdullahi; Isa Aliyu, Aliyu; Hashemi, M. S.

2018-05-01

This paper studies the brusselator reaction diffusion model (BRDM) with time- and constant-dependent coefficients. The soliton solutions for BRDM with time-dependent coefficients are obtained via first integral (FIM), ansatz, and sine-Gordon expansion (SGEM) methods. Moreover, it is well known that stability analysis (SA), symmetry analysis and conservation laws (CLs) give several information for modelling a system of differential equations (SDE). This is because they can be used for investigating the internal properties, existence, uniqueness and integrability of different SDE. For this reason, we investigate the SA via linear stability technique, symmetry analysis and CLs for BRDM with constant-dependent coefficients in order to extract more physics and information on the governing equation. The constraint conditions for the existence of the solutions are also examined. The new solutions obtained in this paper can be useful for describing the concentrations of diffusion problems of the BRDM. It is shown that the examined dependent coefficients are some of the factors that are affecting the diffusion rate. So, the present paper provides much motivational information in comparison to the existing results in the literature.

Design and validation of a self-administered questionnaire as an aid to detection of occupational exposure to lung carcinogens.

PubMed

Pélissier, C; Dutertre, V; Fournel, P; Gendre, I; Michel Vergnon, J; Kalecinski, J; Tinquaut, F; Fontana, L; Chauvin, F

2017-02-01

Ten to thirty percent of lung cancer is thought to be of occupational origin. Lung cancer is under-declared as an occupational disease in Europe, and most declarations of occupational disease concern asbestos. The purpose of this study was to design and validate a short, sensitive self-administered questionnaire, as an aid for physicians in detecting occupational exposure to asbestos and other lung carcinogens in order to remedy occupational lung cancer under-declaration. Cross-sectional study. A short (30-question) self-administered questionnaire was drawn up by oncologist-pneumologists and occupational physicians, covering situations of exposure to proven and probable lung carcinogens. Understanding and acceptability were assessed on 15 lung cancer patients. Validity and reliability were assessed on 70 lung cancer patients by comparison against a semi-directive questionnaire considered as gold standard. Sensitivity and specificity were assessed by comparing responses to items on the two questionnaires. Reliability was assessed by analysing the kappa concordance coefficient for items on the two questionnaires. Sensitivity was 0.85 and specificity 0.875. Concordance between responses on the two questionnaires was 85.7%, with a kappa coefficient of 0.695 [0.52-0.87]. Mean self-administration time was 3.1 min (versus 8.12 min to administer the gold-standard questionnaire). In 16 patients, the self-administered questionnaire detected lung carcinogen exposure meeting the criteria for occupational disease. The present short, easy-to-use self-administered questionnaire should facilitate detection of occupational exposure to lung carcinogens. It could be used in occupational lung cancer screening and increase the presently low rate of application for recognition of lung cancer as an occupational disease. Copyright © 2016 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

One-Dimensional Singlet Exciton Diffusion in Poly(3-hexylthiophene) Crystalline Domains.

PubMed

Tamai, Yasunari; Matsuura, Yuu; Ohkita, Hideo; Benten, Hiroaki; Ito, Shinzaburo

2014-01-16

Singlet exciton dynamics in crystalline domains of regioregular poly(3-hexylthiophene) (P3HT) films was studied by transient absorption spectroscopy. Upon the selective excitation of crystalline P3HT at the absorption edge, no red shift of the singlet exciton band was observed with an elapse of time, suggesting singlet exciton dynamics in relatively homogeneous P3HT crystalline domains without downhill relaxation in the energetic disorder. Even under such selective excitation conditions, the annihilation rate coefficient γ(t) was still dependent on time, γ(t) ∝ t(-1/2), which is attributed to anisotropic exciton diffusion in P3HT crystalline domains. From the annihilation rate coefficient, the singlet exciton diffusion coefficient D and exciton diffusion length LD in the crystalline domains were evaluated to be 7.9 × 10(-3) cm(2) s(-1) and 20 nm, respectively. The origin of the time-dependent exciton dynamics is discussed in terms of dimensionality.

Quantitative characterization of organic diffusion using an analytical diffusion-reaction model and its application to assessing BOD removal when treating municipal wastewater in a plug flow reactor.

PubMed

Fan, Chihhao; Kao, Chen-Fei; Liu, Yu-Hsi

2017-09-15

The present study aimed to derive an analytical formula to quantify the diffusion of organic contaminant in a biofilm. The experiments were conducted to investigate the BOD degradation under the conditions of influent COD concentration from 50 to 300 mg/L, COD:N:P ratios of 100:5:1 and 100:15:3, with and without auxiliary aeration. The BOD removal rate was around 73% for non-aerated influent COD of 50 mg/L with 1-h hydraulic retention time. The BOD removal rate increased as the influent loading and hydraulic retention time increased while the influent COD was no more than 150 mg/L. Without aeration, the removal rate dropped significantly when influent COD increased to the range no less than 200 mg/L, due to the fact that the BOD diffusive flux driven by the biomass uptake was not further enhanced by higher ambient organic loading. The diffusion coefficient was calculated to be 1.12 × 10 -6  m 2 /d with influent COD of 50 mg/L at COD:N:P ratio of 100:5:1 and 1 h hydraulic retention time and aeration, and the coefficient increased to 3.35 × 10 -6  m 2 /d as the influent COD concentration increased to 300 mg/L. The diffusion coefficient decreased to 4.09 × 10 -7  m 2 /d as the retention time increased to 3 h. The overall diffusion coefficients showed an increasing trend as the influent organic loading increased. The difference in diffusion coefficients between 1 and 2 h was apparently greater than that between 2 and 3 h, indicating a smaller overall diffusive flux due to a longer retention time. Further analysis revealed that BOD diffusion activity exhibited a declining trend as the wastewater travelled through the system. An analytical diffusion-reaction model was developed to characterize the diffusion behaviour, and applied to estimating the treatment efficiency for real domestic sewage. The result showed that the estimated effluent BOD concentrations were quite comparable to those from experimental measurements. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diffusion of Sticky Nanoparticles in a Polymer Melt: Crossover from Suppressed to Enhanced Transport

DOE PAGES

Carroll, Bobby; Bocharova, Vera; Carrillo, Jan-Michael Y.; ...

2018-03-09

The self-diffusion of a single large particle in a fluid is usually described by the classic Stokes–Einstein (SE) hydrodynamic relation. However, there are many fluids where the SE prediction for nanoparticles diffusion fails. These systems include diffusion of nanoparticles in porous media, in entangled and unentangled polymer melts and solutions, and protein diffusion in biological environments. A fundamental understanding of the microscopic parameters that govern nanoparticle diffusion is relevant to a wide range of applications. Here in this work, we present experimental measurements of the tracer diffusion coefficient of small and large nanoparticles that experience strong attractions with unentangled andmore » entangled polymer melt matrices. For the small nanoparticle system, a crossover from suppressed to enhanced diffusion is observed with increasing polymer molecular weight. We interpret these observations based on our theoretical and simulation insights of the preceding article (paper 1) as a result of a crossover from an effective hydrodynamic core–shell to a nonhydrodynamic vehicle mechanism of transport, with the latter strongly dependent on polymer–nanoparticle desorption time. In conclusion, a general zeroth-order qualitative picture for small sticky nanoparticle diffusion in polymer melts is proposed.« less

Diffusion of Sticky Nanoparticles in a Polymer Melt: Crossover from Suppressed to Enhanced Transport

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

Carroll, Bobby; Bocharova, Vera; Carrillo, Jan-Michael Y.

The self-diffusion of a single large particle in a fluid is usually described by the classic Stokes–Einstein (SE) hydrodynamic relation. However, there are many fluids where the SE prediction for nanoparticles diffusion fails. These systems include diffusion of nanoparticles in porous media, in entangled and unentangled polymer melts and solutions, and protein diffusion in biological environments. A fundamental understanding of the microscopic parameters that govern nanoparticle diffusion is relevant to a wide range of applications. Here in this work, we present experimental measurements of the tracer diffusion coefficient of small and large nanoparticles that experience strong attractions with unentangled andmore » entangled polymer melt matrices. For the small nanoparticle system, a crossover from suppressed to enhanced diffusion is observed with increasing polymer molecular weight. We interpret these observations based on our theoretical and simulation insights of the preceding article (paper 1) as a result of a crossover from an effective hydrodynamic core–shell to a nonhydrodynamic vehicle mechanism of transport, with the latter strongly dependent on polymer–nanoparticle desorption time. In conclusion, a general zeroth-order qualitative picture for small sticky nanoparticle diffusion in polymer melts is proposed.« less

A first-principles study of elastic and diffusion properties of magnesium based alloys

NASA Astrophysics Data System (ADS)

Ganeshan, Swetha

2011-12-01

In this thesis, the influence of alloying elements on the elastic and diffusion properties of Magnesium (Mg) has been studied based on first-principles density functional theory. The stress-strain method has been used to predict the elastic constants of the Mg based alloys studied herein. This method involves calculating the resultant change in stress due to application of strain. The validity of this method has been successfully tested for both 0K as well as at finite temperatures. The elastic constants predicted in this work have been correlated to ductility, fracture toughness, stiffness, elastic anisotropy and bond directionality, thus providing a better understanding of the influence of alloying elements on the mechanical and physical properties of Mg. Elastic constants, as a function of temperature have been predicted using first-principles quasi-static approximation. In this approach elastic stiffness coefficients calculated with respect to volume (cij( V)) have been correlated to the equilibrium volume as a function of temperature V(T) from phonon calculations to obtain temperature dependence of elastic stiffness coefficients cij(T). To compare our calculated temperature dependent elastic constants with that of experiments an isentropic correction term has been introduced. It is seen that the influence of this isentropic correction term on the elastic constants becomes significant at high temperatures. The quasi-static approximation has been primarily applied to calculate temperature dependent elastic constants of Mg2Ge, Mg2Si, Mg 2Sn and Mg2Pb. In the case of dilute Mg alloys, a 36 atom supercell with 35 atoms of Mg and one atom of the alloying impurity has been used for calculating the corresponding elastic constants. It is seen that there is a direct correspondence between the trends in the elastic constants and the lattice parameters of all the Mg based alloys studied herein. Elements that cause a decrease (increase) in the lattice constants result in an increase (decrease) in the bulk modulus. Self-diffusion calculations of Mg have been performed within both LDA and GGA. It is seen that, in the absence of surface corrections, while results of the two approximations (i.e. LDA and GGA) bound experimental data, better agreement is seen with respect to results from LDA, in comparison with experimental measurements. The effect of thermal expansion on the diffusivity of Mg has been studied using both HA and QHA. It is seen that the influence of anharmonicity on the diffusivity of Mg is negligible. Self-diffusion of Mg is faster in the basal plane than between adjacent basal planes. Partial correlation factors corresponding to the diffusion of a Mg atom from one basal plane to the adjacent basal plane, i.e. fBx and fBz, decrease with temperature whereas the partial correlation factor corresponding to the diffusion of Mg atom within the basal plane, i.e. fAx , increases with temperature. The ratio of jump frequencies w⊥/w∥ for self-diffusion of Mg increase with increase in temperature. The method used to calculate self-diffusion coefficients has been extended to compute impurity diffusion coefficients of Al, Ca, Sn and Zn in Mg. For these calculations, a 36 atom supercell with 1 vacant site and 1 impurity has been used. The 8-frequencey model has been implemented to obtain the different atom jump frequencies in order to calculate impurity diffusion coefficients in Mg. The trend in the impurity diffusion coefficients, with the exception of DZn-Mg is as follows: D Mg-Ca>DMg>DMg-Sn> DMg-Al. For impurity diffusion of Zn in Mg, at high temperatures DMg-Zn overlaps with that of DMg-Al , while at low temperatures it overlaps with that of D Mg-Sn. The different atom jump frequencies computed during the diffusion calculations are seen to be temperature dependent, increasing with increase in temperature. The correlation factors for all the alloy systems considered herein, is close to 1. This is expected to be due to the close packing of Mg lattice. (Abstract shortened by UMI.)

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.

Complex Diffusion Mechanisms for Li in Feldspar: Re-thinking Li-in-Plag Geospeedometry

NASA Astrophysics Data System (ADS)

Holycross, M.; Watson, E. B.

2017-12-01

In recent years, the lithium isotope system has been applied to model processes in a wide variety of terrestrial environments. In igneous settings, Li diffusion gradients have been frequently used to time heating episodes. Lithium partitioning behavior during decompression or cooling events drives Li transfer between phases, but the extent of Li exchange may be limited by its diffusion rate in geologic materials. Lithium is an exceptionally fast diffuser in silicate media, making it uniquely suited to record short-lived volcanic phenomena. The Li-in-plagioclase geospeedometer is often used to time explosive eruptions by applying laboratory-calibrated Li diffusion coefficients to model concentration profiles in magmatic feldspar samples. To quantify Li transport in natural scenarios, experimental measurements are needed that account for changing temperature and oxygen fugacity as well as different feldspar compositions and crystallographic orientation. Ambient pressure experiments were run at RPI to diffuse Li from a powdered spodumene source into polished sanidine, albite, oligoclase or anorthite crystals over the temperature range 500-950 ºC. The resulting 7Li concentration gradients developed in the mineral specimens were evaluated using laser ablation ICP-MS. The new data show that Li diffusion in all feldspar compositions simultaneously operates by both a "fast" and "slow" diffusion mechanism. Fast path diffusivities are similar to those found by Giletti and Shanahan [1997] for Li diffusion in plagioclase and are typically 10 to 20 times greater than slow path diffusivities. Lithium concentration gradients in the feldspar experiments plot in the shape of two superimposed error function curves with the slow diffusion regime in the near-surface of the crystal. Lithium diffusion is most sluggish in sanidine and is significantly faster in the plagioclase feldspars. It is still unclear what diffusion mechanism operates in nature, but the new measurements may impact how Li-in-plagioclase geospeedometry is used to time igneous processes. Giletti, B.J., and T.M. Shanahan (1997) Alkali diffusion in plagioclase feldspar, Chem. Geol., 139, 3-20

On the anisotropic advection-diffusion equation with time dependent coefficients

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

Hernandez-Coronado, Hector; Coronado, Manuel; Del-Castillo-Negrete, Diego B.

The advection-diffusion equation with time dependent velocity and anisotropic time dependent diffusion tensor is examined in regard to its non-classical transport features and to the use of a non-orthogonal coordinate system. Although this equation appears in diverse physical problems, particularly in particle transport in stochastic velocity fields and in underground porous media, a detailed analysis of its solutions is lacking. In order to study the effects of the time-dependent coefficients and the anisotropic diffusion on transport, we solve analytically the equation for an initial Dirac delta pulse. Here, we discuss the solutions to three cases: one based on power-law correlationmore » functions where the pulse diffuses faster than the classical rate ~t, a second case specically designed to display slower rate of diffusion than the classical one, and a third case to describe hydrodynamic dispersion in porous media« less

On the anisotropic advection-diffusion equation with time dependent coefficients

DOE PAGES

Hernandez-Coronado, Hector; Coronado, Manuel; Del-Castillo-Negrete, Diego B.

2017-02-01

The advection-diffusion equation with time dependent velocity and anisotropic time dependent diffusion tensor is examined in regard to its non-classical transport features and to the use of a non-orthogonal coordinate system. Although this equation appears in diverse physical problems, particularly in particle transport in stochastic velocity fields and in underground porous media, a detailed analysis of its solutions is lacking. In order to study the effects of the time-dependent coefficients and the anisotropic diffusion on transport, we solve analytically the equation for an initial Dirac delta pulse. Here, we discuss the solutions to three cases: one based on power-law correlationmore » functions where the pulse diffuses faster than the classical rate ~t, a second case specically designed to display slower rate of diffusion than the classical one, and a third case to describe hydrodynamic dispersion in porous media« less

Evaluating linear response in active systems with no perturbing field

NASA Astrophysics Data System (ADS)

Szamel, Grzegorz

2017-03-01

We present a method for the evaluation of time-dependent linear response functions for systems of active particles propelled by a persistent (colored) noise from unperturbed simulations. The method is inspired by the Malliavin weights sampling method proposed by Warren and Allen (Phys. Rev. Lett., 109 (2012) 250601) for out-of-equilibrium systems of passive Brownian particles. We illustrate our method by evaluating two linear response functions for a single active particle in an external harmonic potential. As an application, we calculate the time-dependent mobility function and an effective temperature, defined through the Einstein relation between the self-diffusion and mobility coefficients, for a system of many active particles interacting via a screened Coulomb potential. We find that this effective temperature decreases with increasing persistence time of the self-propulsion. Initially, for not too large persistence times, it changes rather slowly, but then it decreases markedly when the persistence length of the self-propelled motion becomes comparable with the particle size.

Evaluating linear response in active systems with no perturbing field: Application to the calculation of an effective temperature

NASA Astrophysics Data System (ADS)

Szamel, Grzegorz

We present a method for the evaluation of time-dependent linear response functions for systems of active particles propelled by a persistent (colored) noise from unperturbed simulations. The method is inspired by the Malliavin weights sampling method proposed earlier for systems of (passive) Brownian particles. We illustrate our method by evaluating a linear response function for a single active particle in an external harmonic potential. As an application, we calculate the time-dependent mobility function and an effective temperature, defined through the Einstein relation between the self-diffusion and mobility coefficients, for a system of active particles interacting via a screened-Coulomb potential. We find that this effective temperature decreases with increasing persistence time of the self-propulsion. Initially, for not too large persistence times, it changes rather slowly, but then it decreases markedly when the persistence length of the self-propelled motion becomes comparable with the particle size. Supported by NSF and ERC.

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.

Diffusion models for corona formation in metagabbros from the Western Grenville Province, Canada

NASA Astrophysics Data System (ADS)

Grant, Shona M.

1988-01-01

Metagabbro bodies in SW Grenville Province display a variety of disequilibrium corona textures between spinel-clouded plagioclase and primary olivine or opaque oxide. Textural evidence favours a single-stage, subsolidus origin for the olivine coronas and diffusive mass transfer is believed to have been the rate-controlling process. Irreversible thermodynamics have been used to model two different garnet symplectite-bearing corona sequences in terms of steady state diffusion. In the models the flux of each component is related to the chemical potential gradients of all diffusing species by the Onsager or L-coefficients for diffusion. These coefficients are analogous to experimentally determined diffusion coefficients ( d), but relate the flux of components to chemical potential rather than concentration gradients. The major constraint on the relative values of Onsager coefficients comes from the observed mole fraction, X, of garnet in the symplectites; in (amph-gt) symplectites X {Gt/Sym}˜0.80, compared with ˜0.75 in (cpx-gt) symplectites. Several models using simple oxide components, and two different modifications of the reactant plagioclase composition, give the following qualitative results: the very low mobility of aluminium appears to control the rate of corona formation. Mg and Fe have similar mobility, and Mg can be up to 6 8 times more mobile than sodium. Determination of calcium mobility is problematical because of a proposed interaction with cross-coefficient terms reflecting “uphill” Ca-diffusion, i.e., calcium diffusing up its own chemical potential gradient. If these terms are not introduced, it is difficult to generate the required proportions of garnet in the symplectite. However, at moderate values of the cross-coefficient ratios, Mg can be up to 4 6 times more mobile than calcium ( L MgMg/LCaCa<4 6) and calcium must be 3 4 times more mobile than aluminium ( L CaCa/LAlAl>3).

Validation of drift and diffusion coefficients from experimental data

NASA Astrophysics Data System (ADS)

Riera, R.; Anteneodo, C.

2010-04-01

Many fluctuation phenomena, in physics and other fields, can be modeled by Fokker-Planck or stochastic differential equations whose coefficients, associated with drift and diffusion components, may be estimated directly from the observed time series. Its correct characterization is crucial to determine the system quantifiers. However, due to the finite sampling rates of real data, the empirical estimates may significantly differ from their true functional forms. In the literature, low-order corrections, or even no corrections, have been applied to the finite-time estimates. A frequent outcome consists of linear drift and quadratic diffusion coefficients. For this case, exact corrections have been recently found, from Itô-Taylor expansions. Nevertheless, model validation constitutes a necessary step before determining and applying the appropriate corrections. Here, we exploit the consequences of the exact theoretical results obtained for the linear-quadratic model. In particular, we discuss whether the observed finite-time estimates are actually a manifestation of that model. The relevance of this analysis is put into evidence by its application to two contrasting real data examples in which finite-time linear drift and quadratic diffusion coefficients are observed. In one case the linear-quadratic model is readily rejected while in the other, although the model constitutes a very good approximation, low-order corrections are inappropriate. These examples give warning signs about the proper interpretation of finite-time analysis even in more general diffusion processes.

Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

PubMed Central

Yamamoto, Eiji; Akimoto, Takuma; Kalli, Antreas C.; Yasuoka, Kenji; Sansom, Mark S. P.

2017-01-01

Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations. One is fractional Brownian motion, attributed to the motion of the lipids with which the PH domain interacts. The other is temporally fluctuating diffusivity; that is, the short-time diffusivity of the bound protein changes substantially with time. Moreover, the diffusivity for short-time measurements is intrinsically different from that for long-time measurements. This fluctuating diffusivity results from dynamic changes in interactions between the PH domain and PIP molecules. Our results provide evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces. Changes in the diffusivity of PH domains and related membrane-bound proteins may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:28116358

Transport of Internetwork Magnetic Flux Elements in the Solar Photosphere

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Preparation and characterization of self-crosslinked organic/inorganic proton exchange membranes

NASA Astrophysics Data System (ADS)

Zhong, Shuangling; Cui, Xuejun; Dou, Sen; Liu, Wencong

A series of silicon-containing sulfonated polystyrene/acrylate (Si-sPS/A) nanoparticles are successfully synthesized via simple emulsion polymerization method. The Si-sPS/A latexes show good film-forming capability and the self-crosslinked organic/inorganic proton exchange membranes are prepared by pouring the Si-sPS/A nanoparticle latexes into glass plates and drying at 60 °C for 10 h and 120 °C for 2 h. The potential of the membranes in direct methanol fuel cells (DMFCs) is characterized preliminarily by studying their thermal stability, ion-exchange capacity, water uptake, methanol diffusion coefficient, proton conductivity and selectivity (proton conductivity/methanol diffusion coefficient). The results indicate that these membranes possess excellent thermal stability and methanol barrier due to the existence of self-crosslinked silica network. In addition, the proton conductivity of the membranes is in the range of 10 -3-10 -2 S cm -1 and all the membranes show much higher selectivity in comparison with Nafion ® 117. These results suggest that the self-crosslinked organic/inorganic proton exchange membranes are particularly promising in DMFC applications.

Simple Analytical Forms of the Perpendicular Diffusion Coefficient for Two-component Turbulence. III. Damping Model of Dynamical Turbulence

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

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

2017-10-01

In several astrophysical applications one needs analytical forms of cosmic-ray diffusion parameters. Some examples are studies of diffusive shock acceleration and solar modulation. In the current article we explore perpendicular diffusion based on the unified nonlinear transport theory. While we focused on magnetostatic turbulence in Paper I, we included the effect of dynamical turbulence in Paper II of the series. In the latter paper we assumed that the temporal correlation time does not depend on the wavenumber. More realistic models have been proposed in the past, such as the so-called damping model of dynamical turbulence. In the present paper wemore » derive analytical forms for the perpendicular diffusion coefficient of energetic particles in two-component turbulence for this type of time-dependent turbulence. We present new formulas for the perpendicular diffusion coefficient and we derive a condition for which the magnetostatic result is recovered.« less

Balance in Astronauts Performing Jumps, Walking and Quiet Stance Following Spaceflight

NASA Technical Reports Server (NTRS)

Reschke, Millard F.; Bloomberg, J. J.; Wood, S. J.; Harm, D. L.

2011-01-01

Introduction: Both balance and locomotor ataxia is severe in astronauts returning from spaceflight with serious implications for unassisted landings. As a part of an ongoing effort to demonstrate the functional significance of the postflight ataxia problem our laboratory has evaluated jumping, walking heel-to-toe and quite stance balance immediately following spaceflight. Methods: Six astronauts from 12-16 day flights and three from 6-month flights were asked to perform three self-initiated two-footed jumps from a 30-cm-high platform, walking for 10 steps (three trials) placing the feet heel to toe in tandem, arms folded across the chest and the eyes closed, and lastly, recover from a simulated fall by standing from a prone position on the floor and with eyes open maintain a quiet stance for 3 min with arms relaxed along the side of the body and feet comfortably positioned on a force plate. Crewmembers were tested twice before flight, on landing day (short-duration), and days 1, 6, and 30 following all flight durations. Results/Conclusions: Many of astronauts tested fell on their first postflight jump but recovered by the third jump showing a rapid learning progression. Changes in take-off strategy were clearly evident in duration of time in the air between the platform and the ground (significant reduction in time to land), and also in increased asymmetry in foot latencies on take-off postflight. During the tandem heel-to-toe walking task there was a significant decrease in percentage of correct steps on landing day (short-duration crew) and on first day following landing (long-duration) with only partial recovery the following day. Astronauts for both short and long duration flight times appeared to be unaware of foot position relative to their bodies or the floor. During quite stance most of crewmembers tested exhibited increased stochastic activity (larger short-term COP diffusion coefficients postflight in all planes and increases in mean sway speed).

In situ estimation of the effective chemical diffusion coefficient of a rock matrix in a fractured aquifer

USGS Publications Warehouse

Gebrekristos, R.A.; Shapiro, A.M.; Usher, B.H.

2008-01-01

An in situ method of estimating the effective diffusion coefficient for a chemical constituent that diffuses into the primary porosity of a rock is developed by abruptly changing the concentration of the dissolved constituent in a borehole in contact with the rock matrix and monitoring the time-varying concentration. The experiment was conducted in a borehole completed in mudstone on the campus of the University of the Free State in Bloemfontein, South Africa. Numerous tracer tests were conducted at this site, which left a residual concentration of sodium chloride in boreholes that diffused into the rock matrix over a period of years. Fresh water was introduced into a borehole in contact with the mudstone, and the time-varying increase of chloride was observed by monitoring the electrical conductivity (EC) at various depths in the borehole. Estimates of the effective diffusion coefficient were obtained by interpreting measurements of EC over 34 d. The effective diffusion coefficient at a depth of 36 m was approximately 7.8??10-6 m2/d, but was sensitive to the assumed matrix porosity. The formation factor and mass flux for the mudstone were also estimated from the experiment. ?? Springer-Verlag 2007.

Presence of time-dependent diffusion in the brachial plexus.

PubMed

Mahbub, Zaid B; Peters, Andrew M; Gowland, Penny A

2018-02-01

This work describes the development of a method to measure the variation of apparent diffusion coefficient (ADC) with diffusion time (Δ) in the brachial plexus, as a potential method of probing microstructure. Diffusion-weighted MRI with body signal suppression was used to highlight the nerves from surrounding tissues, and sequence parameters were optimized for sensitivity to change with diffusion time. A porous media-restricted diffusion model based on the Latour-Mitra equation was fitted to the diffusion time-dependent ADC data from the brachial plexus nerves and cord. The ADC was observed to reduce at long diffusion times, confirming that diffusion was restricted in the nerves and cord in healthy subjects. T2 of the nerves was measured to be 80 ± 5 ms, the diffusion coefficient was found to vary from (1.5 ± 0.1) × 10 -3 mm 2 /s at a diffusion time of 18.3 ms to (1.0 ± 0.2) × 10 -3 mm 2 /s at a diffusion time of 81.3 ms. A novel method of probing restricted diffusion in the brachial plexus was developed. Resulting parameters were comparable with values obtained previously on biological systems. Magn Reson Med 79:789-795, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Quantitative Characterization of the Microstructure and Transport Properties of Biopolymer Networks

PubMed Central

Jiao, Yang; Torquato, Salvatore

2012-01-01

Biopolymer networks are of fundamental importance to many biological processes in normal and tumorous tissues. In this paper, we employ the panoply of theoretical and simulation techniques developed for characterizing heterogeneous materials to quantify the microstructure and effective diffusive transport properties (diffusion coefficient De and mean survival time τ) of collagen type I networks at various collagen concentrations. In particular, we compute the pore-size probability density function P(δ) for the networks and present a variety of analytical estimates of the effective diffusion coefficient De for finite-sized diffusing particles, including the low-density approximation, the Ogston approximation, and the Torquato approximation. The Hashin-Strikman upper bound on the effective diffusion coefficient De and the pore-size lower bound on the mean survival time τ are used as benchmarks to test our analytical approximations and numerical results. Moreover, we generalize the efficient first-passage-time techniques for Brownian-motion simulations in suspensions of spheres to the case of fiber networks and compute the associated effective diffusion coefficient De as well as the mean survival time τ, which is related to nuclear magnetic resonance (NMR) relaxation times. Our numerical results for De are in excellent agreement with analytical results for simple network microstructures, such as periodic arrays of parallel cylinders. Specifically, the Torquato approximation provides the most accurate estimates of De for all collagen concentrations among all of the analytical approximations we consider. We formulate a universal curve for τ for the networks at different collagen concentrations, extending the work of Yeong and Torquato [J. Chem. Phys. 106, 8814 (1997)]. We apply rigorous cross-property relations to estimate the effective bulk modulus of collagen networks from a knowledge of the effective diffusion coefficient computed here. The use of cross-property relations to link other physical properties to the transport properties of collagen networks is also discussed. PMID:22683739

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient.

PubMed

Wang, Junmei; Hou, Tingjun

2011-12-01

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. Copyright © 2011 Wiley Periodicals, Inc.

Understanding of the Elemental Diffusion Behavior in Concentrated Solid Solution Alloys

DOE PAGES

Zhang, Chuan; Zhang, Fan; Jin, Ke; ...

2017-07-13

As one of the core effects on the high-temperature structural stability, the so-called “sluggish diffusion effect” in high-entropy alloy (HEA) has attracted much attention. Experimental investigations on the diffusion kinetics have been carried out in a few HEA systems, such as Al-Co-Cr-Fe-Ni and Co-Cr-Fe-Mn-Ni. However, the mechanisms behind this effect remain unclear. To better understand the diffusion kinetics of the HEAs, a combined computational/experimental approach is employed in the current study. In the present work, a self-consistent atomic mobility database is developed for the face-centered cubic (fcc) phase of the Co-Cr-Fe-Mn-Ni quinary system. The simulated diffusion coefficients and concentration profilesmore » using this database can well describe the experimental data both from this work and the literatures. The validated mobility database is then used to calculate the tracer diffusion coefficients of Ni in the subsystems of the Co-Cr-Fe-Mn-Ni system with equiatomic ratios. The comparisons of these calculated diffusion coefficients reveal that the diffusion of Ni is not inevitably more sluggish with increasing number of components in the subsystem even with homologous temperature. Taking advantage of computational thermodynamics, the diffusivities of alloying elements with composition and/or temperature are also calculated. Furthermore, these calculations provide us an overall picture of the diffusion kinetics within the Co-Cr-Fe-Mn-Ni system.« less

Probability distribution of financial returns in a model of multiplicative Brownian motion with stochastic diffusion coefficient

NASA Astrophysics Data System (ADS)

Silva, Antonio

2005-03-01

It is well-known that the mathematical theory of Brownian motion was first developed in the Ph. D. thesis of Louis Bachelier for the French stock market before Einstein [1]. In Ref. [2] we studied the so-called Heston model, where the stock-price dynamics is governed by multiplicative Brownian motion with stochastic diffusion coefficient. We solved the corresponding Fokker-Planck equation exactly and found an analytic formula for the time-dependent probability distribution of stock price changes (returns). The formula interpolates between the exponential (tent-shaped) distribution for short time lags and the Gaussian (parabolic) distribution for long time lags. The theoretical formula agrees very well with the actual stock-market data ranging from the Dow-Jones index [2] to individual companies [3], such as Microsoft, Intel, etc. [] [1] Louis Bachelier, ``Th'eorie de la sp'eculation,'' Annales Scientifiques de l''Ecole Normale Sup'erieure, III-17:21-86 (1900).[] [2] A. A. Dragulescu and V. M. Yakovenko, ``Probability distribution of returns in the Heston model with stochastic volatility,'' Quantitative Finance 2, 443--453 (2002); Erratum 3, C15 (2003). [cond-mat/0203046] [] [3] A. C. Silva, R. E. Prange, and V. M. Yakovenko, ``Exponential distribution of financial returns at mesoscopic time lags: a new stylized fact,'' Physica A 344, 227--235 (2004). [cond-mat/0401225

The rate of equilibration of viscous aerosol particles

NASA Astrophysics Data System (ADS)

O'Meara, Simon; Topping, David O.; McFiggans, Gordon

2016-04-01

The proximity of atmospheric aerosol particles to equilibrium with their surrounding condensable vapours can substantially impact their transformations, fate and impacts and is the subject of vibrant research activity. In this study we first compare equilibration timescales estimated by three different models for diffusion through aerosol particles to assess any sensitivity to choice of model framework. Equilibration times for diffusion coefficients with varying dependencies on composition are compared for the first time. We show that even under large changes in the saturation ratio of a semi-volatile component (es) of 1-90 % predicted equilibration timescales are in agreement, including when diffusion coefficients vary with composition. For condensing water and a diffusion coefficient dependent on composition, a plasticising effect is observed, leading to a decreased estimated equilibration time with increasing final es. Above 60 % final es maximum equilibration times of around 1 s are estimated for comparatively large particles (10 µm) containing a relatively low diffusivity component (1 × 10-25 m2 s-1 in pure form). This, as well as other results here, questions whether particle-phase diffusion through water-soluble particles can limit hygroscopic growth in the ambient atmosphere. In the second part of this study, we explore sensitivities associated with the use of particle radius measurements to infer diffusion coefficient dependencies on composition using a diffusion model. Given quantified similarities between models used in this study, our results confirm considerations that must be taken into account when designing such experiments. Although quantitative agreement of equilibration timescales between models is found, further work is necessary to determine their suitability for assessing atmospheric impacts, such as their inclusion in polydisperse aerosol simulations.

Comparison of self-reported versus accelerometer-measured physical activity.

PubMed

Dyrstad, Sindre M; Hansen, Bjørge H; Holme, Ingar M; Anderssen, Sigmund A

2014-01-01

The International Physical Activity Questionnaire (IPAQ) is one of the most widely used questionnaires to assess physical activity (PA). Validation studies for the IPAQ have been executed, but still there is a need for studies comparing absolute values between IPAQ and accelerometer in large population studies. To compare PA and sedentary time from the self-administered, short version of the IPAQ with data from ActiGraph accelerometer in a large national sample. A total of 1751 adults (19-84 yr) wore an accelerometer (ActiGraph GT1M) for seven consecutive days and completed the IPAQ-Short Form. Sedentary time, total PA, and time spent in moderate to vigorous activity were compared in relation to sex, age, and education. Men and women reported, on average, 131 min·d (SE = 4 min·d) less sedentary time compared with the accelerometer measurements. The difference between self-reported and measured sedentary time and vigorous-intensity PA was greatest among men with a lower education level and for men 65 yr and older. Although men reported 47% more moderate to vigorous physical activity (MVPA) compared with women, there were no differences between sexes in accelerometer-determined MVPA. Accelerometer-determined moderate PA was reduced from 110 to 42 min·d (62%) when analyzed in blocks of 10 min (P < 0.0001) compared with 1-min blocks. The main correlation coefficients between self-reported variables and accelerometer measures of physical activity were between 0.20 and 0.46. The participants report through IPAQ-Short Form more vigorous PA and less sedentary time compared with the accelerometer. The difference between self-reported and accelerometer-measured MVPA increased with higher activity and intensity levels. Associations between the methods were affected by sex, age, and education, but not body mass index.

Structural relaxation in a binary metallic melt: Molecular dynamics computer simulation of undercooled Al80Ni20

NASA Astrophysics Data System (ADS)

Das, Subir K.; Horbach, Jürgen; Voigtmann, Thomas

2008-08-01

Molecular dynamics computer simulations are performed to study structure and structural relaxation in the glassforming metallic alloy Al80Ni20 . The interactions between the particles are modeled by an effective potential of the embedded atom type. Our model of Al80Ni20 exhibits chemical short-range order (CSRO) that is reflected in a broad prepeak around a wave number of 1.8Å-1 in the partial static structure factor for the Ni-Ni correlations. The CSRO is due to the preference of Ni atoms to have Al rather than Ni atoms as nearest neighbors. By analyzing incoherent and coherent intermediate scattering functions as well as self-diffusion constants and shear viscosity, we discuss how the chemical ordering is reflected in the dynamics of the deeply undercooled melt. The q dependence of the α relaxation time as well as the Debye-Waller factor for the Al-Al correlations show oscillations at the location of the prepeak in the partial static structure factor for the Ni-Ni correlations. The latter feature of the Debye-Waller factor is well reproduced by a calculation in the framework of the mode coupling theory (MCT) of the glass transition, using the partial static structure factors from the simulation as input. We also check the validity of the Stokes-Einstein-Sutherland formula that relates the self-diffusion coefficients with the shear viscosity. We show that it breaks down already far above the mode coupling critical temperature Tc . The failure of the Stokes-Einstein-Sutherland relation is not related to the specific chemical ordering in Al80Ni20 .

Superdiffusion revisited in view of collisionless reconnection

NASA Astrophysics Data System (ADS)

Treumann, R. A.; Baumjohann, W.

2014-06-01

The concept of diffusion in collisionless space plasmas like those near the magnetopause and in the geomagnetic tail during reconnection is reexamined making use of the division of particle orbits into waiting orbits and break-outs into ballistic motion lying at the bottom, for instance, of Lévy flights. The rms average displacement in this case increases with time, describing superdiffusion, though faster than classical, is still a weak process, being however strong enough to support fast reconnection. Referring to two kinds of numerical particle-in-cell simulations we determine the anomalous diffusion coefficient, the anomalous collision frequency on which the diffusion process is based, and construct a relation between the diffusion coefficients and the resistive scale. The anomalous collision frequency from electron pseudo-viscosity in reconnection turns out to be of the order of the lower-hybrid frequency with the latter providing a lower limit, thus making similar assumptions physically meaningful. Tentative though not completely justified use of the κ distribution yields κ ≈ 6 in the reconnection diffusion region and, for the anomalous diffusion coefficient, the order of several times Bohm diffusivity.

Self-excitation of a nonlinear scalar field in a random medium

PubMed Central

Zeldovich, Ya. B.; Molchanov, S. A.; Ruzmaikin, A. A.; Sokoloff, D. D.

1987-01-01

We discuss the evolution in time of a scalar field under the influence of a random potential and diffusion. The cases of a short-correlation in time and of stationary potentials are considered. In a linear approximation and for sufficiently weak diffusion, the statistical moments of the field grow exponentially in time at growth rates that progressively increase with the order of the moment; this indicates the intermittent nature of the field. Nonlinearity halts this growth and in some cases can destroy the intermittency. However, in many nonlinear situations the intermittency is preserved: high, persistent peaks of the field exist against the background of a smooth field distribution. These widely spaced peaks may make a major contribution to the average characteristics of the field. PMID:16593872

Molecular dynamics of lipid bilayers studied by incoherent quasi-elastic neutron scattering

NASA Astrophysics Data System (ADS)

König, S.; Pfeiffer, W.; Bayerl, T.; Richter, D.; Sackmann, E.

1992-08-01

Molecular motions in highly oriented multilayers of dipalmitoylphosphatidylcholine were studied as a function of temperature and hydration using incoherent quasi-elastic neutron scattering (QENS). The short range diffusive motions of the lipid molecules and the chain/headgroup dynamics were evaluated : 1) by measurement of the dependence of the elastic incoherent structure factor (EISF), the line-width Γ and the dynamic structure factors on the scattering vector Q for two orientations of the sample. The orientations were chosen such that the scattering vecto Q was either predominantly perpendicular or parallel to the membrane normal ; 2) by comparing data from protonated and chain deuterated lipids and 3) by the use of instruments of different energy resolution (i.e. time-of-flight and backscattering spectrometers exploring time regimes of 10^{-13} s to 10^{-11} s and 10^{-11} s to 10^{-9} s respectively). In the fluid phase the time-of-flight spectra revealed a restricted isotropic in-plane and out-of-plane diffusion of the hydrocarbon chain and headgroup protons. The mean displacements range from ≈ 0.6 Å for methylene protons near the glycerol backbone to 7 Å for protons near the chain ends. These values are obtained for a water content of 23 wt%. The values are somewhat increased at 30wt% of water. Measurements of the temperature variation of the EISF and the line-width Γ revealed a remarkably high degree of chain dynamics in the gel (L{β '})-phase. The total elastic intensity as observed with the backscattering instrument showed that L{α}-L{β '}-phase transition is only well expressed at Q-values around 1 Å^{-1}, while the number and mobility of the chain defects characterized at Q≈ 2 Å^{-1} (possibly gtg-kinks) increase continuously between 2 °C and 70 °C. In the time regime explored by the backscattering instrument, motions of the whole lipid molecules are also seen. It was interpreted in terms of a superposition of local in-plane and out-of-plane diffusion and lateral diffusional jumps between adjacent sites as predicted by the free volume model. For a sample containing 12 wt% of water at 60 °C the diffusion coefficient for the out-of-plane motion is D^{allel}=6× 10^{-6} cm2/s with an amplitude of 2.25 Å. In-plane the diffusion coefficients range from D_{min}^{perp}=1.5× 10^{-7} cm2/s to D_{max}^{perp}=6× 10^{-6} cm2/s. The lateral diffusion coefficient is D_lat=9.7× 10^{-8} cm2/s in reasonable agreement with FRAP measurements. The strong increase of the lateral mobility with increasing water content yielded an exponential law for the variation of the diffusion coefficient with excess area per lipid (i.e. hydration) in agreement with the free volume model. The out-of-plane motion is characterized by an amplitude of about 0.5 Å in the time-of-flight time regime and of 2-3 Å in the backscattering time regime. The origin of this discrepancy could be the thermally excited membrane undulations since their relaxation times of ≈ 3× 10^{-9} s (obtained in a separate spin-echo study) agree roughly with the reciprocal line-width of 2.5× 10^{-9} s for the backscattering instrument at Qto 0. The time-of-flight result of 0.5 Å can be attributed to a dynamic surface roughness.

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.

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

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.

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.

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

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

Yang, J.; Martí, J., E-mail: jordi.marti@upc.edu; Calero, C.

2014-03-14

Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in themore » membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10{sup −5} cm{sup 2}/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10{sup −8} cm{sup 2}/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2–8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a “wagging of the tails” frequency around 30 cm{sup −1}, which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.« less

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.

Mode coupling theory for nonequilibrium glassy dynamics of thermal self-propelled particles.

PubMed

Feng, Mengkai; Hou, Zhonghuai

2017-06-28

We present a mode coupling theory study for the relaxation and glassy dynamics of a system of strongly interacting self-propelled particles, wherein the self-propulsion force is described by Ornstein-Uhlenbeck colored noise and thermal noises are included. Our starting point is an effective Smoluchowski equation governing the distribution function of particle positions, from which we derive a memory function equation for the time dependence of density fluctuations in nonequilibrium steady states. With the basic assumption of the absence of macroscopic currents and standard mode coupling approximation, we can obtain expressions for the irreducible memory function and other relevant dynamic terms, wherein the nonequilibrium character of the active system is manifested through an averaged diffusion coefficient D[combining macron] and a nontrivial structural function S 2 (q) with q being the magnitude of wave vector q. D[combining macron] and S 2 (q) enter the frequency term and the vertex term for the memory function, and thus influence both the short time and the long time dynamics of the system. With these equations obtained, we study the glassy dynamics of this thermal self-propelled particle system by investigating the Debye-Waller factor f q and relaxation time τ α as functions of the persistence time τ p of self-propulsion, the single particle effective temperature T eff as well as the number density ρ. Consequently, we find the critical density ρ c for given τ p shifts to larger values with increasing magnitude of propulsion force or effective temperature, in good accordance with previously reported simulation work. In addition, the theory facilitates us to study the critical effective temperature T for fixed ρ as well as its dependence on τ p . We find that T increases with τ p and in the limit τ p → 0, it approaches the value for a simple passive Brownian system as expected. Our theory also well recovers the results for passive systems and can be easily extended to more complex systems such as active-passive mixtures.

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.

Fractal analysis of lateral movement in biomembranes.

PubMed

Gmachowski, Lech

2018-04-01

Lateral movement of a molecule in a biomembrane containing small compartments (0.23-μm diameter) and large ones (0.75 μm) is analyzed using a fractal description of its walk. The early time dependence of the mean square displacement varies from linear due to the contribution of ballistic motion. In small compartments, walking molecules do not have sufficient time or space to develop an asymptotic relation and the diffusion coefficient deduced from the experimental records is lower than that measured without restrictions. The model makes it possible to deduce the molecule step parameters, namely the step length and time, from data concerning confined and unrestricted diffusion coefficients. This is also possible using experimental results for sub-diffusive transport. The transition from normal to anomalous diffusion does not affect the molecule step parameters. The experimental literature data on molecular trajectories recorded at a high time resolution appear to confirm the modeled value of the mean free path length of DOPE for Brownian and anomalous diffusion. Although the step length and time give the proper values of diffusion coefficient, the DOPE speed calculated as their quotient is several orders of magnitude lower than the thermal speed. This is interpreted as a result of intermolecular interactions, as confirmed by lateral diffusion of other molecules in different membranes. The molecule step parameters are then utilized to analyze the problem of multiple visits in small compartments. The modeling of the diffusion exponent results in a smooth transition to normal diffusion on entering a large compartment, as observed in experiments.

Time-dependent models for blazar emission with the second-order Fermi acceleration

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

Asano, Katsuaki; Takahara, Fumio; Toma, Kenji

The second-order Fermi acceleration (Fermi-II) driven by turbulence may be responsible for the electron acceleration in blazar jets. We test this model with time-dependent simulations. The hard electron spectrum predicted by the Fermi-II process agrees with the hard photon spectrum of 1ES 1101–232. For other blazars that show softer spectra, the Fermi-II model requires radial evolution of the electron injection rate and/or diffusion coefficient in the outflow. Such evolutions can yield a curved electron spectrum, which can reproduce the synchrotron spectrum of Mrk 421 from the radio to the X-ray regime. The photon spectrum in the GeV energy range ofmore » Mrk 421 is hard to fit with a synchrotron self-Compton model. However, if we introduce an external radio photon field with a luminosity of 4.9 × 10{sup 38} erg s{sup –1}, GeV photons are successfully produced via inverse Compton scattering. The temporal variability of the diffusion coefficient or injection rate causes flare emission. The observed synchronicity of X-ray and TeV flares implies a decrease of the magnetic field in the flaring source region.« less

Simulations of Cyclic Voltammetry for Electric Double Layers in Asymmetric Electrolytes: A Generalized Modified Poisson-Nernst-Planck Model

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

Wang, Hainan; Thiele, Alexander; Pilon, Laurent

2013-11-15

This paper presents a generalized modified Poisson–Nernst–Planck (MPNP) model derived from first principles based on excess chemical potential and Langmuir activity coefficient to simulate electric double-layer dynamics in asymmetric electrolytes. The model accounts simultaneously for (1) asymmetric electrolytes with (2) multiple ion species, (3) finite ion sizes, and (4) Stern and diffuse layers along with Ohmic potential drop in the electrode. It was used to simulate cyclic voltammetry (CV) measurements for binary asymmetric electrolytes. The results demonstrated that the current density increased significantly with decreasing ion diameter and/or increasing valency |z i| of either ion species. By contrast, the ionmore » diffusion coefficients affected the CV curves and capacitance only at large scan rates. Dimensional analysis was also performed, and 11 dimensionless numbers were identified to govern the CV measurements of the electric double layer in binary asymmetric electrolytes between two identical planar electrodes of finite thickness. A self-similar behavior was identified for the electric double-layer integral capacitance estimated from CV measurement simulations. Two regimes were identified by comparing the half cycle period τ CV and the “RC time scale” τ RC corresponding to the characteristic time of ions’ electrodiffusion. For τ RC ← τ CV, quasi-equilibrium conditions prevailed and the capacitance was diffusion-independent while for τ RC → τ CV, the capacitance was diffusion-limited. The effect of the electrode was captured by the dimensionless electrode electrical conductivity representing the ratio of characteristic times associated with charge transport in the electrolyte and that in the electrode. The model developed here will be useful for simulating and designing various practical electrochemical, colloidal, and biological systems for a wide range of applications.« less

Diffusion of water in the endosperm tissue of wheat grains as studied by pulsed field gradient nuclear magnetic resonance.

PubMed

Callaghan, P T; Jolley, K W; Lelievre, J

1979-10-01

Pulsed field gradient nuclear magnetic resonance has been used to measure water self-diffusion coefficients in the endosperm tissue of wheat grains as a function of the tissue water content. A model that confines the water molecules to a randomly oriented array of capillaries with both transverse dimension less than 100 nm has been used to fit the data and give a unique diffusion coefficient at each water content. The diffusion rates vary from 1.8 x 10(-10) m2s-1 at the lowest to 1.2 x 10(-9) m2s-1 at the highest moisture content. This variation can be explained in terms of an increase in water film thickness from approximately 0.5 to approximately 2.5 nm over the moisture range investigated (200-360 mg g-1).

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

PubMed Central

2015-01-01

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

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

PubMed

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

2014-06-05

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

Experimental measurement of self-diffusion in a strongly coupled plasma

DOE PAGES

Strickler, Trevor S.; Langin, Thomas K.; McQuillen, Paul; ...

2016-05-17

Here, we present a study of the collisional relaxation of ion velocities in a strongly coupled, ultracold neutral plasma on short time scales compared to the inverse collision rate. The measured average velocity of a tagged population of ions is shown to be equivalent to the ion-velocity autocorrelation function. We thus gain access to fundamental aspects of the single-particle dynamics in strongly coupled plasmas and to the ion self-diffusion constant under conditions where experimental measurements have been lacking. Nonexponential decay towards equilibrium of the average velocity heralds non-Markovian dynamics that are not predicted by traditional descriptions of weakly coupled plasmas.more » This demonstrates the utility of ultracold neutral plasmas for studying the effects of strong coupling on collisional processes, which is of interest for dense laboratory and astrophysical plasmas.« less

Light attenuation characteristics of glacially-fed lakes

NASA Astrophysics Data System (ADS)

Rose, Kevin C.; Hamilton, David P.; Williamson, Craig E.; McBride, Chris G.; Fischer, Janet M.; Olson, Mark H.; Saros, Jasmine E.; Allan, Mathew G.; Cabrol, Nathalie

2014-07-01

Transparency is a fundamental characteristic of aquatic ecosystems and is highly responsive to changes in climate and land use. The transparency of glacially-fed lakes may be a particularly sensitive sentinel characteristic of these changes. However, little is known about the relative contributions of glacial flour versus other factors affecting light attenuation in these lakes. We sampled 18 glacially-fed lakes in Chile, New Zealand, and the U.S. and Canadian Rocky Mountains to characterize how dissolved absorption, algal biomass (approximated by chlorophyll a), water, and glacial flour contributed to attenuation of ultraviolet radiation (UVR) and photosynthetically active radiation (PAR, 400-700 nm). Variation in attenuation across lakes was related to turbidity, which we used as a proxy for the concentration of glacial flour. Turbidity-specific diffuse attenuation coefficients increased with decreasing wavelength and distance from glaciers. Regional differences in turbidity-specific diffuse attenuation coefficients were observed in short UVR wavelengths (305 and 320 nm) but not at longer UVR wavelengths (380 nm) or PAR. Dissolved absorption coefficients, which are closely correlated with diffuse attenuation coefficients in most non-glacially-fed lakes, represented only about one quarter of diffuse attenuation coefficients in study lakes here, whereas glacial flour contributed about two thirds across UVR and PAR. Understanding the optical characteristics of substances that regulate light attenuation in glacially-fed lakes will help elucidate the signals that these systems provide of broader environmental changes and forecast the effects of climate change on these aquatic ecosystems.

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.

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.

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.

Influence of the sediment on lead speciation in the Tagus estuary.

PubMed

Mota, A M; Cruz, P; Vilhena, C; Gonçalves, M L S

2005-04-01

The aim of this work is to study the influence of the Tagus estuarine sediment on lead speciation in the overlying natural water. The water sample in the presence of the sediment was contaminated three times with Pb(II) in a laboratory experiment. In different periods of time, at 1-7 days after each contamination, small volumes of water were titrated with lead. The titration was followed by anodic stripping voltammetry in differential pulse mode. Before and after contamination systematic analysis of the voltammetric parameters (peak current, peak potential and peak width) were carried out to get a clear picture of Pb(II) complexation in the soluble fraction in contact with the sediment. Two main types of organic ligands, macromolecular ligands and small compounds, were detected before contamination. Both of them form labile complexes (degree of lability within the timescale of some milliseconds). The small compounds, with a diffusion coefficient similar to that of the free metal ion, present a homogeneous behaviour in terms of Pb complexation. On the other hand macromolecular ligands, with a diffusion coefficient of 1.2 x 10(-6) cm2s(-1), can be described by two different binding groups, which might be of phenolic and carboxylic type as presented by humic matter. The sediment eliminated lead contamination (10(-6) moldm(-3) was the maximum concentration added) from 12 dm3 of water (surface of 8 dm2) within 2 days. It was also found that the sediment released organic ligands responsible for both labile and inert Pb complexes "seen" by voltammetry. The release of organic ligands that decreases the bioavailability of Pb(II) was clearly detected 1 week after contamination. Therefore, the sediment acts as a buffer for lead through two mechanisms against lead contamination: removing lead ions from the solution and releasing organic ligands to the water column. In a short period of time the sediment responds as a self-cleaning system for Pb(II) contamination in the estuarine water, which may have a very important influence in environmental pollution.

NMR investigation of the short-chain ionic surfactant-water systems.

PubMed

Popova, M V; Tchernyshev, Y S; Michel, D

2004-02-03

The structure and dynamics of surfactant molecules [CH3(CH2)7COOK] in heavy water solutions were investigated by 1H and 2H NMR. A double-exponential attenuation of the spin-echo amplitude in a Carr-Purcell-Meiboom-Gill experiment was found. We expect correspondence to both bounded and monomeric states. At high concentrations in the NMR self-diffusion measurements also a double-exponential decay of the spin-echo signal versus the square of the dc magnetic gradient was observed. The slow component of the diffusion process is caused by micellar aggregates, while the fast component is the result of the self-diffusion of the monomers through the micelles. The self-diffusion studies indicate that the form of micelles changes with increasing total surfactant concentration. The critical temperature range for self-association is reflected in the 1H transverse relaxation.

Single-File Escape of Colloidal Particles from Microfluidic Channels

NASA Astrophysics Data System (ADS)

Locatelli, Emanuele; Pierno, Matteo; Baldovin, Fulvio; Orlandini, Enzo; Tan, Yizhou; Pagliara, Stefano

2016-07-01

Single-file diffusion is a ubiquitous physical process exploited by living and synthetic systems to exchange molecules with their environment. It is paramount to quantify the escape time needed for single files of particles to exit from constraining synthetic channels and biological pores. This quantity depends on complex cooperative effects, whose predominance can only be established through a strict comparison between theory and experiments. By using colloidal particles, optical manipulation, microfluidics, digital microscopy, and theoretical analysis we uncover the self-similar character of the escape process and provide closed-formula evaluations of the escape time. We find that the escape time scales inversely with the diffusion coefficient of the last particle to leave the channel. Importantly, we find that at the investigated microscale, bias forces as tiny as 10-15 N determine the magnitude of the escape time by drastically reducing interparticle collisions. Our findings provide crucial guidelines to optimize the design of micro- and nanodevices for a variety of applications including drug delivery, particle filtering, and transport in geometrical constrictions.

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.

Insertion and self-diffusion of a monotopic protein, the Aquifex aeolicus sulfide quinone reductase, in supported lipid bilayers.

PubMed

Harb, Frédéric; Prunetti, Laurence; Giudici-Orticoni, Marie-Thérèse; Guiral, Marianne; Tinland, Bernard

2015-10-01

Monotopic proteins constitute a class of membrane proteins that bind tightly to cell membranes, but do not span them. We present a FRAPP (Fluorescence Recovery After Patterned Photobleaching) study of the dynamics of a bacterial monotopic protein, SQR (sulfide quinone oxidoreductase) from the thermophilic bacteria Aquifex aeolicus, inserted into two different types of lipid bilayers (EggPC: L-α-phosphatidylcholine (Egg, Chicken) and DMPC: 1,2-dimyristoyl-sn-glycero-3-phosphocholine) supported on two different types of support (mica or glass). It sheds light on the behavior of a monotopic protein inside the bilayer. The insertion of SQR is more efficient when the bilayer is in the fluid phase than in the gel phase. We observed diffusion of the protein, with no immobile fraction, and deduced from the diffusion coefficient measurements that the resulting inserted object is the same whatever the incubation conditions, i.e. homogeneous in terms of oligomerization state. As expected, the diffusion coefficient of the SQR is smaller in the gel phase than in the fluid phase. In the supported lipid bilayer, the diffusion coefficient of the SQR is smaller than the diffusion coefficient of phospholipids in both gel and fluid phase. SQR shows a diffusion behavior different from the transmembrane protein α-hemolysin, and consistent with its monotopic character. Preliminary experiments in the presence of the substrate of SQR, DecylUbiquinone, an analogue of quinone, component of transmembrane electrons transport systems of eukaryotic and prokaryotic organisms, have been carried out. Finally, we studied the behavior of SQR, in terms of insertion and diffusion, in bilayers formed with lipids from Aquifex aeolicus. All the conclusions that we have found in the biomimetic systems applied to the biological system.

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.

Self-consistent approach to the solution of the light transfer problem for irradiances in marine waters with arbitrary turbidity, depth, and surface illumination. I. Case of absorption and elastic scattering.

PubMed

Haltrin, V I

1998-06-20

A self-consistent variant of the two-flow approximation that takes into account strong anisotropy of light scattering in seawater of finite depth and arbitrary turbidity is presented. To achieve an appropriate accuracy, this approach uses experimental dependencies between downward and total mean cosines. It calculates irradiances, diffuse attenuation coefficients, and diffuse reflectances in waters with arbitrary values of scattering, backscattering, and attenuation coefficients. It also takes into account arbitrary conditions of illumination and reflection from the bottom with the Lambertian albedo. This theory can be used for the calculation of apparent optical properties in both open and coastal oceanic waters, lakes, and rivers. It can also be applied to other types of absorbing and scattering medium such as paints, photographic emulsions, and biological tissues.

Oxygen diffusion in alpha-Al2O3. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Cawley, J. D.; Halloran, J. W.; Cooper, A. R.

1984-01-01

Oxygen self diffusion coefficients were determined in single crystal alpha-Al2O3 using the gas exchange technique. The samples were semi-infinite slabs cut from five different boules with varying background impurities. The diffusion direction was parallel to the c-axis. The tracer profiles were determined by two techniques, single spectrum proton activation and secondary ion mass spectrometry. The SIMS proved to be a more useful tool. The determined diffusion coefficients, which were insensitive to impurity levels and oxygen partial pressure, could be described by D = .00151 exp (-572kJ/RT) sq m/s. The insensitivities are discussed in terms of point defect clustering. Two independent models are consistent with the findings, the first considers the clusters as immobile point defect traps which buffer changes in the defect chemistry. The second considers clusters to be mobile and oxygen diffusion to be intrinsic behavior, the mechanism for oxygen transport involving neutral clusters of Schottky quintuplets.

Impact of casein gel microstructure on self-diffusion coefficient of molecular probes measured by 1H PFG-NMR.

PubMed

Le Feunteun, Steven; Mariette, François

2007-12-26

The translational dynamics of poly(ethylene glycol) (PEG) polymers with molecular weights (Mw) varying from 6x10(2) to 5x10(5) were investigated by pulsed field gradient NMR in casein suspensions and in gels induced by acidification, enzyme action, and a combination of both. For molecules with Mwor=8000, there was strong dependence of diffusion on PEG size and on the casein network structure as revealed by scanning electron microscopy images. The diffusion coefficients of the two largest PEGs were increased after coagulation by amounts that depended on the internal structure of the gel. In addition, the 527,000 g/mol PEG was found to deviate from Gaussian diffusion behavior to greater or lesser extents according to the casein concentration and the sample microstructure. The results are discussed in terms of network rearrangements.

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.

Calibration schemes of a field-compatible optical spectroscopic system to quantify neovascular changes in the dysplastic cervix

NASA Astrophysics Data System (ADS)

Chang, Vivide Tuan-Chyan; Merisier, Delson; Yu, Bing; Walmer, David K.; Ramanujam, Nirmala

2011-03-01

A significant challenge in detecting cervical pre-cancer in low-resource settings is the lack of effective screening facilities and trained personnel to detect the disease before it is advanced. Light based technologies, particularly quantitative optical spectroscopy, have the potential to provide an effective, low cost, and portable solution for cervical pre-cancer screening in these communities. We have developed and characterized a portable USB-powered optical spectroscopic system to quantify total hemoglobin content, hemoglobin saturation, and reduced scattering coefficient of cervical tissue in vivo. The system consists of a high-power LED as light source, a bifurcated fiber optic assembly, and two USB spectrometers for sample and calibration spectra acquisitions. The system was subsequently tested in Leogane, Haiti, where diffuse reflectance spectra from 33 colposcopically normal sites in 21 patients were acquired. Two different calibration methods, i.e., a post-study diffuse reflectance standard measurement and a real time self-calibration channel were studied. Our results suggest that a self-calibration channel enabled more accurate extraction of scattering contrast through simultaneous real-time correction of intensity drifts in the system. A self-calibration system also minimizes operator bias and required training. Hence, future contact spectroscopy or imaging systems should incorporate a selfcalibration channel to reliably extract scattering contrast.

Liquid- and Gas-Phase Diffusion of Ferrocene in Thin Films of Metal-Organic Frameworks

PubMed Central

Zhou, Wencai; Wöll, Christof; Heinke, Lars

2015-01-01

The mass transfer of the guest molecules in nanoporous host materials, in particular in metal-organic frameworks (MOFs), is among the crucial features of their applications. By using thin surface-mounted MOF films in combination with a quartz crystal microbalance (QCM), the diffusion of ferrocene vapor and of ethanolic and hexanic ferrocene solution in HKUST-1 was investigated. For the first time, liquid- and gas-phase diffusion in MOFs was compared directly in the identical sample. The diffusion coefficients are in the same order of magnitude (~10−16 m2·s−1), whereas the diffusion coefficient of ferrocene in the empty framework is roughly 3-times smaller than in the MOF which is filled with ethanol or n-hexane.

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.

Resonant thickening of self-gravitating discs: imposed or self-induced orbital diffusion in the tightly wound limit

NASA Astrophysics Data System (ADS)

Fouvry, Jean-Baptiste; Pichon, Christophe; Chavanis, Pierre-Henri; Monk, Laura

2017-11-01

The secular thickening of a self-gravitating stellar galactic disc is investigated using the dressed collisionless Fokker-Planck equation and the inhomogeneous multicomponent Balescu-Lenard equation. The thick WKB limits for the diffusion fluxes are found using the epicyclic approximation, while assuming that only radially tightly wound transient spirals are sustained by the disc. This yields simple quadratures for the drift and diffusion coefficients, providing a clear understanding of the positions of maximum vertical orbital diffusion within the disc, induced by fluctuations either external or due to the finite number of particles. These thick limits also offer a consistent derivation of a thick disc Toomre parameter, which is shown to be exponentially boosted by the ratio of the vertical to radial scaleheights. Dressed potential fluctuations within the disc statistically induce a vertical bending of a subset of resonant orbits, triggering the corresponding increase in vertical velocity dispersion. When applied to a tepid stable tapered disc perturbed by shot noise, these two frameworks reproduce qualitatively the formation of ridges of resonant orbits towards larger vertical actions, as found in direct numerical simulations, but overestimates the time-scale involved in their appearance. Swing amplification is likely needed to resolve this discrepancy, as demonstrated in the case of razor-thin discs. Other sources of thickening are also investigated, such as fading sequences of slowing bars, or the joint evolution of a population of giant molecular clouds within the disc.

Diffusion in confinement: kinetic simulations of self- and collective diffusion behavior of adsorbed gases

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

Abouelnasr, MKF; Smit, B

2012-01-01

The self- and collective-diffusion behaviors of adsorbed methane, helium, and isobutane in zeolite frameworks LTA, MFI, AFI, and SAS were examined at various concentrations using a range of molecular simulation techniques including Molecular Dynamics (MD), Monte Carlo (MC), Bennett-Chandler (BC), and kinetic Monte Carlo (kMC). This paper has three main results. (1) A novel model for the process of adsorbate movement between two large cages was created, allowing the formulation of a mixing rule for the re-crossing coefficient between two cages of unequal loading. The predictions from this mixing rule were found to agree quantitatively with explicit simulations. (2) Amore » new approach to the dynamically corrected Transition State Theory method to analytically calculate self-diffusion properties was developed, explicitly accounting for nanoscale fluctuations in concentration. This approach was demonstrated to quantitatively agree with previous methods, but is uniquely suited to be adapted to a kMC simulation that can simulate the collective-diffusion behavior. (3) While at low and moderate loadings the self- and collective-diffusion behaviors in LTA are observed to coincide, at higher concentrations they diverge. A change in the adsorbate packing scheme was shown to cause this divergence, a trait which is replicated in a kMC simulation that explicitly models this behavior. These phenomena were further investigated for isobutane in zeolite MFI, where MD results showed a separation in self- and collective-diffusion behavior that was reproduced with kMC simulations.« less

Diffusion in confinement: kinetic simulations of self- and collective diffusion behavior of adsorbed gases.

PubMed

Abouelnasr, Mahmoud K F; Smit, Berend

2012-09-07

The self- and collective-diffusion behaviors of adsorbed methane, helium, and isobutane in zeolite frameworks LTA, MFI, AFI, and SAS were examined at various concentrations using a range of molecular simulation techniques including Molecular Dynamics (MD), Monte Carlo (MC), Bennett-Chandler (BC), and kinetic Monte Carlo (kMC). This paper has three main results. (1) A novel model for the process of adsorbate movement between two large cages was created, allowing the formulation of a mixing rule for the re-crossing coefficient between two cages of unequal loading. The predictions from this mixing rule were found to agree quantitatively with explicit simulations. (2) A new approach to the dynamically corrected Transition State Theory method to analytically calculate self-diffusion properties was developed, explicitly accounting for nanoscale fluctuations in concentration. This approach was demonstrated to quantitatively agree with previous methods, but is uniquely suited to be adapted to a kMC simulation that can simulate the collective-diffusion behavior. (3) While at low and moderate loadings the self- and collective-diffusion behaviors in LTA are observed to coincide, at higher concentrations they diverge. A change in the adsorbate packing scheme was shown to cause this divergence, a trait which is replicated in a kMC simulation that explicitly models this behavior. These phenomena were further investigated for isobutane in zeolite MFI, where MD results showed a separation in self- and collective- diffusion behavior that was reproduced with kMC simulations.

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.

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.

Electrotransfer in Liquid Binary Aluminum Alloys

NASA Astrophysics Data System (ADS)

Tekuchev, V. V.; Kalinkin, D. P.; Ivanova, I. V.

2018-07-01

The mobility of ions in a liquid binary metal system based on aluminum is calculated for the first time in a wide range of concentrations, based on studies of its resistivity and self-diffusion coefficient. It is established that in an Al-Cu system, the ions of aluminum move to the anode, while Al-Mg, Al-Sn, and Al-Sb move to the cathode; i.e., there is inversion of the electrotransfer of aluminum ions. When the concentration of a component is reduced, the mobility of its ions is increased by the module.

Self-Diffusion and Heteroassociation in an Acetone-Chloroform Mixture at 298 K

NASA Astrophysics Data System (ADS)

Golubev, V. A.; Gurina, D. L.; Kumeev, R. S.

2018-01-01

The self-diffusion coefficients of acetone and chloroform in a binary acetone-chloroform mixture at 298 K are determined via pulsed field gradient NMR spectroscopy. It is estimated that the hydrodynamic radii of the mixture's components, calculated using the Stokes-Einstein equation, grow as the concentrations of the components fall. It is shown that such behavior of hydrodynamic radii is due to acetone-chloroform heteroassociation. The hydrodynamic radii of monomers and heteroassociates in a 1: 1 ratio are determined along with the constant of heteroassociation, using the proposed model of an associated solution.

Bulk dynamics of Brownian hard disks: Dynamical density functional theory versus experiments on two-dimensional colloidal hard spheres

NASA Astrophysics Data System (ADS)

Stopper, Daniel; Thorneywork, Alice L.; Dullens, Roel P. A.; Roth, Roland

2018-03-01

Using dynamical density functional theory (DDFT), we theoretically study Brownian self-diffusion and structural relaxation of hard disks and compare to experimental results on quasi two-dimensional colloidal hard spheres. To this end, we calculate the self-van Hove correlation function and distinct van Hove correlation function by extending a recently proposed DDFT-approach for three-dimensional systems to two dimensions. We find that the theoretical results for both self-part and distinct part of the van Hove function are in very good quantitative agreement with the experiments up to relatively high fluid packing fractions of roughly 0.60. However, at even higher densities, deviations between the experiment and the theoretical approach become clearly visible. Upon increasing packing fraction, in experiments, the short-time self-diffusive behavior is strongly affected by hydrodynamic effects and leads to a significant decrease in the respective mean-squared displacement. By contrast, and in accordance with previous simulation studies, the present DDFT, which neglects hydrodynamic effects, shows no dependence on the particle density for this quantity.

Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient

PubMed Central

Sigaut, Lorena; Pearson, John E.; Colman-Lerner, Alejandro; Ponce Dawson, Silvina

2014-01-01

The gradient of Bicoid (Bcd) is key for the establishment of the anterior-posterior axis in Drosophila embryos. The gradient properties are compatible with the SDD model in which Bcd is synthesized at the anterior pole and then diffuses into the embryo and is degraded with a characteristic time. Within this model, the Bcd diffusion coefficient is critical to set the timescale of gradient formation. This coefficient has been measured using two optical techniques, Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS), obtaining estimates in which the FCS value is an order of magnitude larger than the FRAP one. This discrepancy raises the following questions: which estimate is "correct''; what is the reason for the disparity; and can the SDD model explain Bcd gradient formation within the experimentally observed times? In this paper, we use a simple biophysical model in which Bcd diffuses and interacts with binding sites to show that both the FRAP and the FCS estimates may be correct and compatible with the observed timescale of gradient formation. The discrepancy arises from the fact that FCS and FRAP report on different effective (concentration dependent) diffusion coefficients, one of which describes the spreading rate of the individual Bcd molecules (the messengers) and the other one that of their concentration (the message). The latter is the one that is more relevant for the gradient establishment and is compatible with its formation within the experimentally observed times. PMID:24901638

Messages do diffuse faster than messengers: reconciling disparate estimates of the morphogen bicoid diffusion coefficient.

PubMed

Sigaut, Lorena; Pearson, John E; Colman-Lerner, Alejandro; Ponce Dawson, Silvina

2014-06-01

The gradient of Bicoid (Bcd) is key for the establishment of the anterior-posterior axis in Drosophila embryos. The gradient properties are compatible with the SDD model in which Bcd is synthesized at the anterior pole and then diffuses into the embryo and is degraded with a characteristic time. Within this model, the Bcd diffusion coefficient is critical to set the timescale of gradient formation. This coefficient has been measured using two optical techniques, Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS), obtaining estimates in which the FCS value is an order of magnitude larger than the FRAP one. This discrepancy raises the following questions: which estimate is "correct''; what is the reason for the disparity; and can the SDD model explain Bcd gradient formation within the experimentally observed times? In this paper, we use a simple biophysical model in which Bcd diffuses and interacts with binding sites to show that both the FRAP and the FCS estimates may be correct and compatible with the observed timescale of gradient formation. The discrepancy arises from the fact that FCS and FRAP report on different effective (concentration dependent) diffusion coefficients, one of which describes the spreading rate of the individual Bcd molecules (the messengers) and the other one that of their concentration (the message). The latter is the one that is more relevant for the gradient establishment and is compatible with its formation within the experimentally observed times.

Oxide ion diffusion mechanism related to Co and Fe ions in (Ba0.5Sr0.5)(Co0.8Fe0.2)O3-δ using in-situ X-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Itoh, Takanori; Imai, Hideto

2018-03-01

The time changes of the white line and pre-edge intensities of Co and Fe K-edge in (Ba0.5Sr0.5)(Co0.8Fe0.2)O3-δ (BSCF) were observed to estimate the oxide ion diffusion related to Co and Fe ions by using in - situ X-ray absorption spectroscopy (XAS) during oxidation. The 20 μm self-standing BSCF film was prepared for in - situ XAS measurements. The time changes of absorption were fitted to the exponential decay function with two terms. The longer relaxation time (τ), related to the oxide ion diffusion during the oxidation of BSCF, is dependent on temperature. The oxide ion diffusion coefficients (D) were calculated from the τ s estimated by in - situ XAS. The values of the activation energy (Ea) for D related to Co K-edge white line, Co pre-edge, and Fe pre-edge were 1.8-2.0 eV. The value of Ea for D related to Fe K-edge white line, however, was higher than other absorption values at approximately 2.3 eV. We discussed the oxide ion diffusion mechanism related to Co and Fe ions in BSCF using in - situ XAS.

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

Non-Markovian Effects in Turbulent Diffusion in Magnetized Plasmas

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

Zagorodny, Anatoly; Weiland, Jan

2009-10-08

The derivation of the kinetic equations for inhomogeneous plasma in an external magnetic field is presented. The Fokker-Planck-type equations with the non-Markovian kinetic coefficients are proposed. In the time-local limit (small correlation times with respect to the distribution function relaxation time) the relations obtained recover the results known from the appropriate quasilinear theory and the Dupree-Weinstock theory of plasma turbulence. The equations proposed are used to describe zonal flow generation and to estimate the diffusion coefficient for saturated turbulence.

Mapping Diffusion in a Living Cell via the Phasor Approach

PubMed Central

Ranjit, Suman; Lanzano, Luca; Gratton, Enrico

2014-01-01

Diffusion of a fluorescent protein within a cell has been measured using either fluctuation-based techniques (fluorescence correlation spectroscopy (FCS) or raster-scan image correlation spectroscopy) or particle tracking. However, none of these methods enables us to measure the diffusion of the fluorescent particle at each pixel of the image. Measurement using conventional single-point FCS at every individual pixel results in continuous long exposure of the cell to the laser and eventual bleaching of the sample. To overcome this limitation, we have developed what we believe to be a new method of scanning with simultaneous construction of a fluorescent image of the cell. In this believed new method of modified raster scanning, as it acquires the image, the laser scans each individual line multiple times before moving to the next line. This continues until the entire area is scanned. This is different from the original raster-scan image correlation spectroscopy approach, where data are acquired by scanning each frame once and then scanning the image multiple times. The total time of data acquisition needed for this method is much shorter than the time required for traditional FCS analysis at each pixel. However, at a single pixel, the acquired intensity time sequence is short; requiring nonconventional analysis of the correlation function to extract information about the diffusion. These correlation data have been analyzed using the phasor approach, a fit-free method that was originally developed for analysis of FLIM images. Analysis using this method results in an estimation of the average diffusion coefficient of the fluorescent species at each pixel of an image, and thus, a detailed diffusion map of the cell can be created. PMID:25517145

A model for shrinkage strain in photo polymerization of dental composites.

PubMed

Petrovic, Ljubomir M; Atanackovic, Teodor M

2008-04-01

We formulate a new model for the shrinkage strain developed during photo polymerization in dental composites. The model is based on the diffusion type fractional order equation, since it has been proved that polymerization reaction is diffusion controlled (Atai M, Watts DC. A new kinetic model for the photo polymerization shrinkage-strain of dental composites and resin-monomers. Dent Mater 2006;22:785-91). Our model strongly confirms the observation by Atai and Watts (see reference details above) and their experimental results. The shrinkage strain is modeled by a nonlinear differential equation in (see reference details above) and that equation must be solved numerically. In our approach, we use the linear fractional order differential equation to describe the strain rate due to photo polymerization. This equation is solved exactly. As shrinkage is a consequence of the polymerization reaction and polymerization reaction is diffusion controlled, we postulate that shrinkage strain rate is described by a diffusion type equation. We find explicit form of solution to this equation and determine the strain in the resin monomers. Also by using equations of linear viscoelasticity, we determine stresses in the polymer due to the shrinkage. The time evolution of stresses implies that the maximal stresses are developed at the very beginning of the polymerization process. The stress in a dental composite that is light treated has the largest value short time after the treatment starts. The strain settles at the constant value in the time of about 100s (for the cases treated in Atai and Watts). From the model developed here, the shrinkage strain of dental composites and resin monomers is analytically determined. The maximal value of stresses is important, since this value must be smaller than the adhesive bond strength at cavo-restoration interface. The maximum stress determined here depends on the diffusivity coefficient. Since diffusivity coefficient increases as polymerization proceeds, it follows that the periods of light treatments should be shorter at the beginning of the treatment and longer at the end of the treatment, with dark interval between the initial low intensity and following high intensity curing. This is because at the end of polymerization the stress relaxation cannot take place.

Variations in Static Force Control and Motor Unit Behavior with Error Amplification Feedback in the Elderly.

PubMed

Chen, Yi-Ching; Lin, Linda L; Lin, Yen-Ting; Hu, Chia-Ling; Hwang, Ing-Shiou

2017-01-01

Error amplification (EA) feedback is a promising approach to advance visuomotor skill. As error detection and visuomotor processing at short time scales decline with age, this study examined whether older adults could benefit from EA feedback that included higher-frequency information to guide a force-tracking task. Fourteen young and 14 older adults performed low-level static isometric force-tracking with visual guidance of typical visual feedback and EA feedback containing augmented high-frequency errors. Stabilogram diffusion analysis was used to characterize force fluctuation dynamics. Also, the discharge behaviors of motor units and pooled motor unit coherence were assessed following the decomposition of multi-channel surface electromyography (EMG). EA produced different behavioral and neurophysiological impacts on young and older adults. Older adults exhibited inferior task accuracy with EA feedback than with typical visual feedback, but not young adults. Although stabilogram diffusion analysis revealed that EA led to a significant decrease in critical time points for both groups, EA potentiated the critical point of force fluctuations [Formula: see text], short-term effective diffusion coefficients (Ds), and short-term exponent scaling only for the older adults. Moreover, in older adults, EA added to the size of discharge variability of motor units and discharge regularity of cumulative discharge rate, but suppressed the pooled motor unit coherence in the 13-35 Hz band. Virtual EA alters the strategic balance between open-loop and closed-loop controls for force-tracking. Contrary to expectations, the prevailing use of closed-loop control with EA that contained high-frequency error information enhanced the motor unit discharge variability and undermined the force steadiness in the older group, concerning declines in physiological complexity in the neurobehavioral system and the common drive to the motoneuronal pool against force destabilization.

Variations in Static Force Control and Motor Unit Behavior with Error Amplification Feedback in the Elderly

PubMed Central

Chen, Yi-Ching; Lin, Linda L.; Lin, Yen-Ting; Hu, Chia-Ling; Hwang, Ing-Shiou

2017-01-01

Error amplification (EA) feedback is a promising approach to advance visuomotor skill. As error detection and visuomotor processing at short time scales decline with age, this study examined whether older adults could benefit from EA feedback that included higher-frequency information to guide a force-tracking task. Fourteen young and 14 older adults performed low-level static isometric force-tracking with visual guidance of typical visual feedback and EA feedback containing augmented high-frequency errors. Stabilogram diffusion analysis was used to characterize force fluctuation dynamics. Also, the discharge behaviors of motor units and pooled motor unit coherence were assessed following the decomposition of multi-channel surface electromyography (EMG). EA produced different behavioral and neurophysiological impacts on young and older adults. Older adults exhibited inferior task accuracy with EA feedback than with typical visual feedback, but not young adults. Although stabilogram diffusion analysis revealed that EA led to a significant decrease in critical time points for both groups, EA potentiated the critical point of force fluctuations <ΔFc2>, short-term effective diffusion coefficients (Ds), and short-term exponent scaling only for the older adults. Moreover, in older adults, EA added to the size of discharge variability of motor units and discharge regularity of cumulative discharge rate, but suppressed the pooled motor unit coherence in the 13–35 Hz band. Virtual EA alters the strategic balance between open-loop and closed-loop controls for force-tracking. Contrary to expectations, the prevailing use of closed-loop control with EA that contained high-frequency error information enhanced the motor unit discharge variability and undermined the force steadiness in the older group, concerning declines in physiological complexity in the neurobehavioral system and the common drive to the motoneuronal pool against force destabilization. PMID:29167637

Measurement and modeling of diffusion time dependence of apparent diffusion coefficient and fractional anisotropy in prostate tissue ex vivo.

PubMed

Bourne, Roger; Liang, Sisi; Panagiotaki, Eleftheria; Bongers, Andre; Sved, Paul; Watson, Geoffrey

2017-10-01

The purpose of this study was to measure and model the diffusion time dependence of apparent diffusion coefficient (ADC) and fractional anisotropy (FA) derived from conventional prostate diffusion-weighted imaging methods as used in recommended multiparametric MRI protocols. Diffusion tensor imaging (DTI) was performed at 9.4 T with three radical prostatectomy specimens, with diffusion times in the range 10-120 ms and b-values 0-3000 s/mm 2 . ADC and FA were calculated from DTI measurements at b-values of 800 and 1600 s/mm 2 . Independently, a two-component model (restricted isotropic plus Gaussian anisotropic) was used to synthesize DTI data, from which ADC and FA were predicted and compared with the measured values. Measured ADC and FA exhibited a diffusion time dependence, which was closely predicted by the two-component model. ADC decreased by about 0.10-0.15 μm 2 /ms as diffusion time increased from 10 to 120 ms. FA increased with diffusion time at b-values of 800 and 1600 s/mm 2 but was predicted to be independent of diffusion time at b = 3000 s/mm 2 . Both ADC and FA exhibited diffusion time dependence that could be modeled as two unmixed water pools - one having isotropic restricted dynamics, and the other unrestricted anisotropic dynamics. These results highlight the importance of considering and reporting diffusion times in conventional ADC and FA calculations and protocol recommendations, and inform the development of improved diffusion methods for prostate cancer imaging. Copyright © 2017 John Wiley & Sons, Ltd.

Evolution of Edge Pedestal Profiles Over the L-H Transition

NASA Astrophysics Data System (ADS)

Sayer, M. S.; Stacey, W. M.; Floyd, J. P.; Groebner, R. J.

2012-10-01

The detailed time evolution of thermal diffusivities, electromagnetic forces, pressure gradients, particle pinch and momentum transport frequencies (which determine the diffusion coefficient) have been analyzed during the L-H transition in a DIII-D discharge. Density, temperature, rotation velocity and electric field profiles at times just before and after the L-H transition are analyzed in terms of these quantities. The analysis is based on the fluid particle balance, energy balance, force balance and heat conduction equations, as in Ref. [1], but with much greater time resolution and with account for thermal ion orbit loss. The variation of diffusive and non-diffusive transport over the L-H transition is determined from the variation in the radial force balance (radial electric field, VxB force, and pressure gradient) and the variation in the interpreted diffusive transport coefficients. 6pt [1] W.M. Stacey and R.J. Groebner, Phys. Plasmas 17, 112512 (2010).

Superionic Phases of the 1:1 Water–Ammonia Mixture

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

Bethkenhagen, Mandy; Cebulla, Daniel; Redmer, Ronald

We report four structures for the 1:1 water–ammonia mixture showing superionic behavior at high temperature with the space groups P4/ nmm, Ima2, Pma2, and Pm, which have been identified from evolutionary random structure search calculations at 0 K. Analyzing the respective pair distribution functions and diffusive properties the superionic phase is found to be stable in a temperature range between 1000 and 6000 K for pressures up to 800 GPa. We propose a high-pressure phase diagram of the water–ammonia mixture for the first time and compare the self-diffusion coefficients in the mixture to the ones found in water and ammonia.more » Lastly, possible implications on the interior structure of the giant planets Uranus and Neptune are discussed.« less

Superionic Phases of the 1:1 Water–Ammonia Mixture

DOE PAGES

Bethkenhagen, Mandy; Cebulla, Daniel; Redmer, Ronald; ...

2015-09-21

We report four structures for the 1:1 water–ammonia mixture showing superionic behavior at high temperature with the space groups P4/ nmm, Ima2, Pma2, and Pm, which have been identified from evolutionary random structure search calculations at 0 K. Analyzing the respective pair distribution functions and diffusive properties the superionic phase is found to be stable in a temperature range between 1000 and 6000 K for pressures up to 800 GPa. We propose a high-pressure phase diagram of the water–ammonia mixture for the first time and compare the self-diffusion coefficients in the mixture to the ones found in water and ammonia.more » Lastly, possible implications on the interior structure of the giant planets Uranus and Neptune are discussed.« less

Spatially dependent diffusion coefficient as a model for pH sensitive microgel particles in microchannels

PubMed Central

Pieprzyk, S.; Heyes, D. M.; Brańka, A. C.

2016-01-01

Solute transport and intermixing in microfluidic devices is strongly dependent on diffusional processes. Brownian Dynamics simulations of pressure-driven flow of model microgel particles in microchannels have been carried out to explore these processes and the factors that influence them. The effects of a pH-field that induces a spatial dependence of particle size and consequently the self-diffusion coefficient and system thermodynamic state were focused on. Simulations were carried out in 1D to represent some of the cross flow dependencies, and in 2D and 3D to include the effects of flow and particle concentration, with typical stripe-like diffusion coefficient spatial variations. In 1D, the mean square displacement and particle displacement probability distribution function agreed well with an analytically solvable model consisting of infinitely repulsive walls and a discontinuous pH-profile in the middle of the channel. Skew category Brownian motion and non-Gaussian dynamics were observed, which follows from correlations of step lengths in the system, and can be considered to be an example of so-called “diffusing diffusivity.” In Poiseuille flow simulations, the particles accumulated in regions of larger diffusivity and the largest particle concentration throughput was found when this region was in the middle of the channel. The trends in the calculated cross-channel diffusional behavior were found to be very similar in 2D and 3D. PMID:27795750

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

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.

Enhanced Diffusion of Chlorinated Organic Compounds into Aquitards due to Cracking

NASA Astrophysics Data System (ADS)

Ayral, D.; Otero, M.; Chung, S.; Goltz, M. N.; Huang, J.; Demond, A. H.

2012-12-01

Despite great efforts, remediation of sites contaminated with dense non-aqueous phase liquids (DNAPLs) is very challenging because, even at residual saturations, DNAPLs can act as a long-term source for a dissolved phase contaminant plume. Current models consider the possibility of diffusion and storage of these compounds in unfractured low permeability layers. However, there is a need to consider the impact of cracks, whether naturally occurring or induced by the interaction between low permeable layers and DNAPLs. To evaluate the impact on diffusive fluxes, diffusion coefficients were measured in low permeability materials representative of aquitards at steady-state using the time-lag method. The experimental setup comprised silty soil, packed into a retaining ring, sandwiched in between two reservoirs. The analytical solution for the time-lag method requires constant conditions in the upper and lower reservoirs. The lower reservoir contained pure trichloroethylene (TCE), while the upper reservoir was maintained at a concentration of zero by bubbling air through it, sweeping TCE into toluene trap. In order to predict the flux, the experimental effective diffusion coefficients were used to calculate the flux through uncracked matrix whereas bulk diffusion coefficient was used to calculate flux through the cracks. By using the experimentally-obtained diffusion coefficients and experimentally-measured crack intensity factors (the ratio of the area of cracks to the uncracked area), the total flux was estimated over extended time periods. These calculations, based on experimental data, were used to evaluate if diffusive-based fluxes in the presence of cracks were significantly greater than in the case of diffusion into an uncracked matrix. The enhanced diffusive fluxes were evaluated to determine whether there is the potential for significantly greater storage in the low permeable layers in the case of cracks, or whether the possibility of advective fluxes into the cracks needs to be considered as well.

Noise and diffusion of a vibrated self-propelled granular particle

NASA Astrophysics Data System (ADS)

Walsh, Lee; Wagner, Caleb G.; Schlossberg, Sarah; Olson, Christopher; Baskaran, Aparna; Menon, Narayanan

Granular materials are an important physical realization of active matter. In vibration-fluidized granular matter, both diffusion and self-propulsion derive from the same collisional forcing, unlike many other active systems where there is a clean separation between the origin of single-particle mobility and the coupling to noise. Here we present experimental studies of single-particle motion in a vibrated granular monolayer, along with theoretical analysis that compares grain motion at short and long time scales to the assumptions and predictions, respectively, of the active Brownian particle (ABP) model. The results demonstrate that despite the unique relation between noise and propulsion, granular media do show the generic features predicted by the ABP model and indicate that this is a valid framework to predict collective phenomena. Additionally, our scheme of analysis for validating the inputs and outputs of the model can be applied to other granular and non-granular systems.

Collision statistics, thermodynamics, and transport coefficients of hard hyperspheres in three, four, and five dimensions

NASA Astrophysics Data System (ADS)

Lue, L.

2005-01-01

The collision statistics of hard hyperspheres are investigated. An exact, analytical formula is developed for the distribution of speeds of a sphere on collision, which is shown to be related to the average time between collisions for a sphere with a particular velocity. In addition, the relationship between the collision rate and the compressibility factor is generalized to arbitrary dimensions. Molecular dynamics simulations are performed for d=3, 4, and 5 dimensional hard-hypersphere fluids. From these simulations, the equation of state of these systems, the self-diffusion coefficient, the shear viscosity, and the thermal conductivity are determined as a function of density. Various aspects of the collision statistics and their dependence on the density and dimensionality of the system are also studied.

Small effect of water on upper-mantle rheology based on silicon self-diffusion coefficients.

PubMed

Fei, Hongzhan; Wiedenbeck, Michael; Yamazaki, Daisuke; Katsura, Tomoo

2013-06-13

Water has been thought to affect the dynamical processes in the Earth's interior to a great extent. In particular, experimental deformation results suggest that even only a few tens of parts per million of water by weight enhances the creep rates in olivine by orders of magnitude. However, those deformation studies have limitations, such as considering only a limited range of water concentrations and very high stresses, which might affect the results. Rock deformation can also be understood as an effect of silicon self-diffusion, because the creep rates of minerals at temperatures as high as those in the Earth's interior are limited by self-diffusion of the slowest species. Here we experimentally determine the silicon self-diffusion coefficient DSi in forsterite at 8 GPa and 1,600 K to 1,800 K as a function of water content CH2O from less than 1 to about 800 parts per million of water by weight, yielding the relationship, DSi ≈ (CH2O)(1/3). This exponent is strikingly lower than that obtained by deformation experiments (1.2; ref. 7). The high nominal creep rates in the deformation studies under wet conditions may be caused by excess grain boundary water. We conclude that the effect of water on upper-mantle rheology is very small. Hence, the smooth motion of the Earth's tectonic plates cannot be caused by mineral hydration in the asthenosphere. Also, water cannot cause the viscosity minimum zone in the upper mantle. And finally, the dominant mechanism responsible for hotspot immobility cannot be water content differences between their source and surrounding regions.

Permeability of Concrete with Recycled Concrete Aggregate and Pozzolanic Materials under Stress

PubMed Central

Wang, Hailong; Sun, Xiaoyan; Wang, Junjie; Monteiro, Paulo J.M.

2016-01-01

The research reported herein studied the permeability of concrete containing recycled-concrete aggregate (RA), superfine phosphorous slag (PHS), and ground granulated blast-furnace slag (GGBS) with and without stress. Test results showed that the chloride diffusion coefficient of RA concrete (RAC) without external loads decreased with time, and the permeability of RAC is much lower than that of the reference concrete due to the on-going hydration and the pozzolanic reaction provided by the PHS and GGBS additives in the RAC mixture. The permeability of chloride under flexural load is much more sensitive than that under compressive load due to the differences in porosity and cracking pattern. At low compressive stress levels, the permeability of chloride decreased by the closing of pores and microcracks within RAC specimens. However, in a relatively short time the chloride diffusion coefficient and the chloride content increased rapidly with the increase of compressive stress when it exceeded a threshold stress level of approximate 35% of the ultimate compressive strength. Under flexural stress, the chloride transport capability increased with the increase of stress level and time. At high compressive and flexural stress levels, creep had a significant effect on the permeability of chloride in the RAC specimens due to the damage from the nucleation and propagation of microcracks over time. It is apparent that mortar cracking has more of a significant effect on the chloride transport in concrete than cracking in the interfacial transition zone (ITZ). PMID:28773376

Permeability of Concrete with Recycled Concrete Aggregate and Pozzolanic Materials under Stress.

PubMed

Wang, Hailong; Sun, Xiaoyan; Wang, Junjie; Monteiro, Paulo J M

2016-03-30

The research reported herein studied the permeability of concrete containing recycled-concrete aggregate (RA), superfine phosphorous slag (PHS), and ground granulated blast-furnace slag (GGBS) with and without stress. Test results showed that the chloride diffusion coefficient of RA concrete (RAC) without external loads decreased with time, and the permeability of RAC is much lower than that of the reference concrete due to the on-going hydration and the pozzolanic reaction provided by the PHS and GGBS additives in the RAC mixture. The permeability of chloride under flexural load is much more sensitive than that under compressive load due to the differences in porosity and cracking pattern. At low compressive stress levels, the permeability of chloride decreased by the closing of pores and microcracks within RAC specimens. However, in a relatively short time the chloride diffusion coefficient and the chloride content increased rapidly with the increase of compressive stress when it exceeded a threshold stress level of approximate 35% of the ultimate compressive strength. Under flexural stress, the chloride transport capability increased with the increase of stress level and time. At high compressive and flexural stress levels, creep had a significant effect on the permeability of chloride in the RAC specimens due to the damage from the nucleation and propagation of microcracks over time. It is apparent that mortar cracking has more of a significant effect on the chloride transport in concrete than cracking in the interfacial transition zone (ITZ).

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.

Molecular dynamic simulations of selective self-diffusion of CH4/CO2/H2O/N2 in coal

NASA Astrophysics Data System (ADS)

Song, Y.; Jiang, B.; Li, F. L.

2017-06-01

The self-diffusion coefficients (D) of CH4/CO2/H2O/N2 at a relatively broad range of temperatures(298.15∼ 458.15K)and pressures (1∼6MPa) under the NPT, NPH, NVE, and NVT ensembles were obtained after the calculations of molecular mechanics(MM), annealing kinetics(AK), giant canonical Monte Carlo(GCMC), and molecular dynamics (MD) based on Wiser bituminous coal model (WM). The Ds of the adsorbates at the saturated adsorption configurations are D CH4418K. The average swelling ratios manifest as H2O (14.7∼35.18%)>CO2 (13.38∼32.25%)>CH4 (15.35∼23.71%)> N2 (11.47∼22.14%) (NPH, 1∼6MPa). There exits differences in D, swelling ratios and E among various ensembles, indicating that the selection of ensembles has an important influence on the MD calculations for self-diffusion coefficients.

Electrostatic Interactions Influence Protein Adsorption (but Not Desorption) at the Silica-Aqueous Interface.

PubMed

McUmber, Aaron C; Randolph, Theodore W; Schwartz, Daniel K

2015-07-02

High-throughput single-molecule total internal reflection fluorescence microscopy was used to investigate the effects of pH and ionic strength on bovine serum albumin (BSA) adsorption, desorption, and interfacial diffusion at the aqueous-fused silica interface. At high pH and low ionic strength, negatively charged BSA adsorbed slowly to the negatively charged fused silica surface. At low pH and low ionic strength, where BSA was positively charged, or in solutions at higher ionic strength, adsorption was approximately 1000 times faster. Interestingly, neither surface residence times nor the interfacial diffusion coefficients of BSA were influenced by pH or ionic strength. These findings suggested that adsorption kinetics were dominated by energy barriers associated with electrostatic interactions, but once adsorbed, protein-surface interactions were dominated by short-range nonelectrostatic interactions. These results highlight the ability of single-molecule techniques to isolate elementary processes (e.g., adsorption and desorption) under steady-state conditions, which would be impossible to measure using ensemble-averaging methods.

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Interdiffusion in the Ni/TD-NiCr and Cr/TD-NiCr systems

NASA Technical Reports Server (NTRS)

Pawar, A. V.; Tenney, D. R.

1974-01-01

The diffusion of Ni and Cr into TD-NiCr has been studied over the 900 to 1100 C temperature range. The diffusion couples were prepared by electroplating Cr and Ni on polished TD-NiCr wafers. Concentration profiles produced as a result of isothermal diffusion at 905, 1000, and 1100 C were determined by electron microprobe analysis. The Boltzmann-Matano analysis was used to determine concentration-dependent diffusion coefficients which were found to compare favorably with previously reported values. These data suggest that 2 vol % ThO2 distribution has no appreciable effect on the rates of diffusion in TD-NiCr with a large grain size. This supports the view that an inert dispersoid in an alloy matrix will not in itself lead to enhanced diffusion unless a short-circuit diffusion structure is stabilized.

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.

Equilibrium sorption and diffusion rate studies with halogenated organic chemical and sandy aquifer material

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

Ball, W.P.

1990-01-01

Concepts for rate limitation of sorptive uptake of hydrophobic organic solutes by aquifer solids are reviewed, emphasizing physical diffusion models and in the context of effects on contaminant transport. Data for the sorption of tetrachloroethene (PCE) and 1,2,4,5-tetrachlorobenzene (TeCB) on Borden sand are presented, showing that equilibrium is attained very slowly, requiring equilibration times on the order of tens of days for PCE and hundreds of days for TeCB. The rate of approach to equilibrium decreased with increasing particle size and sorption distribution coefficient, in accordance with retarded intragranular diffusion models. Pulverization of the samples significantly decreased the required timemore » to equilibrium without changing the sorption capacity of the solids. Batch sorption methodology was refined to allow accurate measurement of long-term distribution coefficients, using purified {sup 14}C-labelled solute spikes and sealed glass ampules. Sorption isotherms for PCE and TeCB were conducted with size fractions of Borden sand over four to five orders of magnitude in aqueous concentration, and were found to be slightly nonlinear (Freundlich exponent = 0.8). A concentrated set of data in the low concentration range (<50 ug/L) revealed that sorption in this range could be equally well described by a linear isotherm. Distribution coefficients of the two solutes with seven size fractions of Borden sand, measured at low concentration and at full equilibrium, were between seven and sixty times the value predicted on the basis of recent correlations with organic carbon content. Rate results for coarse size fractions support a simple pore diffusion model, with pore diffusion coefficients estimated to be approximately 3 {times} 10{sup {minus}8} cm{sup 2}/sec, more than 200{times} lower than the aqueous diffusivities.« less

Simulation of stochastic diffusion via first exit times

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

Lötstedt, Per, E-mail: perl@it.uu.se; Meinecke, Lina, E-mail: lina.meinecke@it.uu.se

2015-11-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a methodmore » based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions.« less

Simulation of stochastic diffusion via first exit times

PubMed Central

Lötstedt, Per; Meinecke, Lina

2015-01-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a method based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions. PMID:26600600

Effect of the scattering delay on time-dependent photon migration in turbid media.

PubMed

Yaroslavsky, I V; Yaroslavsky, A N; Tuchin, V V; Schwarzmaier, H J

1997-09-01

We modified the diffusion approximation of the time-dependent radiative transfer equation to account for a finite scattering delay time. Under the usual assumptions of the diffusion approximation, the effect of the scattering delay leads to a simple renormalization of the light velocity that appears in the diffusion equation. Accuracy of the model was evaluated by comparison with Monte Carlo simulations in the frequency domain for a semi-infinite geometry. A good agreement is demonstrated for both matched and mismatched boundary conditions when the distance from the source is sufficiently large. The modified diffusion model predicts that the neglect of the scattering delay when the optical properties of the turbid material are derived from normalized frequency- or time-domain measurements should result in an underestimation of the absorption coefficient and an overestimation of the transport coefficient. These observations are consistent with the published experimental data.

Photon migration through a turbid slab described by a model based on diffusion approximation. I. Theory.

PubMed

Contini, D; Martelli, F; Zaccanti, G

1997-07-01

The diffusion approximation of the radiative transfer equation is a model used widely to describe photon migration in highly diffusing media and is an important matter in biological tissue optics. An analysis of the time-dependent diffusion equation together with its solutions for the slab geometry and for a semi-infinite diffusing medium are reported. These solutions, presented for both the time-dependent and the continuous wave source, account for the refractive index mismatch between the turbid medium and the surrounding medium. The results have been compared with those obtained when different boundary conditions were assumed. The comparison has shown that the effect of the refractive index mismatch cannot be disregarded. This effect is particularly important for the transmittance. The discussion of results also provides an analysis of the role of the absorption coefficient in the expression of the diffusion coefficient.

Dynamics of a magnetic active Brownian particle under a uniform magnetic field.

PubMed

Vidal-Urquiza, Glenn C; Córdova-Figueroa, Ubaldo M

2017-11-01

The dynamics of a magnetic active Brownian particle undergoing three-dimensional Brownian motion, both translation and rotation, under the influence of a uniform magnetic field is investigated. The particle self-propels at a constant speed along its magnetic dipole moment, which reorients due to the interplay between Brownian and magnetic torques, quantified by the Langevin parameter α. In this work, the time-dependent active diffusivity and the crossover time (τ^{cross})-from ballistic to diffusive regimes-are calculated through the time-dependent correlation function of the fluctuations of the propulsion direction. The results reveal that, for any value of α, the particle undergoes a directional (or ballistic) propulsive motion at very short times (t≪τ^{cross}). In this regime, the correlation function decreases linearly with time, and the active diffusivity increases with it. It the opposite time limit (t≫τ^{cross}), the particle moves in a purely diffusive regime with a correlation function that decays asymptotically to zero and an active diffusivity that reaches a constant value equal to the long-time active diffusivity of the particle. As expected in the absence of a magnetic field (α=0), the crossover time is equal to the characteristic time scale for rotational diffusion, τ_{rot}. In the presence of a magnetic field (α>0), the correlation function, the active diffusivity, and the crossover time decrease with increasing α. The magnetic field regulates the regimes of propulsion of the particle. Here, the field reduces the period of time at which the active particle undergoes a directional motion. Consequently, the active particle rapidly reaches a diffusive regime at τ^{cross}≪τ_{rot}. In the limit of weak fields (α≪1), the crossover time decreases quadratically with α, while in the limit of strong fields (α≫1) it decays asymptotically as α^{-1}. The results are in excellent agreement with those obtained by Brownian dynamics simulations.

Dynamics of a magnetic active Brownian particle under a uniform magnetic field

NASA Astrophysics Data System (ADS)

Vidal-Urquiza, Glenn C.; Córdova-Figueroa, Ubaldo M.

2017-11-01

The dynamics of a magnetic active Brownian particle undergoing three-dimensional Brownian motion, both translation and rotation, under the influence of a uniform magnetic field is investigated. The particle self-propels at a constant speed along its magnetic dipole moment, which reorients due to the interplay between Brownian and magnetic torques, quantified by the Langevin parameter α . In this work, the time-dependent active diffusivity and the crossover time (τcross)—from ballistic to diffusive regimes—are calculated through the time-dependent correlation function of the fluctuations of the propulsion direction. The results reveal that, for any value of α , the particle undergoes a directional (or ballistic) propulsive motion at very short times (t ≪τcross ). In this regime, the correlation function decreases linearly with time, and the active diffusivity increases with it. It the opposite time limit (t ≫τcross ), the particle moves in a purely diffusive regime with a correlation function that decays asymptotically to zero and an active diffusivity that reaches a constant value equal to the long-time active diffusivity of the particle. As expected in the absence of a magnetic field (α =0 ), the crossover time is equal to the characteristic time scale for rotational diffusion, τrot. In the presence of a magnetic field (α >0 ), the correlation function, the active diffusivity, and the crossover time decrease with increasing α . The magnetic field regulates the regimes of propulsion of the particle. Here, the field reduces the period of time at which the active particle undergoes a directional motion. Consequently, the active particle rapidly reaches a diffusive regime at τcross≪τrot . In the limit of weak fields (α ≪1 ), the crossover time decreases quadratically with α , while in the limit of strong fields (α ≫1 ) it decays asymptotically as α-1. The results are in excellent agreement with those obtained by Brownian dynamics simulations.

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

Lung Morphometry with Hyperpolarized 129Xe: Theoretical Background

PubMed Central

Sukstanskii, A.L.; Yablonskiy, D.A.

2011-01-01

The 3He lung morphometry technique, based on MRI measurements of hyperpolarized 3He gas diffusion in lung airspaces, provides unique information on the lung microstructure at the alveolar level. In vivo 3D tomographic images of standard morphological parameters (airspace chord length, lung parenchyma surface-to-volume ratio, number of alveoli per unit volume) can be generated from a rather short (several seconds) MRI scan. The technique is based on a theory of gas diffusion in lung acinar airways and experimental measurements of diffusion attenuated MRI signal. The present work aims at developing the theoretical background of a similar technique based on hyperpolarized 129Xe gas. As the diffusion coefficient and gyromagnetic ratio of 129Xe gas are substantially different from those of 3He gas, the specific details of the theory and experimental measurements with 129Xe should be amended. We establish phenomenological relationships between acinar airway geometrical parameters and the diffusion attenuated MR signal for human and small animal lungs, both normal lungs and lungs with mild emphysema. Optimal diffusion times are shown to be about 5 ms for human and 1.3 ms for small animals. The expected uncertainties in measuring main morphometrical parameters of the lungs are estimated in the framework of Bayesian probability theory. PMID:21713985

Diffusion across the modified polyethylene separator GX in the heat-sterilizable AgO-Zn battery

NASA Technical Reports Server (NTRS)

Lutwack, R.

1973-01-01

Models of diffusion across an inert membrane have been studied using the computer program CINDA. The models were constructed to simulate various conditions obtained in the consideration of the diffusion of Ag (OH)2 ions in the AgO-Zn battery. The effects on concentrations across the membrane at the steady state and on the fluxout as a function of time were used to examine the consequences of stepwise reducing the number of sources of ions, of stepwise blocking the source and sink surfaces, of varying the magnitude of the diffusion coefficient for a uniform membrane, of varying the diffusion coefficient across the membrane, and of excluding volumes to diffusion.

Determination of carrier lifetime and diffusion length in Al-doped 4H-SiC epilayers by time-resolved optical techniques

NASA Astrophysics Data System (ADS)

Liaugaudas, Gediminas; Dargis, Donatas; Kwasnicki, Pawel; Arvinte, Roxana; Zielinski, Marcin; Jarašiūnas, Kęstutis

2015-01-01

A series of p-type 4H-SiC epilayers with aluminium concentration ranging from 2  ×  1016 to 8  ×  1019 cm-3 were investigated by time-resolved optical techniques in order to determine the effect of aluminium doping on high-injection carrier lifetime at room temperature and the diffusion coefficient at different injections (from ≈3  ×  1018 to ≈5  ×  1019 cm-3) and temperatures (from 78 to 730 K). We find that the defect limited carrier lifetime τSRH decreases from 20 ns in the low-doped samples down to ≈0.6 ns in the heavily doped epilayers. Accordingly, the ambipolar diffusion coefficient decreases from Da = 3.5 cm2 s-1 down to ≈0.6 cm2 s-1, corresponding to the hole mobility of µh = 70 cm2 Vs-1 and 12 cm2 Vs-1, respectively. In the highly doped epilayers, the injection-induced decrease of the diffusion coefficient, due to the transition from the minority carrier diffusion to the ambipolar diffusion, provided the electron diffusion coefficient of De ≈ 3 cm2 s-1. The Al-doping resulted in the gradual decrease of the ambipolar diffusion length, from LD = 2.7 µm down to LD = 0.25 µm in the epilayers with the lowest and highest aluminium concentrations.

Nondestructive quantification of analyte diffusion in cornea and sclera using optical coherence tomography.

PubMed

Ghosn, Mohamad G; Tuchin, Valery V; Larin, Kirill V

2007-06-01

Noninvasive functional imaging, monitoring, and quantification of analytes transport in epithelial ocular tissues are extremely important for therapy and diagnostics of many eye diseases. In this study the authors investigated the capability of optical coherence tomography (OCT) for noninvasive monitoring and quantification of diffusion of different analytes in sclera and cornea of rabbit eyes. A portable time-domain OCT system with wavelength of 1310 +/- 15 nm, output power of 3.5 mW, and resolution of 25 mum was used in this study. Diffusion of different analytes was monitored and quantified in rabbit cornea and sclera of whole eyeballs. Diffusion of water, metronidazole (0.5%), dexamethasone (0.2%), ciprofloxacin (0.3%), mannitol (20%), and glucose solution (20%) were examined, and their permeability coefficients were calculated by using OCT signal slope and depth-resolved amplitude methods. Permeability coefficients were calculated as a function of time and tissue depth. For instance, mannitol was found to have a permeability coefficient of (8.99 +/- 1.43) x 10(-6) cm/s in cornea and (6.18 +/- 1.08) x 10(-6) cm/s in sclera. The permeability coefficient of drugs with small concentrations (where water was the major solvent) was found to be in the range of that of water in the same tissue type, whereas permeability coefficients of higher concentrated solutions varied significantly. Results suggest that the OCT technique might be a powerful tool for noninvasive diffusion studies of different analytes in ocular tissues. However, additional methods of OCT signal acquisition and processing are required to study the diffusion of agents of small concentrations.

Measuring restriction sizes using diffusion weighted magnetic resonance imaging: a review.

PubMed

Martin, Melanie

2013-01-01

This article reviews a new concept in magnetic resonance as applied to cellular and biological systems. Diffusion weighted magnetic resonance imaging can be used to infer information about restriction sizes of samples being measured. The measurements rely on the apparent diffusion coefficient changing with diffusion times as measurements move from restricted to free diffusion regimes. Pulsed gradient spin echo (PGSE) measurements are limited in the ability to shorten diffusion times and thus are limited in restriction sizes which can be probed. Oscillating gradient spin echo (OGSE) measurements could provide shorter diffusion times so smaller restriction sizes could be probed.

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

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.

Diffusion anisotropy of poor metal solute atoms in hcp-Ti

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

Scotti, Lucia, E-mail: lxs234@bham.ac.uk; Mottura, Alessandro, E-mail: a.mottura@bham.ac.uk

2015-05-28

Atom migration mechanisms influence a wide range of phenomena: solidification kinetics, phase equilibria, oxidation kinetics, precipitation of phases, and high-temperature deformation. In particular, solute diffusion mechanisms in α-Ti alloys can help explain their excellent high-temperature behaviour. The purpose of this work is to study self- and solute diffusion in hexagonal close-packed (hcp)-Ti, and its anisotropy, from first-principles using the 8-frequency model. The calculated diffusion coefficients show that diffusion energy barriers depend more on bonding characteristics of the solute rather than the size misfit with the host, while the extreme diffusion anisotropy of some solute elements in hcp-Ti is a resultmore » of the bond angle distortion.« less

Influence of compositional complexity on interdiffusion in Ni-containing concentrated solid-solution alloys

DOE PAGES

Jin, Ke; Zhang, Chuan; Zhang, Fan; ...

2018-03-07

To investigate the compositional effects on thermal-diffusion kinetics in concentrated solid-solution alloys, interdiffusion in seven diffusion couples with alloys from binary to quinary is systematically studied. The alloys with higher compositional complexity exhibit in general lower diffusion coefficients against homologous temperature, however, an exception is found that diffusion in NiCoFeCrPd is faster than in NiCoFeCr and NiCoCr. While the derived diffusion parameters suggest that diffusion in medium and high entropy alloys is overall more retarded than in pure metals and binary alloys, they strongly depend on specific constituents. The comparative features are captured by computational thermodynamics approaches using a self-consistentmore » database.« less

Quasielastic neutron scattering measurements and ab initio MD-simulations on single ion motions in molten NaF

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

Demmel, F.; Mukhopadhyay, S.; Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ

2016-01-07

The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusionmore » coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.« less

Flat-plate solar array project process development area: Process research of non-CZ silicon material

NASA Technical Reports Server (NTRS)

Campbell, R. B.

1986-01-01

Several different techniques to simultaneously diffuse the front and back junctions in dendritic web silicon were investigated. A successful simultaneous diffusion reduces the cost of the solar cell by reducing the number of processing steps, the amount of capital equipment, and the labor cost. The three techniques studied were: (1) simultaneous diffusion at standard temperatures and times using a tube type diffusion furnace or a belt furnace; (2) diffusion using excimer laser drive-in; and (3) simultaneous diffusion at high temperature and short times using a pulse of high intensity light as the heat source. The use of an excimer laser and high temperature short time diffusion experiment were both more successful than the diffusion at standard temperature and times. The three techniques are described in detail and a cost analysis of the more successful techniques is provided.

Entropy as a measure of diffusion

NASA Astrophysics Data System (ADS)

Aghamohammadi, Amir; Fatollahi, Amir H.; Khorrami, Mohammad; Shariati, Ahmad

2013-10-01

The time variation of entropy, as an alternative to the variance, is proposed as a measure of the diffusion rate. It is shown that for linear and time-translationally invariant systems having a large-time limit for the density, at large times the entropy tends exponentially to a constant. For systems with no stationary density, at large times the entropy is logarithmic with a coefficient specifying the speed of the diffusion. As an example, the large-time behaviors of the entropy and the variance are compared for various types of fractional-derivative diffusions.

Transport properties of carbon dioxide and methane from molecular dynamics simulations.

PubMed

Aimoli, C G; Maginn, E J; Abreu, C R A

2014-10-07

Transport properties of carbon dioxide and methane are predicted for temperatures between (273.15 and 573.15) K and pressures up to 800 MPa by molecular dynamics simulations. Viscosities and thermal conductivities were obtained through the Green-Kubo formalism, whereas the Einstein relation was used to provide self-diffusion coefficient estimates. The differences in property predictions due to the force field nature and parametrization were investigated by the comparison of seven different CO2 models (two single-site models, three rigid three-site models, and two fully flexible three-site models) and three different CH4 models (two single-site models and one fully flexible five-site model). The simulation results show good agreement with experimental data, except for thermal conductivities at low densities. The molecular structure and force field parameters play an important role in the accuracy of the simulations, which is within the experimental deviations reported for viscosities and self-diffusion coefficients considering the most accurate CO2 and CH4 models studied. On the other hand, the molecular flexibility does not seem to improve accuracy, since the explicit account of vibrational and bending degrees of freedom in the CO2 flexible models leads to slightly less accurate results. Nonetheless, the use of a correctional term to account for vibrational modes in rigid models generally improves estimations of thermal conductivity values. At extreme densities, the caging effect observed with single-site representations of the molecules restrains mobility and leads to an unphysical overestimation of viscosities and, conversely, to the underestimation of self-diffusion coefficients. This result may help to better understand the limits of applicability of such force fields concerning structural and transport properties of dense systems.

On the factors affecting porosity dissolution in selective laser sintering process

NASA Astrophysics Data System (ADS)

Ly, H.-B.; Monteiro, E.; Dal, M.; Regnier, G.

2018-05-01

Selective Laser Sintering process is one of the additive manufacturing techniques in which parts are manufactured layer by layer. During such process, gas bubbles are formed in the melted polymer due to faster polymer grains coalescence at surface than deeper in the powder bed. Although gas diffusion is possible through the polymer melt, it's usual that some porosities remain in the final part if their initial sizes are too big and solidification time too short. In this contribution, a bubble dissolution model involving fluid dynamics and mass transport has been developed to study factors affecting porosity resorption kinetic. In this model, gas diffusion follows Fick's laws and the melted polymer is supposed Newtonian. At the polymer/gas interface, surface tension is considered and Henry's law is used to relate the partial pressure of gas with its concentration in the fluid. This problem is solved numerically by means of the finite element method in 1D. After validation of the numerical tool, the influence on dissolution time of several parameters (e.g. the initial size and form of gas porosities, the viscosity, the diffusion coefficient, the surface tension constant or the ambient pressure) has been examined.

Revealing mesoscopic structural universality with diffusion.

PubMed

Novikov, Dmitry S; Jensen, Jens H; Helpern, Joseph A; Fieremans, Els

2014-04-08

Measuring molecular diffusion is widely used for characterizing materials and living organisms noninvasively. This characterization relies on relations between macroscopic diffusion metrics and structure at the mesoscopic scale commensurate with the diffusion length. Establishing such relations remains a fundamental challenge, hindering progress in materials science, porous media, and biomedical imaging. Here we show that the dynamical exponent in the time dependence of the diffusion coefficient distinguishes between the universality classes of the mesoscopic structural complexity. Our approach enables the interpretation of diffusion measurements by objectively selecting and modeling the most relevant structural features. As an example, the specific values of the dynamical exponent allow us to identify the relevant mesoscopic structure affecting MRI-measured water diffusion in muscles and in brain, and to elucidate the structural changes behind the decrease of diffusion coefficient in ischemic stroke.

Ion transport with charge-protected and non-charge-protected cations using the compensated Arrhenius formalism. Part 2. Relationship between ionic conductivity and diffusion.

PubMed

Petrowsky, Matt; Fleshman, Allison; Bopege, Dharshani N; Frech, Roger

2012-08-09

Temperature-dependent ionic conductivities and cation/anion self-diffusion coefficients are measured for four electrolyte families: TbaTf-linear primary alcohols, LiTf-linear primary alcohols, TbaTf-n-alkyl acetates, and LiTf-n-alkyl acetates. The Nernst-Einstein equation does not adequately describe the data. Instead, the compensated Arrhenius formalism is applied to both conductivity and diffusion data. General trends based on temperature and alkyl chain length are observed when conductivity is plotted against cation or anion diffusion coefficient, but there is no clear pattern to the data. However, plotting conductivity exponential prefactors against those for diffusion results in four distinct curves, one each for the alcohol and acetate families described above. Furthermore, the TbaTf-alcohol and TbaTf-acetate data are "in line" with each other. The conductivity prefactors for the LiTf-alcohol data are smaller than those for the TbaTf data. The LiTf-acetate data have the lowest conductivity prefactors. This trend in prefactors mirrors the observed trend in degree of ionic association for these electrolytes.

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

NASA Astrophysics Data System (ADS)

Arendt, V.; Shalchi, A.

2018-06-01

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

Diffusion-weighted imaging of breast lesions: Region-of-interest placement and different ADC parameters influence apparent diffusion coefficient values.

PubMed

Bickel, Hubert; Pinker, Katja; Polanec, Stephan; Magometschnigg, Heinrich; Wengert, Georg; Spick, Claudio; Bogner, Wolfgang; Bago-Horvath, Zsuzsanna; Helbich, Thomas H; Baltzer, Pascal

2017-05-01

To investigate the influence of region-of-interest (ROI) placement and different apparent diffusion coefficient (ADC) parameters on ADC values, diagnostic performance, reproducibility and measurement time in breast tumours. In this IRB-approved, retrospective study, 149 histopathologically proven breast tumours (109 malignant, 40 benign) in 147 women (mean age 53.2) were investigated. Three radiologists independently measured minimum, mean and maximum ADC, each using three ROI placement approaches:1 - small 2D-ROI, 2 - large 2D-ROI and 3 - 3D-ROI covering the whole lesion. One reader performed all measurements twice. Median ADC values, diagnostic performance, reproducibility, and measurement time were calculated and compared between all combinations of ROI placement approaches and ADC parameters. Median ADC values differed significantly between the ROI placement approaches (p < .001). Minimum ADC showed the best diagnostic performance (AUC .928-.956), followed by mean ADC obtained from 2D ROIs (.926-.94). Minimum and mean ADC showed high intra- (ICC .85-.94) and inter-reader reproducibility (ICC .74-.94). Median measurement time was significantly shorter for the 2D ROIs (p < .001). ROI placement significantly influences ADC values measured in breast tumours. Minimum and mean ADC acquired from 2D-ROIs are useful for the differentiation of benign and malignant breast lesions, and are highly reproducible, with rapid measurement. • Region of interest placement significantly influences apparent diffusion coefficient of breast tumours. • Minimum and mean apparent diffusion coefficient perform best and are reproducible. • 2D regions of interest perform best and provide rapid measurement times.

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.

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.

Do TFSA anions slither? Pressure exposes the role of TFSA conformational exchange in self-diffusion

DOE PAGES

Suarez, Sophia N.; Wishart, James F.; Rua, Armando; ...

2015-10-28

Multi-nuclear ( 1H, 2H, and 19F) magnetic resonance spectroscopy techniques as functions of temperature and pressure were applied to the study of selectively deuterated 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (EMIM TFSA) ionic liquid isotopologues and related ionic liquids. For EMIM TFSA, temperature-dependent 2H T 1 data indicate stronger electric field gradients in the alkyl chain region compared to the imidazolium ring. Most significantly, the pressure dependences of the EMIM and TFSA self-diffusion coefficients revealed that the displacements of the cations and anions are independent, with diffusion of the TFSA anions being slowed much more by increasing pressure than for the EMIM cations, asmore » shown by their respective activation volumes (28.8 ± 2.5 cm³/mol for TFSA vs. 14.6 ± 1.3 cm³/mol for EMIM). Increasing pressure may lower the mobility of the TFSA anion by hindering its interconversion between trans and cis conformers, a process that is coupled to diffusion according to published molecular dynamics simulations. Measured activation volumes (ΔV ‡) for ion self-diffusion in EMIM bis(fluoromethylsulfonyl)amide and EMIM tetrafluoroborate support this hypothesis.« less

Do TFSA anions slither? Pressure exposes the role of TFSA conformational exchange in self-diffusion

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

Suarez, Sophia N.; Wishart, James F.; Rua, Armando

Multi-nuclear ( 1H, 2H, and 19F) magnetic resonance spectroscopy techniques as functions of temperature and pressure were applied to the study of selectively deuterated 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (EMIM TFSA) ionic liquid isotopologues and related ionic liquids. For EMIM TFSA, temperature-dependent 2H T 1 data indicate stronger electric field gradients in the alkyl chain region compared to the imidazolium ring. Most significantly, the pressure dependences of the EMIM and TFSA self-diffusion coefficients revealed that the displacements of the cations and anions are independent, with diffusion of the TFSA anions being slowed much more by increasing pressure than for the EMIM cations, asmore » shown by their respective activation volumes (28.8 ± 2.5 cm³/mol for TFSA vs. 14.6 ± 1.3 cm³/mol for EMIM). Increasing pressure may lower the mobility of the TFSA anion by hindering its interconversion between trans and cis conformers, a process that is coupled to diffusion according to published molecular dynamics simulations. Measured activation volumes (ΔV ‡) for ion self-diffusion in EMIM bis(fluoromethylsulfonyl)amide and EMIM tetrafluoroborate support this hypothesis.« less

Short-Path Statistics and the Diffusion Approximation

NASA Astrophysics Data System (ADS)

Blanco, Stéphane; Fournier, Richard

2006-12-01

In the field of first return time statistics in bounded domains, short paths may be defined as those paths for which the diffusion approximation is inappropriate. This is at the origin of numerous open questions concerning the characterization of residence time distributions. We show here how general integral constraints can be derived that make it possible to address short-path statistics indirectly by application of the diffusion approximation to long paths. Application to the moments of the distribution at the low-Knudsen limit leads to simple practical results and novel physical pictures.

Classical transport in disordered systems

NASA Astrophysics Data System (ADS)

Papaioannou, Antonios

This thesis reports on the manifestation of structural disorder on molecular transport and it consists of two parts. Part I discusses the relations between classical transport and the underlying structural complexity of the system. Both types of molecular diffusion, namely Gaussian and non- Gaussian are presented and the relevant time regimes are discussed. In addition the concept of structural universality is introduced and connected with the diffusion metrics. One of the most robust techniques for measuring molecular mean square displacements is magnetic resonance. This method requires encoding and subsequently reading out after an experimentally controlled time, a phase φ to the spins using magnetic field gradients. The main limitation for probing short diffusion lengths L(t) ˜ 1micro m with magnetic resonance is the requirement to encode and decode the phase φ in very short time intervals. Therefore, to probe such displacements a special probe was developed equipped with a gradient coil capable of delivering magnetic field gradients of approximately 90 G/cmA . The design of the probe is reported. Part I also includes a discussion of experiments of transport in two qualitatively different disordered phantoms and reports on a direct observation of universality in one-dimension. The results reveal the universal power law scaling of the diffusion coefficient at the long-time regime and illustrate the essence of structural universality by experimentally determining the structure correlation function of the phantoms. In addition, the scaling of the diffusive permeability of the phantoms with respect to the pore size is investigated. Additional work presented includes a detailed study of adsorption of methane gas in Vycor disordered glass. The techniques described in Part I of this thesis are widely used for measuring structural parameters of porous media, such as the surface-to-volume ratio or diffusive permeability. Part II of this thesis discusses the biophysical application of diffusion in disordered systems in the field of bioengineering. Elastin-based bioengineered scaffolds, which are mainly used for tissue and bone regeneration, must be able to deliver nutrients to the native tissue. It is therefore essential to quantitatively assess their structural parameters such as their surface-to-volume ratio and diffusive permeability. Part II focuses on a detailed study of structure and dynamics of elastin, the principle protein component found in tissues and one of the main components for scaffold engineering, using NMR 13C-MAS techniques. Lastly, the second half of Part II, discusses preliminary experiments of diffusion in elastin-based films.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Motoneuron membrane potentials follow a time inhomogeneous jump diffusion process.

PubMed

Jahn, Patrick; Berg, Rune W; Hounsgaard, Jørn; Ditlevsen, Susanne

2011-11-01

Stochastic leaky integrate-and-fire models are popular due to their simplicity and statistical tractability. They have been widely applied to gain understanding of the underlying mechanisms for spike timing in neurons, and have served as building blocks for more elaborate models. Especially the Ornstein-Uhlenbeck process is popular to describe the stochastic fluctuations in the membrane potential of a neuron, but also other models like the square-root model or models with a non-linear drift are sometimes applied. Data that can be described by such models have to be stationary and thus, the simple models can only be applied over short time windows. However, experimental data show varying time constants, state dependent noise, a graded firing threshold and time-inhomogeneous input. In the present study we build a jump diffusion model that incorporates these features, and introduce a firing mechanism with a state dependent intensity. In addition, we suggest statistical methods to estimate all unknown quantities and apply these to analyze turtle motoneuron membrane potentials. Finally, simulated and real data are compared and discussed. We find that a square-root diffusion describes the data much better than an Ornstein-Uhlenbeck process with constant diffusion coefficient. Further, the membrane time constant decreases with increasing depolarization, as expected from the increase in synaptic conductance. The network activity, which the neuron is exposed to, can be reasonably estimated to be a threshold version of the nerve output from the network. Moreover, the spiking characteristics are well described by a Poisson spike train with an intensity depending exponentially on the membrane potential.

Diffusion of GPI-anchored proteins is influenced by the activity of dynamic cortical actin

PubMed Central

Saha, Suvrajit; Lee, Il-Hyung; Polley, Anirban; Groves, Jay T.; Rao, Madan; Mayor, Satyajit

2015-01-01

Molecular diffusion at the surface of living cells is believed to be predominantly driven by thermal kicks. However, there is growing evidence that certain cell surface molecules are driven by the fluctuating dynamics of cortical cytoskeleton. Using fluorescence correlation spectroscopy, we measure the diffusion coefficient of a variety of cell surface molecules over a temperature range of 24–37°C. Exogenously incorporated fluorescent lipids with short acyl chains exhibit the expected increase of diffusion coefficient over this temperature range. In contrast, we find that GPI-anchored proteins exhibit temperature-independent diffusion over this range and revert to temperature-dependent diffusion on cell membrane blebs, in cells depleted of cholesterol, and upon acute perturbation of actin dynamics and myosin activity. A model transmembrane protein with a cytosolic actin-binding domain also exhibits the temperature-independent behavior, directly implicating the role of cortical actin. We show that diffusion of GPI-anchored proteins also becomes temperature dependent when the filamentous dynamic actin nucleator formin is inhibited. However, changes in cortical actin mesh size or perturbation of branched actin nucleator Arp2/3 do not affect this behavior. Thus cell surface diffusion of GPI-anchored proteins and transmembrane proteins that associate with actin is driven by active fluctuations of dynamic cortical actin filaments in addition to thermal fluctuations, consistent with expectations from an “active actin-membrane composite” cell surface. PMID:26378258

Psychometric properties of the Chinese version of the pediatric quality of life inventory 4.0 Generic core scales among children with short stature.

PubMed

Wu, Hua-hong; Li, Hui; Gao, Qian

2013-05-30

The quality of life in children with short stature was rarely studied in China, so we explore these children's quality of life and psychometric properties of the Chinese version of the Pediatric Quality of Life Inventory 4.0(PedsQL4.0) Generic Core Scales among children with short stature. A total of 201 children aged 8 ~ 18 years from the short stature clinic and other clinics of capital institute of pediatrics attended this study. The questionnaires include demographic information and PedsQL4.0 generic core scales. According to children's height, we divided them into three groups: short stature, normal short and normal group, then compared the score of scales by the height category. Moreover, we analyzed the reliability and validity of PedsQL4.0 generic core scales in these 201 children. The child self-report total PedsQL mean score, for the short stature, normal short and normal groups were 77.77 ± 9.69, 83.50 ± 8.56 and 87.36 ± 7.23; the parent-proxy total PedsQL mean score were 77.62 ± 10.50, 82.69 ± 8.35 and 84.91 ± 9.96 respectively. Both for children self- and parent proxy-reports, the Cronbach's α coefficients of total scale, psychosocial health and social functioning ranged between 0.74 and 0.80, it ranged between 0.51 and 0.66 in other dimensions. For child self-reports, the correlation coefficients of 17 items' scores (total 23 items) with the scores of dimensions they belong to were above 0.5, with the highest 0.759; the other 6 items' correlation coefficients were below 0.5, with the lowest 0.280. For parent proxy-reports, the correlation coefficients of 19 items' scores with the scores of dimension they belong to were above 0.5, with the highest 0.793, the other 4 items' below 0.5 with the lowest 0.243. The quality of life in children with short stature is worse than their normal peers by Peds QL4.0 generic core scales, the statues of their quality of life was positively related to their stature.

Response of radiation belt simulations to different radial diffusion coefficients for relativistic and ultra-relativistic electrons

NASA Astrophysics Data System (ADS)

Drozdov, Alexander; Mann, Ian; Baker, Daniel N.; Subbotin, Dmitriy; Ozeke, Louis; Shprits, Yuri; Kellerman, Adam

Two parameterizations of the resonant wave-particle interactions of electrons with ULF waves in the magnetosphere by Brautigam and Albert [2000] and Ozeke et al. [2012] are evaluated using the Versatile Electron Radiation Belt (VERB) diffusion code to estimate the effect of changing a diffusion coefficient on the radiation belt simulation. The period of investigation includes geomagnetically quiet and active time. The simulations take into account wave-particle interactions represented by radial diffusion transport, local acceleration, losses due to pitch-angle diffusion, and mixed diffusion. 1. Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999JA900344 2. Ozeke, L. G., I. R. Mann, K. R. Murphy, I. J. Rae, D. K. Milling, S. R. Elkington, A. A. Chan, and H. J. Singer (2012), ULF wave derived radiation belt radial diffusion coefficients, J. Geophys. Res., 117, A04222, doi:10.1029/2011JA017463.