The continued value of disk diffusion for assessing antimicrobial susceptibility in clinical laboratories: report from the Clinical and Laboratory Standards Institute Methods Development and Standardization Working Group.

PubMed

Humphries, Romney M; Kircher, Susan; Ferrell, Andrea; Krause, Kevin M; Malherbe, Rianna; Hsiung, Andre; Burnham, C A

2018-05-09

Expedited pathways to antimicrobial agent approval by the United States Food and Drug Administration (FDA) have led to increased delays between drug approval and the availability of FDA-cleared antimicrobial susceptibility testing (AST) devices. Antimicrobial disks for use with disk diffusion testing are among the first AST devices available to clinical laboratories. However, many laboratories are reluctant to implement a disk diffusion method for a variety of reasons, including dwindling proficiency with this method, interruptions to laboratory workflow, uncertainty surrounding the quality and reliability of a disk diffusion test, and perceived need to report an MIC to clinicians. This mini-review provides a report from the Clinical and Laboratory Standards Institute Working Group on Methods Development and Standardization on the current standards and clinical utility of disk diffusion testing. Copyright © 2018 American Society for Microbiology.

Diffusion Weighted Image Denoising Using Overcomplete Local PCA

PubMed Central

Manjón, José V.; Coupé, Pierrick; Concha, Luis; Buades, Antonio; Collins, D. Louis; Robles, Montserrat

2013-01-01

Diffusion Weighted Images (DWI) normally shows a low Signal to Noise Ratio (SNR) due to the presence of noise from the measurement process that complicates and biases the estimation of quantitative diffusion parameters. In this paper, a new denoising methodology is proposed that takes into consideration the multicomponent nature of multi-directional DWI datasets such as those employed in diffusion imaging. This new filter reduces random noise in multicomponent DWI by locally shrinking less significant Principal Components using an overcomplete approach. The proposed method is compared with state-of-the-art methods using synthetic and real clinical MR images, showing improved performance in terms of denoising quality and estimation of diffusion parameters. PMID:24019889

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.

First-Order Hyperbolic System Method for Time-Dependent Advection-Diffusion Problems

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Nishikawa, Hiroaki

2014-01-01

A time-dependent extension of the first-order hyperbolic system method for advection-diffusion problems is introduced. Diffusive/viscous terms are written and discretized as a hyperbolic system, which recovers the original equation in the steady state. The resulting scheme offers advantages over traditional schemes: a dramatic simplification in the discretization, high-order accuracy in the solution gradients, and orders-of-magnitude convergence acceleration. The hyperbolic advection-diffusion system is discretized by the second-order upwind residual-distribution scheme in a unified manner, and the system of implicit-residual-equations is solved by Newton's method over every physical time step. The numerical results are presented for linear and nonlinear advection-diffusion problems, demonstrating solutions and gradients produced to the same order of accuracy, with rapid convergence over each physical time step, typically less than five Newton iterations.

Divergent series and memory of the initial condition in the long-time solution of some anomalous diffusion problems.

PubMed

Yuste, S Bravo; Borrego, R; Abad, E

2010-02-01

We consider various anomalous d -dimensional diffusion problems in the presence of an absorbing boundary with radial symmetry. The motion of particles is described by a fractional diffusion equation. Their mean-square displacement is given by r(2) proportional, variant t(gamma)(00 , the emergence of such series in the long-time domain is a specific feature of subdiffusion problems. We present a method to regularize such series, and, in some cases, validate the procedure by using alternative techniques (Laplace transform method and numerical simulations). In the normal diffusion case, we find that the signature of the initial condition on the approach to the steady state rapidly fades away and the solution approaches a single (the main) decay mode in the long-time regime. In remarkable contrast, long-time memory of the initial condition is present in the subdiffusive case as the spatial part Psi1(r) describing the long-time decay of the solution to the steady state is determined by a weighted superposition of all spatial modes characteristic of the normal diffusion problem, the weight being dependent on the initial condition. Interestingly, Psi1(r) turns out to be independent of the anomalous diffusion exponent gamma .

Diffusion processes of fragmentary information on scale-free networks

NASA Astrophysics Data System (ADS)

Li, Xun; Cao, Lang

2016-05-01

Compartmental models of diffusion over contact networks have proven representative of real-life propagation phenomena among interacting individuals. However, there is a broad class of collective spreading mechanisms departing from compartmental representations, including those for diffusive objects capable of fragmentation and transmission unnecessarily as a whole. Here, we consider a continuous-state susceptible-infected-susceptible (SIS) model as an ideal limit-case of diffusion processes of fragmentary information on networks, where individuals possess fractions of the information content and update them by selectively exchanging messages with partners in the vicinity. Specifically, we incorporate local information, such as neighbors' node degrees and carried contents, into the individual partner choice, and examine the roles of a variety of such strategies in the information diffusion process, both qualitatively and quantitatively. Our method provides an effective and flexible route of modulating continuous-state diffusion dynamics on networks and has potential in a wide array of practical applications.

Study on monostable and bistable reaction-diffusion equations by iteration of travelling wave maps

NASA Astrophysics Data System (ADS)

Yi, Taishan; Chen, Yuming

2017-12-01

In this paper, based on the iterative properties of travelling wave maps, we develop a new method to obtain spreading speeds and asymptotic propagation for monostable and bistable reaction-diffusion equations. Precisely, for Dirichlet problems of monostable reaction-diffusion equations on the half line, by making links between travelling wave maps and integral operators associated with the Dirichlet diffusion kernel (the latter is NOT invariant under translation), we obtain some iteration properties of the Dirichlet diffusion and some a priori estimates on nontrivial solutions of Dirichlet problems under travelling wave transformation. We then provide the asymptotic behavior of nontrivial solutions in the space-time region for Dirichlet problems. These enable us to develop a unified method to obtain results on heterogeneous steady states, travelling waves, spreading speeds, and asymptotic spreading behavior for Dirichlet problem of monostable reaction-diffusion equations on R+ as well as of monostable/bistable reaction-diffusion equations on R.

Development of Methods for Low Temperature Diffusion Bonding.

DTIC Science & Technology

1987-09-01

Hazlett, T. H., " High Strength Low Temperature Bonding of Beryllium and Other Metals," Welding Journal, 60(11), pp. 301-s to 310-s, 1970. 12. 1986 Annual...34CIPLU’q *flBQ~ P 0.(4 ".Oq’J 4 Low Temperature , Methods for Diffusion Rl ,’..’S olid deveoped ~’~ ~ ’State Bonding, or Diffusion Welding An apparatus lor...low t’empeaur R~u on’ nding of dissimilar metals has been develped.Experiments varying the bonding temperature at constant pressure and time were

Aluminum base alloy powder metallurgy process and product

NASA Technical Reports Server (NTRS)

Paris, Henry G. (Inventor)

1986-01-01

A metallurgical method including cooling molten aluminum particles and consolidating resulting solidified particles into a multiparticle body, wherein the improvement comprises the provision of greater than 0.15% of a metal which diffuses in the aluminum solid state at a rate less than that of Mn. Aluminum containing greater than 0.15% of a metal which diffuses in the aluminum solid state at a rate less than that of Mn.

An enriched finite element method to fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Luan, Shengzhi; Lian, Yanping; Ying, Yuping; Tang, Shaoqiang; Wagner, Gregory J.; Liu, Wing Kam

2017-08-01

In this paper, an enriched finite element method with fractional basis [ 1,x^{α }] for spatial fractional partial differential equations is proposed to obtain more stable and accurate numerical solutions. For pure fractional diffusion equation without advection, the enriched Galerkin finite element method formulation is demonstrated to simulate the exact solution successfully without any numerical oscillation, which is advantageous compared to the traditional Galerkin finite element method with integer basis [ 1,x] . For fractional advection-diffusion equation, the oscillatory behavior becomes complex due to the introduction of the advection term which can be characterized by a fractional element Peclet number. For the purpose of addressing the more complex numerical oscillation, an enriched Petrov-Galerkin finite element method is developed by using a dimensionless fractional stabilization parameter, which is formulated through a minimization of the residual of the nodal solution. The effectiveness and accuracy of the enriched finite element method are demonstrated by a series of numerical examples of fractional diffusion equation and fractional advection-diffusion equation, including both one-dimensional and two-dimensional, steady-state and time-dependent cases.

Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin.

PubMed

Shadrina, Maria S; English, Ann M; Peslherbe, Gilles H

2012-07-11

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the parameters to greatly increase the simulation efficiency. The method is carefully validated against standard molecular dynamics (MD) simulations and available experimental structural and kinetic data on ligand diffusion in T-state deoxyHbA. The methodology provides a viable alternative approach to traditional MD simulations and/or potential of mean force calculations for: (i) characterizing kinetically accessible diffusion tunnels and escape routes for light ligands in porous proteins; (ii) very large systems when realistic simulations require the inclusion of multiple subunits of a protein; and (iii) proteins that access short-lived conformations relative to the simulation time. In the case of T-state deoxyHbA, we find distinct ligand diffusion tunnels consistent with the experimentally observed disparate Xe cavities in the α- and β-subunits. We identify two distal barriers including the distal histidine (E7) that control access to the heme. The multiple escape routes uncovered by our simulations call for a review of the current popular hypothesis on ligand escape from hemoglobin. Larger deviations from the crystal structure during simulated diffusion in isolated α- and β-subunits highlight the dampening effects of subunit interactions and the importance of including all subunits of multisubunit proteins to map realistic kinetically accessible diffusion tunnels and escape routes.

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

PubMed

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

2007-04-02

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

Quantifying Multistate Cytoplasmic Molecular Diffusion in Bacterial Cells via Inverse Transform of Confined Displacement Distribution.

PubMed

Chen, Tai-Yen; Jung, Won; Santiago, Ace George; Yang, Feng; Krzemiński, Łukasz; Chen, Peng

2015-11-12

Single-molecule tracking (SMT) of fluorescently tagged cytoplasmic proteins can provide valuable information on the underlying biological processes in living cells via subsequent analysis of the displacement distributions; however, the confinement effect originated from the small size of a bacterial cell skews the protein's displacement distribution and complicates the quantification of the intrinsic diffusive behaviors. Using the inverse transformation method, we convert the skewed displacement distribution (for both 2D and 3D imaging conditions) back to that in free space for systems containing one or multiple (non)interconverting Brownian diffusion states, from which we can reliably extract the number of diffusion states as well as their intrinsic diffusion coefficients and respective fractional populations. We further demonstrate a successful application to experimental SMT data of a transcription factor in living E. coli cells. This work allows a direct quantitative connection between cytoplasmic SMT data with diffusion theory for analyzing molecular diffusive behavior in live bacteria.

Quantifying Multistate Cytoplasmic Molecular Diffusion in Bacterial Cells via Inverse Transform of Confined Displacement Distribution

PubMed Central

2016-01-01

Single-molecule tracking (SMT) of fluorescently tagged cytoplasmic proteins can provide valuable information on the underlying biological processes in living cells via subsequent analysis of the displacement distributions; however, the confinement effect originated from the small size of a bacterial cell skews the protein’s displacement distribution and complicates the quantification of the intrinsic diffusive behaviors. Using the inverse transformation method, we convert the skewed displacement distribution (for both 2D and 3D imaging conditions) back to that in free space for systems containing one or multiple (non)interconverting Brownian diffusion states, from which we can reliably extract the number of diffusion states as well as their intrinsic diffusion coefficients and respective fractional populations. We further demonstrate a successful application to experimental SMT data of a transcription factor in living E. coli cells. This work allows a direct quantitative connection between cytoplasmic SMT data with diffusion theory for analyzing molecular diffusive behavior in live bacteria. PMID:26491971

Anisotropic diffusion in mesh-free numerical magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.

2017-04-01

We extend recently developed mesh-free Lagrangian methods for numerical magnetohydrodynamics (MHD) to arbitrary anisotropic diffusion equations, including: passive scalar diffusion, Spitzer-Braginskii conduction and viscosity, cosmic ray diffusion/streaming, anisotropic radiation transport, non-ideal MHD (Ohmic resistivity, ambipolar diffusion, the Hall effect) and turbulent 'eddy diffusion'. We study these as implemented in the code GIZMO for both new meshless finite-volume Godunov schemes (MFM/MFV). We show that the MFM/MFV methods are accurate and stable even with noisy fields and irregular particle arrangements, and recover the correct behaviour even in arbitrarily anisotropic cases. They are competitive with state-of-the-art AMR/moving-mesh methods, and can correctly treat anisotropic diffusion-driven instabilities (e.g. the MTI and HBI, Hall MRI). We also develop a new scheme for stabilizing anisotropic tensor-valued fluxes with high-order gradient estimators and non-linear flux limiters, which is trivially generalized to AMR/moving-mesh codes. We also present applications of some of these improvements for SPH, in the form of a new integral-Godunov SPH formulation that adopts a moving-least squares gradient estimator and introduces a flux-limited Riemann problem between particles.

Hybrid diffusion-P3 equation in N-layered turbid media: steady-state domain.

PubMed

Shi, Zhenzhi; Zhao, Huijuan; Xu, Kexin

2011-10-01

This paper discusses light propagation in N-layered turbid media. The hybrid diffusion-P3 equation is solved for an N-layered finite or infinite turbid medium in the steady-state domain for one point source using the extrapolated boundary condition. The Fourier transform formalism is applied to derive the analytical solutions of the fluence rate in Fourier space. Two inverse Fourier transform methods are developed to calculate the fluence rate in real space. In addition, the solutions of the hybrid diffusion-P3 equation are compared to the solutions of the diffusion equation and the Monte Carlo simulation. For the case of small absorption coefficients, the solutions of the N-layered diffusion equation and hybrid diffusion-P3 equation are almost equivalent and are in agreement with the Monte Carlo simulation. For the case of large absorption coefficients, the model of the hybrid diffusion-P3 equation is more precise than that of the diffusion equation. In conclusion, the model of the hybrid diffusion-P3 equation can replace the diffusion equation for modeling light propagation in the N-layered turbid media for a wide range of absorption coefficients.

Diffusion accessibility as a method for visualizing macromolecular surface geometry.

PubMed

Tsai, Yingssu; Holton, Thomas; Yeates, Todd O

2015-10-01

Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/. © 2015 The Protein Society.

Modeling boundary measurements of scattered light using the corrected diffusion approximation

PubMed Central

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

2012-01-01

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

On a common critical state in localized and diffuse failure modes

NASA Astrophysics Data System (ADS)

Zhu, Huaxiang; Nguyen, Hien N. G.; Nicot, François; Darve, Félix

2016-10-01

Accurately modeling the critical state mechanical behavior of granular material largely relies on a better understanding and characterizing the critical state fabric in different failure modes, i.e. localized and diffuse failure modes. In this paper, a mesoscopic scale is introduced, in which the organization of force-transmission paths (force-chains) and cells encompassed by contacts (meso-loops) can be taken into account. Numerical drained biaxial tests using a discrete element method are performed with different initial void ratios, in order to investigate the critical state fabric on the meso-scale in both localized and diffuse failure modes. According to the displacement and strain fields extracted from tests, the failure mode and failure area of each specimen are determined. Then convergent critical state void ratios are observed in failure area of specimens. Different mechanical features of two kinds of meso-structures (force-chains and meso-loops) are investigated, to clarify whether there exists a convergent meso-structure inside the failure area of granular material, as the signature of critical state. Numerical results support a positive answer. Failure area of both localized and diffuse failure modes therefore exhibits the same fabric in critical state. Hence, these two failure modes prove to be homological with respect to the concept of the critical state.

Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen.

PubMed

Sodeifian, Gholamhossein; Razmimanesh, Fariba

2018-05-10

In this research, for the first time, molecular dynamics (MD) method was used to simulate aspirin and ibuprofen at various concentrations and in neutral and charged states. Effects of the concentration (dosage), charge state, and existence of an integral protein in the membrane on the diffusion rate of drug molecules into lipid bilayer membrane were investigated on 11 systems, for which the parameters indicating diffusion rate and those affecting the rate were evaluated. Considering the diffusion rate, a suitable score was assigned to each system, based on which, analysis of variance (ANOVA) was performed. By calculating the effect size of the indicative parameters and total scores, an optimum system with the highest diffusion rate was determined. Consequently, diffusion rate controlling parameters were obtained: the drug-water hydrogen bond in protein-free systems and protein-drug hydrogen bond in the systems containing protein.

Cyclic steady states in diffusion-induced plasticity with applications to lithium-ion batteries

NASA Astrophysics Data System (ADS)

Peigney, Michaël

2018-02-01

Electrode materials in lithium-ion batteries offer an example of medium in which stress and plastic flow are generated by the diffusion of guest atoms. In such a medium, deformation and diffusion are strongly coupled processes. For designing electrodes with improved lifetime and electro-mechanical efficiency, it is crucial to understand how plasticity and diffusion evolve over consecutive charging-recharging cycles. With such questions in mind, this paper provides general results for the large-time behavior of media coupling plasticity with diffusion when submitted to cyclic chemo-mechanical loadings. Under suitable assumptions, we show that the stress, the plastic strain rate, the chemical potential and the flux of guest atoms converge to a cyclic steady state which is largely independent of the initial state. A special emphasis is laid on the special case of elastic shakedown, which corresponds to the situation where the plastic strain stops evolving after a sufficiently large number of cycles. Elastic shakedown is expected to be beneficial for the fatigue behavior and - in the case of lithium-ion batteries - for the electro-chemical efficiency. We provide a characterization of the chemo-mechanical loadings for which elastic shakedown occurs. Building on that characterization, we suggest a general method for designing structures in such fashion that they operate in the elastic shakedown regime, whatever the initial state is. An attractive feature of the proposed method is that incremental analysis of the fully coupled plasticity-diffusion problem is avoided. The results obtained are applied to the model problem of a battery electrode cylinder particle under cyclic charging. Closed-form expressions are obtained for the set of charging rates and charging amplitudes for which elastic shakedown occurs, as well as for the corresponding cyclic steady states of stress, lithium concentration and chemical potential. Some results for a spherical particle are also presented.

Diffusion of 99-technetium in compacted bentonite under aerobic and anaerobic conditions

NASA Astrophysics Data System (ADS)

Večerník, P.; Jedináková-Křížová, V.

2006-01-01

The main aim of this study was to investigate diffusion of technetium 99Tc under different conditions. Because technetium represents one of the most dangerous fission products due to its very long halftime and high mobility in aerobic conditions diffusion experiments of technetium (as 99TcO 4 - anion) in Czech bentonite from Rokle locality have been carried out. For performance and evaluation of experiments the through-diffusion method was chosen and apparent (Da) and effective (De) diffusion coefficients were evaluated. The effects of particle mesh-size, dry bulk density and aerobic or anaerobic conditions on diffusion were studied. In the presence of oxygen, technetium occurs in oxidation state VII, as an anion, soluble and mobile in the environment. However, under reducing conditions it occurs in a lower oxidation states, mainly as insoluble oxides or hydroxides. Aerobic experiments were carried out under laboratory conditions and anaerobic experiments were performed in a nitrogen atmosphere in a glove box, to simulate the real underground conditions.

A finite elements method to solve the Bloch-Torrey equation applied to diffusion magnetic resonance imaging

NASA Astrophysics Data System (ADS)

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

2014-04-01

The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch-Torrey partial differential equation (PDE). In addition, steady-state Laplace PDEs can be formulated to produce the homogenized diffusion tensor that describes the diffusion characteristics of the medium in the long time limit. In spatial domains that model biological tissues at the cellular level, these two types of PDEs have to be completed with permeability conditions on the cellular interfaces. To solve these PDEs, we implemented a finite elements method that allows jumps in the solution at the cell interfaces by using double nodes. Using a transformation of the Bloch-Torrey PDE we reduced oscillations in the searched-for solution and simplified the implementation of the boundary conditions. The spatial discretization was then coupled to the adaptive explicit Runge-Kutta-Chebyshev time-stepping method. Our proposed method is second order accurate in space and second order accurate in time. We implemented this method on the FEniCS C++ platform and show time and spatial convergence results. Finally, this method is applied to study some relevant questions in diffusion MRI.

Risk Assessment of Alzheimer's Disease using the Information Diffusion Model from Structural Magnetic Resonance Imaging.

PubMed

Beheshti, Iman; Olya, Hossain G T; Demirel, Hasan

2016-04-05

Recently, automatic risk assessment methods have been a target for the detection of Alzheimer's disease (AD) risk. This study aims to develop an automatic computer-aided AD diagnosis technique for risk assessment of AD using information diffusion theory. Information diffusion is a fuzzy mathematics logic of set-value that is used for risk assessment of natural phenomena, which attaches fuzziness (uncertainty) and incompleteness. Data were obtained from voxel-based morphometry analysis of structural magnetic resonance imaging. The information diffusion model results revealed that the risk of AD increases with a reduction of the normalized gray matter ratio (p > 0.5, normalized gray matter ratio <40%). The information diffusion model results were evaluated by calculation of the correlation of two traditional risk assessments of AD, the Mini-Mental State Examination and the Clinical Dementia Rating. The correlation results revealed that the information diffusion model findings were in line with Mini-Mental State Examination and Clinical Dementia Rating results. Application of information diffusion model contributes to the computerization of risk assessment of AD, which has a practical implication for the early detection of AD.

Solubility and diffusion of oxygen in phospholipid membranes.

PubMed

Möller, Matías N; Li, Qian; Chinnaraj, Mathivanan; Cheung, Herbert C; Lancaster, Jack R; Denicola, Ana

2016-11-01

The transport of oxygen and other nonelectrolytes across lipid membranes is known to depend on both diffusion and solubility in the bilayer, and to be affected by changes in the physical state and by the lipid composition, especially the content of cholesterol and unsaturated fatty acids. However, it is not known how these factors affect diffusion and solubility separately. Herein we measured the partition coefficient of oxygen in liposome membranes of dilauroyl-, dimiristoyl- and dipalmitoylphosphatidylcholine in buffer at different temperatures using the equilibrium-shift method with electrochemical detection. The apparent diffusion coefficient was measured following the fluorescence quenching of 1-pyrenedodecanoate inserted in the liposome bilayers under the same conditions. The partition coefficient varied with the temperature and the physical state of the membrane, from below 1 in the gel state to above 2.8 in the liquid-crystalline state in DMPC and DPPC membranes. The partition coefficient was directly proportional to the partial molar volume and was then associated to the increase in free-volume in the membrane as a function of temperature. The apparent diffusion coefficients were corrected by the partition coefficients and found to be nearly the same, with a null dependence on viscosity and physical state of the membrane, probably because the pyrene is disturbing the surrounding lipids and thus becoming insensitive to changes in membrane viscosity. Combining our results with those of others, it is apparent that both solubility and diffusion increase when increasing the temperature or when comparing a membrane in the gel to one in the fluid state. Copyright © 2016 Elsevier B.V. All rights reserved.

Monte Carlo sampling in diffusive dynamical systems

NASA Astrophysics Data System (ADS)

Tapias, Diego; Sanders, David P.; Altmann, Eduardo G.

2018-05-01

We introduce a Monte Carlo algorithm to efficiently compute transport properties of chaotic dynamical systems. Our method exploits the importance sampling technique that favors trajectories in the tail of the distribution of displacements, where deviations from a diffusive process are most prominent. We search for initial conditions using a proposal that correlates states in the Markov chain constructed via a Metropolis-Hastings algorithm. We show that our method outperforms the direct sampling method and also Metropolis-Hastings methods with alternative proposals. We test our general method through numerical simulations in 1D (box-map) and 2D (Lorentz gas) systems.

Local modification of the surface state properties at dilute coverages: CO/Cu(111)

NASA Astrophysics Data System (ADS)

Zaum, Ch.; Meyer-auf-der-Heide, K. M.; Morgenstern, K.

2018-04-01

We follow the diffusion of CO molecules on Cu(111) by time-lapsed low-temperature scanning tunneling microscopy. The diffusivity of individual CO molecules oscillates with the distance to its nearest neighbor due to the long-range interaction mediated by the surface state electrons. The markedly different wavelengths of the oscillation at a coverage of 0.6% ML as compared to the one at 6% ML coverage correspond to two different wavelengths of the surface state electrons, consistent with a shift of the surface state by 340 meV. This surprisingly large shift as compared to results of averaging methods suggests a local modification of the surface state properties.

Existence and instability of steady states for a triangular cross-diffusion system: A computer-assisted proof

NASA Astrophysics Data System (ADS)

Breden, Maxime; Castelli, Roberto

2018-05-01

In this paper, we present and apply a computer-assisted method to study steady states of a triangular cross-diffusion system. Our approach consist in an a posteriori validation procedure, that is based on using a fixed point argument around a numerically computed solution, in the spirit of the Newton-Kantorovich theorem. It allows to prove the existence of various non homogeneous steady states for different parameter values. In some situations, we obtain as many as 13 coexisting steady states. We also apply the a posteriori validation procedure to study the linear stability of the obtained steady states, proving that many of them are in fact unstable.

Interplay between inhibited transport and reaction in nanoporous materials

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

Ackerman, David Michael

2013-01-01

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

Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles.

PubMed

Zhu, Jie; Qin, Yufang; Liu, Taigang; Wang, Jun; Zheng, Xiaoqi

2013-01-01

Identification of gene-phenotype relationships is a fundamental challenge in human health clinic. Based on the observation that genes causing the same or similar phenotypes tend to correlate with each other in the protein-protein interaction network, a lot of network-based approaches were proposed based on different underlying models. A recent comparative study showed that diffusion-based methods achieve the state-of-the-art predictive performance. In this paper, a new diffusion-based method was proposed to prioritize candidate disease genes. Diffusion profile of a disease was defined as the stationary distribution of candidate genes given a random walk with restart where similarities between phenotypes are incorporated. Then, candidate disease genes are prioritized by comparing their diffusion profiles with that of the disease. Finally, the effectiveness of our method was demonstrated through the leave-one-out cross-validation against control genes from artificial linkage intervals and randomly chosen genes. Comparative study showed that our method achieves improved performance compared to some classical diffusion-based methods. To further illustrate our method, we used our algorithm to predict new causing genes of 16 multifactorial diseases including Prostate cancer and Alzheimer's disease, and the top predictions were in good consistent with literature reports. Our study indicates that integration of multiple information sources, especially the phenotype similarity profile data, and introduction of global similarity measure between disease and gene diffusion profiles are helpful for prioritizing candidate disease genes. Programs and data are available upon request.

Revisiting the diffusion mechanism of helium in UO2: A DFT+U study

NASA Astrophysics Data System (ADS)

Liu, X.-Y.; Andersson, D. A.

2018-01-01

The understanding of migration properties of helium atoms after their generation through α-decay of actinides in spent nuclear fuels is important for the safety of nuclear fuel storage and disposal. The diffusion of helium in UO2 is revisited by using the DFT+U simulation methodology employing the "U-ramping" method to address the issue of metastable energy states. A novel diffusion mechanism by helium interstitials, the "asymmetric hop" mechanism, is reported and compared to other diffusion mechanisms including an oxygen vacancy mediated mechanism and available experimental diffusion data. The new mechanism is shown to be the dominant one over a wide temperature range.

A fast and sensitive method for evaluating nuclides migration characteristics in rock medium by using micro-channel reactor concept

NASA Astrophysics Data System (ADS)

Okuyama, Keita; Sasahira, Akira; Noshita, Kenji; Yoshida, Takuma; Kato, Kazuyuki; Nagasaki, Shinya; Ohe, Toshiaki

Experimental effort to evaluate the barrier performance of geologic disposal requires relatively long testing periods and chemically stable conditions. We have developed a new technique, the micro mock-up method, to present a fast and sensitive method to measure both nuclide diffusivity and sorption coefficient within a day to overcome such disadvantage of the conventional method. In this method, a Teflon plate having a micro channel (10-200 μm depth, 2, 4 mm width) is placed just beneath the rock sample plate, radionuclide solution is injected into the channel with constant rate. The breakthrough curve is being measured until a steady state. The outlet flux in the steady state however does not meet the inlet flux because of the matrix diffusion into the rock body. This inlet-outlet difference is simply related to the effective diffusion coefficient ( De) and the distribution coefficient ( Kd) of rock sample. Then, we adopt a fitting procedure to speculate Kd and De values by comparing the observation to the theoretical curve of the two-dimensional diffusion-advection equation. In the present study, we measured De of 3H by using both the micro mock-up method and the conventional through-diffusion method for comparison. The obtained values of De by two different ways for granite sample (Inada area of Japan) were identical: 1.0 × 10 -11 and 9.0 × 10 -12 m 2/s but the testing period was much different: 10 h and 3 days, respectively. We also measured the breakthrough curve of 85Sr and the resulting Kd and De agreed well to the previous study obtained by the batch sorption experiments with crushed samples. The experimental evidence and the above advantages reveal that the micro mock-up method based on the microreactor concept is powerful and much advantageous when compared to the conventional method.

Reflexion measurements for inverse characterization of steel diffusion bond mechanical properties

NASA Astrophysics Data System (ADS)

Le Bourdais, Florian; Cachon, Lionel; Rigal, Emmanuel

2017-02-01

The present work describes a non-destructive testing method aimed at securing high manufacturing quality of the innovative compact heat exchanger developed under the framework of the CEA R&D program dedicated to the Advanced Sodium Technological Reactor for Industrial Demonstration (ASTRID). The heat exchanger assembly procedure currently proposed involves high temperature and high pressure diffusion welding of stainless steel plates. The aim of the non-destructive method presented herein is to characterize the quality of the welds obtained through this assembly process. Based on a low-frequency model developed by Baik and Thompson [1], pulse-echo normal incidence measurements are calibrated according to a specific procedure and allow the determination of the welding interface stiffness using a nonlinear fitting procedure in the frequency domain. Performing the characterization of plates after diffusion welding using this method allows a useful assessment of the material state as a function of the diffusion bonding process.

A novel method for calculating the energy barriers for carbon diffusion in ferrite under heterogeneous stress

NASA Astrophysics Data System (ADS)

Tchitchekova, Deyana S.; Morthomas, Julien; Ribeiro, Fabienne; Ducher, Roland; Perez, Michel

2014-07-01

A novel method for accurate and efficient evaluation of the change in energy barriers for carbon diffusion in ferrite under heterogeneous stress is introduced. This method, called Linear Combination of Stress States, is based on the knowledge of the effects of simple stresses (uniaxial or shear) on these diffusion barriers. Then, it is assumed that the change in energy barriers under a complex stress can be expressed as a linear combination of these already known simple stress effects. The modifications of energy barriers by either uniaxial traction/compression and shear stress are determined by means of atomistic simulations with the Climbing Image-Nudge Elastic Band method and are stored as a set of functions. The results of this method are compared to the predictions of anisotropic elasticity theory. It is shown that, linear anisotropic elasticity fails to predict the correct energy barrier variation with stress (especially with shear stress) whereas the proposed method provides correct energy barrier variation for stresses up to ˜3 GPa. This study provides a basis for the development of multiscale models of diffusion under non-uniform stress.

A novel method for calculating the energy barriers for carbon diffusion in ferrite under heterogeneous stress.

PubMed

Tchitchekova, Deyana S; Morthomas, Julien; Ribeiro, Fabienne; Ducher, Roland; Perez, Michel

2014-07-21

A novel method for accurate and efficient evaluation of the change in energy barriers for carbon diffusion in ferrite under heterogeneous stress is introduced. This method, called Linear Combination of Stress States, is based on the knowledge of the effects of simple stresses (uniaxial or shear) on these diffusion barriers. Then, it is assumed that the change in energy barriers under a complex stress can be expressed as a linear combination of these already known simple stress effects. The modifications of energy barriers by either uniaxial traction/compression and shear stress are determined by means of atomistic simulations with the Climbing Image-Nudge Elastic Band method and are stored as a set of functions. The results of this method are compared to the predictions of anisotropic elasticity theory. It is shown that, linear anisotropic elasticity fails to predict the correct energy barrier variation with stress (especially with shear stress) whereas the proposed method provides correct energy barrier variation for stresses up to ∼3 GPa. This study provides a basis for the development of multiscale models of diffusion under non-uniform stress.

Light diffusion in N-layered turbid media: steady-state domain.

PubMed

Liemert, André; Kienle, Alwin

2010-01-01

We deal with light diffusion in N-layered turbid media. The steady-state diffusion equation is solved for N-layered turbid media having a finite or an infinitely thick N'th layer. Different refractive indices are considered in the layers. The Fourier transform formalism is applied to derive analytical solutions of the fluence rate in Fourier space. The inverse Fourier transform is calculated using four different methods to test their performance and accuracy. Further, to avoid numerical errors, approximate formulas in Fourier space are derived. Fast solutions for calculation of the spatially resolved reflectance and transmittance from the N-layered turbid media ( approximately 10 ms) with small relative differences (<10(-7)) are found. Additionally, the solutions of the diffusion equation are compared to Monte Carlo simulations for turbid media having up to 20 layers.

Lossy radial diffusion of relativistic Jovian electrons. [calculation of synchrotron radiation and electron radiation for Jupiter

NASA Technical Reports Server (NTRS)

Barbosa, D. D.; Coroniti, F. V.

1976-01-01

The radial diffusion equation with synchrotron losses was solved by the Laplace transform method for near-equatorially mirroring relativistic electrons. The evolution of a power law distribution function was found and the characteristics of synchrotron burn-off are stated in terms of explicit parameters for an arbitrary diffusion coefficient. Emissivity from the radiation belts of Jupiter was studied. Asymptotic forms for the distribution in the strong synchrotron loss regime are provided.

Correlation and prediction of gaseous diffusion coefficients.

NASA Technical Reports Server (NTRS)

Marrero, T. R.; Mason, E. A.

1973-01-01

A new correlation method for binary gaseous diffusion coefficients from very low temperatures to 10,000 K is proposed based on an extended principle of corresponding states, and having greater range and accuracy than previous correlations. There are two correlation parameters that are related to other physical quantities and that are predictable in the absence of diffusion measurements. Quantum effects and composition dependence are included, but high-pressure effects are not. The results are directly applicable to multicomponent mixtures.

Detection of Diffusion Heterogeneity in Single Particle Tracking Trajectories Using a Hidden Markov Model with Measurement Noise Propagation

PubMed Central

Slator, Paddy J.; Cairo, Christopher W.; Burroughs, Nigel J.

2015-01-01

We develop a Bayesian analysis framework to detect heterogeneity in the diffusive behaviour of single particle trajectories on cells, implementing model selection to classify trajectories as either consistent with Brownian motion or with a two-state (diffusion coefficient) switching model. The incorporation of localisation accuracy is essential, as otherwise false detection of switching within a trajectory was observed and diffusion coefficient estimates were inflated. Since our analysis is on a single trajectory basis, we are able to examine heterogeneity between trajectories in a quantitative manner. Applying our method to the lymphocyte function-associated antigen 1 (LFA-1) receptor tagged with latex beads (4 s trajectories at 1000 frames s−1), both intra- and inter-trajectory heterogeneity were detected; 12–26% of trajectories display clear switching between diffusive states dependent on condition, whilst the inter-trajectory variability is highly structured with the diffusion coefficients being related by D 1 = 0.68D 0 − 1.5 × 104 nm2 s−1, suggestive that on these time scales we are detecting switching due to a single process. Further, the inter-trajectory variability of the diffusion coefficient estimates (1.6 × 102 − 2.6 × 105 nm2 s−1) is very much larger than the measurement uncertainty within trajectories, suggesting that LFA-1 aggregation and cytoskeletal interactions are significantly affecting mobility, whilst the timescales of these processes are distinctly different giving rise to inter- and intra-trajectory variability. There is also an ‘immobile’ state (defined as D < 3.0 × 103 nm2 s−1) that is rarely involved in switching, immobility occurring with the highest frequency (47%) under T cell activation (phorbol-12-myristate-13-acetate (PMA) treatment) with enhanced cytoskeletal attachment (calpain inhibition). Such ‘immobile’ states frequently display slow linear drift, potentially reflecting binding to a dynamic actin cortex. Our methods allow significantly more information to be extracted from individual trajectories (ultimately limited by time resolution and time-series length), and allow statistical comparisons between trajectories thereby quantifying inter-trajectory heterogeneity. Such methods will be highly informative for the construction and fitting of molecule mobility models within membranes incorporating aggregation, binding to the cytoskeleton, or traversing membrane microdomains. PMID:26473352

Influence of doping on thermal diffusivity of single crystals used in photonics: measurements based on thermal wave methods.

PubMed

Bodzenta, Jerzy; Kaźmierczak-Bałata, Anna; Wokulska, Krystyna B; Kucytowski, Jacek; Łukasiewicz, Tadeusz; Hofman, Władysław

2009-03-01

Three crystals used in solid-state lasers, namely, yttrium aluminum garnet (YAG), yttrium orthovanadate (YVO(4)), and gadolinium calcium oxoborate (GdCOB), were investigated to determine the influence of dopants on their thermal diffusivity. The thermal diffusivity was measured by thermal wave method with a signal detection based on mirage effect. The YAG crystals were doped with Yb or V, the YVO(4) with Nd or Ca and Tm, and the GdCOB crystals contained Nd or Yb. In all cases, the doping caused a decrease in thermal diffusivity. The analysis of complementary measurements of ultrasound velocity changes caused by dopants leads to the conclusion that impurities create phonon scattering centers. This additional scattering reduces the phonon mean free path and accordingly results in the decrease of the thermal diffusivity of the crystal. The influence of doping on lattice parameters was investigated, additionally.

Assessment of diffuser pressure loss on WWTPs in Baden-Württemberg.

PubMed

Krampe, J

2011-01-01

Aeration of activated sludge is a critical treatment step for the operation of activated sludge plants. To achieve a cost effective treatment process, assessing and benchmarking of aeration system performance are important measures. A simple means of gauging the relative condition of a fine bubble diffused aeration system is to evaluate the pressure loss of the diffusers as oxygen transfer tests are rarely applied during the lifetime of an aeration system. This paper shows an assessment of fine bubble diffuser systems in Baden-Württemberg, Germany, based on the results of a questionnaire sent to 941 WWTPs. Apart from the results with regards to the diffuser pressure loss, this paper also presents information on the current state of diffuser technology such as types and materials as well as the diffuser cleaning methods used in Baden-Württemberg. The majority of the WWTPs were equipped with tube diffusers (71%) with 50% of all plants having EPDM membranes installed. Regular mechanical cleaning is the most common cleaning method followed by regular pressure release/air-bumping programs during operations. With regard to the diffuser pressure loss it was found that 50% of the evaluated plants had a diffuser pressure loss that was twice as high as measured for new diffusers.

Welding and Joining of Titanium Aluminides

PubMed Central

Cao, Jian; Qi, Junlei; Song, Xiaoguo; Feng, Jicai

2014-01-01

Welding and joining of titanium aluminides is the key to making them more attractive in industrial fields. The purpose of this review is to provide a comprehensive overview of recent progress in welding and joining of titanium aluminides, as well as to introduce current research and application. The possible methods available for titanium aluminides involve brazing, diffusion bonding, fusion welding, friction welding and reactive joining. Of the numerous methods, solid-state diffusion bonding and vacuum brazing have been most heavily investigated for producing reliable joints. The current state of understanding and development of every welding and joining method for titanium aluminides is addressed respectively. The focus is on the fundamental understanding of microstructure characteristics and processing–microstructure–property relationships in the welding and joining of titanium aluminides to themselves and to other materials. PMID:28788113

Synchronization criteria for generalized reaction-diffusion neural networks via periodically intermittent control.

PubMed

Gan, Qintao; Lv, Tianshi; Fu, Zhenhua

2016-04-01

In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained.

Local error estimates for adaptive simulation of the Reaction–Diffusion Master Equation via operator splitting

PubMed Central

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2015-01-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity. PMID:26865735

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting.

PubMed

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2014-06-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity.

A finite elements method to solve the Bloch–Torrey equation applied to diffusion magnetic resonance imaging

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

Nguyen, Dang Van; NeuroSpin, Bat145, Point Courrier 156, CEA Saclay Center, 91191 Gif-sur-Yvette Cedex; Li, Jing-Rebecca, E-mail: jingrebecca.li@inria.fr

2014-04-15

The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch–Torrey partial differential equation (PDE). In addition, steady-state Laplace PDEs can be formulated to produce the homogenized diffusion tensor that describes the diffusion characteristics of the medium in the long time limit. In spatial domains that model biological tissues at the cellular level, these two types of PDEs have to be completed with permeability conditions on the cellular interfaces. To solve these PDEs, we implemented a finite elements method that allows jumps in the solution atmore » the cell interfaces by using double nodes. Using a transformation of the Bloch–Torrey PDE we reduced oscillations in the searched-for solution and simplified the implementation of the boundary conditions. The spatial discretization was then coupled to the adaptive explicit Runge–Kutta–Chebyshev time-stepping method. Our proposed method is second order accurate in space and second order accurate in time. We implemented this method on the FEniCS C++ platform and show time and spatial convergence results. Finally, this method is applied to study some relevant questions in diffusion MRI.« less

Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

PubMed

A Rohrdanz, Mary; Zheng, Wenwei; Lambeth, Bradley; Vreede, Jocelyne; Clementi, Cecilia

2014-10-01

The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

Random Walk Particle Tracking For Multiphase Heat Transfer

NASA Astrophysics Data System (ADS)

Lattanzi, Aaron; Yin, Xiaolong; Hrenya, Christine

2017-11-01

As computing capabilities have advanced, direct numerical simulation (DNS) has become a highly effective tool for quantitatively predicting the heat transfer within multiphase flows. Here we utilize a hybrid DNS framework that couples the lattice Boltzmann method (LBM) to the random walk particle tracking (RWPT) algorithm. The main challenge of such a hybrid is that discontinuous fields pose a significant challenge to the RWPT framework and special attention must be given to the handling of interfaces. We derive a method for addressing discontinuities in the diffusivity field, arising at the interface between two phases. Analytical means are utilized to develop an interfacial tracer balance and modify the RWPT algorithm. By expanding the modulus of the stochastic (diffusive) step and only allowing a subset of the tracers within the high diffusivity medium to undergo a diffusive step, the correct equilibrium state can be restored (globally homogeneous tracer distribution). The new RWPT algorithm is implemented within the SUSP3D code and verified against a variety of systems: effective diffusivity of a static gas-solids mixture, hot sphere in unbounded diffusion, cooling sphere in unbounded diffusion, and uniform flow past a hot sphere.

Formation of amorphous materials

DOEpatents

Johnson, William L.; Schwarz, Ricardo B.

1986-01-01

Metastable amorphous or fine crystalline materials are formed by solid state reactions by diffusion of a metallic component into a solid compound or by diffusion of a gas into an intermetallic compound. The invention can be practiced on layers of metals deposited on an amorphous substrate or by intermixing powders with nucleating seed granules. All that is required is that the diffusion of the first component into the second component be much faster than the self-diffusion of the first component. The method is practiced at a temperature below the temperature at which the amorphous phase transforms into one or more crystalline phases and near or below the temperature at which the ratio of the rate of diffusion of the first component to the rate of self-diffusion is at least 10.sup.4. This anomalous diffusion criteria is found in many binary, tertiary and higher ordered systems of alloys and appears to be found in all alloy systems that form amorphous materials by rapid quenching. The method of the invention can totally convert much larger dimensional materials to amorphous materials in practical periods of several hours or less.

Global solutions to a class of multi-species reaction-diffusion systems with cross-diffusions arising in population dynamics

NASA Astrophysics Data System (ADS)

Wen, Zijuan; Fu, Shengmao

2009-08-01

In this paper, an n-species strongly coupled cooperating diffusive system is considered in a bounded smooth domain, subject to homogeneous Neumann boundary conditions. Employing the method of energy estimates, we obtain some conditions on the diffusion matrix and inter-specific cooperatives to ensure the global existence and uniform boundedness of a nonnegative solution. The globally asymptotical stability of the constant positive steady state is also discussed. As a consequence, all the results hold true for multi-species Lotka-Volterra type competition model and prey-predator model.

Simulation of adsorbed hydrogen on tungsten surface

NASA Astrophysics Data System (ADS)

Degtyarenko, N. N.; Pisarev, A. A.

2017-12-01

Calculations of the energy of the H-W system were performed using DFT method based on plane waves. Adsorption energies, equilibrium states, vibration spectra, saddle points, activation energies of jumps, and diffusion paths have been analyzed for H atom on W(100) and W(110). Diffusion coefficient for H on W(110) agrees very well with experimental data.

Estimation of the Thermal Process in the Honeycomb Panel by a Monte Carlo Method

NASA Astrophysics Data System (ADS)

Gusev, S. A.; Nikolaev, V. N.

2018-01-01

A new Monte Carlo method for estimating the thermal state of the heat insulation containing honeycomb panels is proposed in the paper. The heat transfer in the honeycomb panel is described by a boundary value problem for a parabolic equation with discontinuous diffusion coefficient and boundary conditions of the third kind. To obtain an approximate solution, it is proposed to use the smoothing of the diffusion coefficient. After that, the obtained problem is solved on the basis of the probability representation. The probability representation is the expectation of the functional of the diffusion process corresponding to the boundary value problem. The process of solving the problem is reduced to numerical statistical modelling of a large number of trajectories of the diffusion process corresponding to the parabolic problem. It was used earlier the Euler method for this object, but that requires a large computational effort. In this paper the method is modified by using combination of the Euler and the random walk on moving spheres methods. The new approach allows us to significantly reduce the computation costs.

Bessel Fourier orientation reconstruction: an analytical EAP reconstruction using multiple shell acquisitions in diffusion MRI.

PubMed

Hosseinbor, Ameer Pasha; Chung, Moo K; Wu, Yu-Chien; Alexander, Andrew L

2011-01-01

The estimation of the ensemble average propagator (EAP) directly from q-space DWI signals is an open problem in diffusion MRI. Diffusion spectrum imaging (DSI) is one common technique to compute the EAP directly from the diffusion signal, but it is burdened by the large sampling required. Recently, several analytical EAP reconstruction schemes for multiple q-shell acquisitions have been proposed. One, in particular, is Diffusion Propagator Imaging (DPI) which is based on the Laplace's equation estimation of diffusion signal for each shell acquisition. Viewed intuitively in terms of the heat equation, the DPI solution is obtained when the heat distribution between temperatuere measurements at each shell is at steady state. We propose a generalized extension of DPI, Bessel Fourier Orientation Reconstruction (BFOR), whose solution is based on heat equation estimation of the diffusion signal for each shell acquisition. That is, the heat distribution between shell measurements is no longer at steady state. In addition to being analytical, the BFOR solution also includes an intrinsic exponential smootheing term. We illustrate the effectiveness of the proposed method by showing results on both synthetic and real MR datasets.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

NASA Astrophysics Data System (ADS)

Kim, Changho; Nonaka, Andy; Bell, John B.; Garcia, Alejandro L.; Donev, Aleksandar

2017-03-01

We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. By comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

DOE PAGES

Kim, Changho; Nonaka, Andy; Bell, John B.; ...

2017-03-24

Here, we develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules,more » to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. Furthermore, by comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.« less

Revisiting the diffusion mechanism of helium in UO 2 : A DFT+ U study

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

Liu, X. -Y.; Andersson, D. A.

The understanding of migration properties of helium atoms after their generation through α-decay of actinides in spent nuclear fuels is important for the safety of nuclear fuel storage and disposal. The diffusion of helium in UO 2 is revisited by using the DFT+U simulation methodology employing the “U-ramping” method to address the issue of metastable energy states. A novel diffusion mechanism by helium interstitials, the “asymmetric hop” mechanism, is reported and compared to other diffusion mechanisms including an oxygen vacancy mediated mechanism and available experimental diffusion data. We show that the new mechanism is the dominant one over a widemore » temperature range.« less

Revisiting the diffusion mechanism of helium in UO 2 : A DFT+ U study

DOE PAGES

Liu, X. -Y.; Andersson, D. A.

2017-11-03

The understanding of migration properties of helium atoms after their generation through α-decay of actinides in spent nuclear fuels is important for the safety of nuclear fuel storage and disposal. The diffusion of helium in UO 2 is revisited by using the DFT+U simulation methodology employing the “U-ramping” method to address the issue of metastable energy states. A novel diffusion mechanism by helium interstitials, the “asymmetric hop” mechanism, is reported and compared to other diffusion mechanisms including an oxygen vacancy mediated mechanism and available experimental diffusion data. We show that the new mechanism is the dominant one over a widemore » temperature range.« less

Thin-film diffusion brazing of titanium alloys

NASA Technical Reports Server (NTRS)

Mikus, E. B.

1972-01-01

A thin film diffusion brazing technique for joining titanium alloys by use of a Cu intermediate is described. The method has been characterized in terms of static and dynamic mechanical properties on Ti-6Al-4V alloy. These include tensile, fracture toughness, stress corrosion, shear, corrosion fatigue, mechanical fatigue and acoustic fatigue. Most of the properties of titanium joints formed by thin film diffusion brazing are equal or exceed base metal properties. The advantages of thin film diffusion brazing over solid state diffusion bonding and brazing with conventional braze alloys are discussed. The producibility advantages of this process over others provide the potential for producing high efficiency joints in structural components of titanium alloys for the minimum cost.

Indispensable finite time corrections for Fokker-Planck equations from time series data.

PubMed

Ragwitz, M; Kantz, H

2001-12-17

The reconstruction of Fokker-Planck equations from observed time series data suffers strongly from finite sampling rates. We show that previously published results are degraded considerably by such effects. We present correction terms which yield a robust estimation of the diffusion terms, together with a novel method for one-dimensional problems. We apply these methods to time series data of local surface wind velocities, where the dependence of the diffusion constant on the state variable shows a different behavior than previously suggested.

Use of Plastic Capillaries for Macromolecular Crystallization

NASA Technical Reports Server (NTRS)

Potter, Rachel R.; Hong, Young-Soo; Ciszak, Ewa M.

2003-01-01

Methods of crystallization of biomolecules in plastic capillaries (Nalgene 870 PFA tubing) are presented. These crystallization methods used batch, free-interface liquid- liquid diffusion alone, or a combination with vapor diffusion. Results demonstrated growth of crystals of test proteins such as thaumatin and glucose isomerase, as well as protein studied in our laboratory such dihydrolipoamide dehydrogenase. Once the solutions were loaded in capillaries, they were stored in the tubes in frozen state at cryogenic temperatures until the desired time of activation of crystallization experiments.

Separation of specular and diffuse components using tensor voting in color images.

PubMed

Nguyen, Tam; Vo, Quang Nhat; Yang, Hyung-Jeong; Kim, Soo-Hyung; Lee, Guee-Sang

2014-11-20

Most methods for the detection and removal of specular reflections suffer from nonuniform highlight regions and/or nonconverged artifacts induced by discontinuities in the surface colors, especially when dealing with highly textured, multicolored images. In this paper, a novel noniterative and predefined constraint-free method based on tensor voting is proposed to detect and remove the highlight components of a single color image. The distribution of diffuse and specular pixels in the original image is determined using tensors' saliency analysis, instead of comparing color information among neighbor pixels. The achieved diffuse reflectance distribution is used to remove specularity components. The proposed method is evaluated quantitatively and qualitatively over a dataset of highly textured, multicolor images. The experimental results show that our result outperforms other state-of-the-art techniques.

Kinetic Monte Carlo Simulation of Oxygen and Cation Diffusion in Yttria-Stabilized Zirconia

NASA Technical Reports Server (NTRS)

Good, Brian

2011-01-01

Yttria-stabilized zirconia (YSZ) is of interest to the aerospace community, notably for its application as a thermal barrier coating for turbine engine components. In such an application, diffusion of both oxygen ions and cations is of concern. Oxygen diffusion can lead to deterioration of a coated part, and often necessitates an environmental barrier coating. Cation diffusion in YSZ is much slower than oxygen diffusion. However, such diffusion is a mechanism by which creep takes place, potentially affecting the mechanical integrity and phase stability of the coating. In other applications, the high oxygen diffusivity of YSZ is useful, and makes the material of interest for use as a solid-state electrolyte in fuel cells. The kinetic Monte Carlo (kMC) method offers a number of advantages compared with the more widely known molecular dynamics simulation method. In particular, kMC is much more efficient for the study of processes, such as diffusion, that involve infrequent events. We describe the results of kinetic Monte Carlo computer simulations of oxygen and cation diffusion in YSZ. Using diffusive energy barriers from ab initio calculations and from the literature, we present results on the temperature dependence of oxygen and cation diffusivity, and on the dependence of the diffusivities on yttria concentration and oxygen sublattice vacancy concentration. We also present results of the effect on diffusivity of oxygen vacancies in the vicinity of the barrier cations that determine the oxygen diffusion energy barriers.

Convection of tin in a Bridgman system. I - Flow characterization by effective diffusivity measurements

NASA Technical Reports Server (NTRS)

Sears, B.; Narayanan, R.; Anderson, T. J.; Fripp, A. L.

1992-01-01

An electrochemical titration method was used to investigate the dynamic states in a cylindrical layer of convecting tin. The liquid tin was contained in a cell, with curved boundaries made of quartz and flat boundaries made of a solid state electrolyte - yttria-stabilized zirconia (YSZ). The electrolyte acted as a window through which a trace amount of oxygen could be pumped in or out by the application of a constant voltage. The concentration at the YSZ interface was monitored by operating the electrochemical cell in the galvanic mode. Experimentally determined effective diffusivities of oxygen were compared with the molecular diffusivity. Dynamic states in the convective flow were thus inferred. Temperature measurements were simultaneously made in order to identify the onset of oscillations from a steady convective regime. The experiments were conducted for two different aspect ratios for various imposed temperature gradients and two different orientations with respect to gravity. Transcritical states were identified and comparison to two-dimensional numerical models were made.

A Luenberger observer for reaction-diffusion models with front position data

NASA Astrophysics Data System (ADS)

Collin, Annabelle; Chapelle, Dominique; Moireau, Philippe

2015-11-01

We propose a Luenberger observer for reaction-diffusion models with propagating front features, and for data associated with the location of the front over time. Such models are considered in various application fields, such as electrophysiology, wild-land fire propagation and tumor growth modeling. Drawing our inspiration from image processing methods, we start by proposing an observer for the eikonal-curvature equation that can be derived from the reaction-diffusion model by an asymptotic expansion. We then carry over this observer to the underlying reaction-diffusion equation by an ;inverse asymptotic analysis;, and we show that the associated correction in the dynamics has a stabilizing effect for the linearized estimation error. We also discuss the extension to joint state-parameter estimation by using the earlier-proposed ROUKF strategy. We then illustrate and assess our proposed observer method with test problems pertaining to electrophysiology modeling, including with a realistic model of cardiac atria. Our numerical trials show that state estimation is directly very effective with the proposed Luenberger observer, while specific strategies are needed to accurately perform parameter estimation - as is usual with Kalman filtering used in a nonlinear setting - and we demonstrate two such successful strategies.

Diffuse-Interface Capturing Methods for Compressible Two-Phase Flows

NASA Astrophysics Data System (ADS)

Saurel, Richard; Pantano, Carlos

2018-01-01

Simulation of compressible flows became a routine activity with the appearance of shock-/contact-capturing methods. These methods can determine all waves, particularly discontinuous ones. However, additional difficulties may appear in two-phase and multimaterial flows due to the abrupt variation of thermodynamic properties across the interfacial region, with discontinuous thermodynamical representations at the interfaces. To overcome this difficulty, researchers have developed augmented systems of governing equations to extend the capturing strategy. These extended systems, reviewed here, are termed diffuse-interface models, because they are designed to compute flow variables correctly in numerically diffused zones surrounding interfaces. In particular, they facilitate coupling the dynamics on both sides of the (diffuse) interfaces and tend to the proper pure fluid-governing equations far from the interfaces. This strategy has become efficient for contact interfaces separating fluids that are governed by different equations of state, in the presence or absence of capillary effects, and with phase change. More sophisticated materials than fluids (e.g., elastic-plastic materials) have been considered as well.

Information Filtering via Heterogeneous Diffusion in Online Bipartite Networks

PubMed Central

Zhang, Fu-Guo; Zeng, An

2015-01-01

The rapid expansion of Internet brings us overwhelming online information, which is impossible for an individual to go through all of it. Therefore, recommender systems were created to help people dig through this abundance of information. In networks composed by users and objects, recommender algorithms based on diffusion have been proven to be one of the best performing methods. Previous works considered the diffusion process from user to object, and from object to user to be equivalent. We show in this work that it is not the case and we improve the quality of the recommendation by taking into account the asymmetrical nature of this process. We apply this idea to modify the state-of-the-art recommendation methods. The simulation results show that the new methods can outperform these existing methods in both recommendation accuracy and diversity. Finally, this modification is checked to be able to improve the recommendation in a realistic case. PMID:26125631

Information Filtering via Heterogeneous Diffusion in Online Bipartite Networks.

PubMed

Zhang, Fu-Guo; Zeng, An

2015-01-01

The rapid expansion of Internet brings us overwhelming online information, which is impossible for an individual to go through all of it. Therefore, recommender systems were created to help people dig through this abundance of information. In networks composed by users and objects, recommender algorithms based on diffusion have been proven to be one of the best performing methods. Previous works considered the diffusion process from user to object, and from object to user to be equivalent. We show in this work that it is not the case and we improve the quality of the recommendation by taking into account the asymmetrical nature of this process. We apply this idea to modify the state-of-the-art recommendation methods. The simulation results show that the new methods can outperform these existing methods in both recommendation accuracy and diversity. Finally, this modification is checked to be able to improve the recommendation in a realistic case.

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

PubMed

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

2014-01-01

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

A reaction-diffusion model of the Darien Gap Sterile Insect Release Method

NASA Astrophysics Data System (ADS)

Alford, John G.

2015-05-01

The Sterile Insect Release Method (SIRM) is used as a biological control for invasive insect species. SIRM involves introducing large quantities of sterilized male insects into a wild population of invading insects. A fertile/sterile mating produces offspring that are not viable and the wild insect population will eventually be eradicated. A U.S. government program maintains a permanent sterile fly barrier zone in the Darien Gap between Panama and Columbia to control the screwworm fly (Cochliomyia Hominivorax), an insect that feeds off of living tissue in mammals and has devastating effects on livestock. This barrier zone is maintained by regular releases of massive quantities of sterilized male screwworm flies from aircraft. We analyze a reaction-diffusion model of the Darien Gap barrier zone. Simulations of the model equations yield two types of spatially inhomogeneous steady-state solutions representing a sterile fly barrier that does not prevent invasion and a barrier that does prevent invasion. We investigate steady-state solutions using both phase plane methods and monotone iteration methods and describe how barrier width and the sterile fly release rate affects steady-state behavior.

Equation-of-motion coupled-cluster method for doubly ionized states with spin-orbit coupling.

PubMed

Wang, Zhifan; Hu, Shu; Wang, Fan; Guo, Jingwei

2015-04-14

In this work, we report implementation of the equation-of-motion coupled-cluster method for doubly ionized states (EOM-DIP-CC) with spin-orbit coupling (SOC) using a closed-shell reference. Double ionization potentials (DIPs) are calculated in the space spanned by 2h and 3h1p determinants with the EOM-DIP-CC approach at the CC singles and doubles level (CCSD). Time-reversal symmetry together with spatial symmetry is exploited to reduce computational effort. To circumvent the problem of unstable dianion references when diffuse basis functions are included, nuclear charges are scaled. Effect of this stabilization potential on DIPs is estimated based on results from calculations using a small basis set without diffuse basis functions. DIPs and excitation energies of some low-lying states for a series of open-shell atoms and molecules containing heavy elements with two unpaired electrons have been calculated with the EOM-DIP-CCSD approach. Results show that this approach is able to afford a reliable description on SOC splitting. Furthermore, the EOM-DIP-CCSD approach is shown to provide reasonable excitation energies for systems with a dianion reference when diffuse basis functions are not employed.

Equation-of-motion coupled-cluster method for doubly ionized states with spin-orbit coupling

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

Wang, Zhifan; Hu, Shu; Guo, Jingwei

2015-04-14

In this work, we report implementation of the equation-of-motion coupled-cluster method for doubly ionized states (EOM-DIP-CC) with spin-orbit coupling (SOC) using a closed-shell reference. Double ionization potentials (DIPs) are calculated in the space spanned by 2h and 3h1p determinants with the EOM-DIP-CC approach at the CC singles and doubles level (CCSD). Time-reversal symmetry together with spatial symmetry is exploited to reduce computational effort. To circumvent the problem of unstable dianion references when diffuse basis functions are included, nuclear charges are scaled. Effect of this stabilization potential on DIPs is estimated based on results from calculations using a small basis setmore » without diffuse basis functions. DIPs and excitation energies of some low-lying states for a series of open-shell atoms and molecules containing heavy elements with two unpaired electrons have been calculated with the EOM-DIP-CCSD approach. Results show that this approach is able to afford a reliable description on SOC splitting. Furthermore, the EOM-DIP-CCSD approach is shown to provide reasonable excitation energies for systems with a dianion reference when diffuse basis functions are not employed.« less

Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

DOE PAGES

Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean -François; ...

2015-06-16

We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion pathsmore » and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. In conclusion, this study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.« less

Detailed study of the water trimer potential energy surface

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

Fowler, J.E.; Schaefer, H.F. III

The potential energy surface of the water trimer has been studied through the use of ab initio quantum mechanical methods. Five stationary points were located, including one minimum and two transition states. All geometries were optimized at levels up to the double-[Zeta] plus polarization plus diffuse (DZP + diff) single and double excitation coupled cluster (CCSD) level of theory. CCSD single energy points were obtained for the minimum, two transition states, and the water monomer using the triple-[Zeta] plus double polarization plus diffuse (TZ2P + diff) basis at the geometries predicted by the DZP + diff CCSD method. Reported aremore » the following: geometrical parameters, total and relative energies, harmonic vibrational frequencies and infrared intensities for the minimum, and zero point vibrational energies for the minimum, two transition states, and three separated water molecules. 27 refs., 5 figs., 10 tabs.« less

Dissemination of the Phasor Method in Electrical Engineering in China

ERIC Educational Resources Information Center

Zhang, Liangliang; Lei, Yinzhao

2014-01-01

Synchrophasors, widely used in the monitoring and analysis of power systems, evolved from the phasor method presented by Charles Proteus Steinmetz in 1893. The phasor method is a mathematical method for solving linear sinusoidal steady-state circuits and time-varying electromagnetic fields. This paper traces the history and diffusion of the phasor…

Numerical Simulation of Transient Liquid Phase Bonding under Temperature Gradient

NASA Astrophysics Data System (ADS)

Ghobadi Bigvand, Arian

Transient Liquid Phase bonding under Temperature Gradient (TG-TLP bonding) is a relatively new process of TLP diffusion bonding family for joining difficult-to-weld aerospace materials. Earlier studies have suggested that in contrast to the conventional TLP bonding process, liquid state diffusion drives joint solidification in TG-TLP bonding process. In the present work, a mass conservative numerical model that considers asymmetry in joint solidification is developed using finite element method to properly study the TG-TLP bonding process. The numerical results, which are experimentally verified, show that unlike what has been previously reported, solid state diffusion plays a major role in controlling the solidification behavior during TG-TLP bonding process. The newly developed model provides a vital tool for further elucidation of the TG-TLP bonding process.

Thermal Diffusivity and Conductivity in Ceramic Matrix Fiber Composite Materials - Literature Study

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

R.G. Quinn

A technical literature review was conducted to gain an understanding of the state of the art method, problems, results, and future of thermal diffusivity/conductivity of matrix-fiber composites for high temperature applications. This paper summarizes the results of test method development and theory. Results from testing on various sample types are discussed with concentration on the anisotropic characteristics of matrix-fiber composites, barriers to heat flow, and notable microstructure observations. The conclusion presents some observations from the technical literature, drawbacks of current information and discusses potential needs for future testing.

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

PubMed

Wu, Wen; Wu, Zhouhu; Song, Zhiwen

2017-07-01

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

An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping.

PubMed

Koh, Wonryull; Blackwell, Kim T

2011-04-21

Stochastic simulation of reaction-diffusion systems enables the investigation of stochastic events arising from the small numbers and heterogeneous distribution of molecular species in biological cells. Stochastic variations in intracellular microdomains and in diffusional gradients play a significant part in the spatiotemporal activity and behavior of cells. Although an exact stochastic simulation that simulates every individual reaction and diffusion event gives a most accurate trajectory of the system's state over time, it can be too slow for many practical applications. We present an accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems designed to improve the speed of simulation by reducing the number of time-steps required to complete a simulation run. This method is unique in that it employs two strategies that have not been incorporated in existing spatial stochastic simulation algorithms. First, diffusive transfers between neighboring subvolumes are based on concentration gradients. This treatment necessitates sampling of only the net or observed diffusion events from higher to lower concentration gradients rather than sampling all diffusion events regardless of local concentration gradients. Second, we extend the non-negative Poisson tau-leaping method that was originally developed for speeding up nonspatial or homogeneous stochastic simulation algorithms. This method calculates each leap time in a unified step for both reaction and diffusion processes while satisfying the leap condition that the propensities do not change appreciably during the leap and ensuring that leaping does not cause molecular populations to become negative. Numerical results are presented that illustrate the improvement in simulation speed achieved by incorporating these two new strategies.

Analysis of Classes of Singular Steady State Reaction Diffusion Equations

NASA Astrophysics Data System (ADS)

Son, Byungjae

We study positive radial solutions to classes of steady state reaction diffusion problems on the exterior of a ball with both Dirichlet and nonlinear boundary conditions. We study both Laplacian as well as p-Laplacian problems with reaction terms that are p-sublinear at infinity. We consider both positone and semipositone reaction terms and establish existence, multiplicity and uniqueness results. Our existence and multiplicity results are achieved by a method of sub-supersolutions and uniqueness results via a combination of maximum principles, comparison principles, energy arguments and a-priori estimates. Our results significantly enhance the literature on p-sublinear positone and semipositone problems. Finally, we provide exact bifurcation curves for several one-dimensional problems. In the autonomous case, we extend and analyze a quadrature method, and in the nonautonomous case, we employ shooting methods. We use numerical solvers in Mathematica to generate the bifurcation curves.

Stochastic modelling of intermittency.

PubMed

Stemler, Thomas; Werner, Johannes P; Benner, Hartmut; Just, Wolfram

2010-01-13

Recently, methods have been developed to model low-dimensional chaotic systems in terms of stochastic differential equations. We tested such methods in an electronic circuit experiment. We aimed to obtain reliable drift and diffusion coefficients even without a pronounced time-scale separation of the chaotic dynamics. By comparing the analytical solutions of the corresponding Fokker-Planck equation with experimental data, we show here that crisis-induced intermittency can be described in terms of a stochastic model which is dominated by state-space-dependent diffusion. Further on, we demonstrate and discuss some limits of these modelling approaches using numerical simulations. This enables us to state a criterion that can be used to decide whether a stochastic model will capture the essential features of a given time series. This journal is © 2010 The Royal Society

Non-Markovian Quantum State Diffusion for temperature-dependent linear spectra of light harvesting aggregates

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

Ritschel, Gerhard; Möbius, Sebastian; Eisfeld, Alexander, E-mail: eisfeld@mpipks-dresden.mpg.de

2015-01-21

Non-Markovian Quantum State Diffusion (NMQSD) has turned out to be an efficient method to calculate excitonic properties of aggregates composed of organic chromophores, taking into account the coupling of electronic transitions to vibrational modes of the chromophores. NMQSD is an open quantum system approach that incorporates environmental degrees of freedom (the vibrations in our case) in a stochastic way. We show in this paper that for linear optical spectra (absorption, circular dichroism), no stochastics is needed, even for finite temperatures. Thus, the spectra can be obtained by propagating a single trajectory. To this end, we map a finite temperature environmentmore » to the zero temperature case using the so-called thermofield method. The resulting equations can then be solved efficiently by standard integrators.« less

A computational kinetic model of diffusion for molecular systems.

PubMed

Teo, Ivan; Schulten, Klaus

2013-09-28

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

Laboratory longitudinal diffusion tests: 1. Dimensionless formulations and validity of simplified solutions

NASA Astrophysics Data System (ADS)

Takeda, M.; Nakajima, H.; Zhang, M.; Hiratsuka, T.

2008-04-01

To obtain reliable diffusion parameters for diffusion testing, multiple experiments should not only be cross-checked but the internal consistency of each experiment should also be verified. In the through- and in-diffusion tests with solution reservoirs, test interpretation of different phases often makes use of simplified analytical solutions. This study explores the feasibility of steady, quasi-steady, equilibrium and transient-state analyses using simplified analytical solutions with respect to (i) valid conditions for each analytical solution, (ii) potential error, and (iii) experimental time. For increased generality, a series of numerical analyses are performed using unified dimensionless parameters and the results are all related to dimensionless reservoir volume (DRV) which includes only the sorptive parameter as an unknown. This means the above factors can be investigated on the basis of the sorption properties of the testing material and/or tracer. The main findings are that steady, quasi-steady and equilibrium-state analyses are applicable when the tracer is not highly sorptive. However, quasi-steady and equilibrium-state analyses become inefficient or impractical compared to steady state analysis when the tracer is non-sorbing and material porosity is significantly low. Systematic and comprehensive reformulation of analytical models enables the comparison of experimental times between different test methods. The applicability and potential error of each test interpretation can also be studied. These can be applied in designing, performing, and interpreting diffusion experiments by deducing DRV from the available information for the target material and tracer, combined with the results of this study.

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.

Molecular dynamics simulations of hydrogen diffusion in aluminum

DOE PAGES

Zhou, X. W.; El Gabaly, F.; Stavila, V.; ...

2016-03-23

In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

Simulation studies of chemical erosion on carbon based materials at elevated temperatures

NASA Astrophysics Data System (ADS)

Kenmotsu, T.; Kawamura, T.; Li, Zhijie; Ono, T.; Yamamura, Y.

1999-06-01

We simulated the fluence dependence of methane reaction yield in carbon with hydrogen bombardment using the ACAT-DIFFUSE code. The ACAT-DIFFUSE code is a simulation code based on a Monte Carlo method with a binary collision approximation and on solving diffusion equations. The chemical reaction model in carbon was studied by Roth or other researchers. Roth's model is suitable for the steady state methane reaction. But this model cannot estimate the fluence dependence of the methane reaction. Then, we derived an empirical formula based on Roth's model for methane reaction. In this empirical formula, we assumed the reaction region where chemical sputtering due to methane formation takes place. The reaction region corresponds to the peak range of incident hydrogen distribution in the target material. We adopted this empirical formula to the ACAT-DIFFUSE code. The simulation results indicate the similar fluence dependence compared with the experiment result. But, the fluence to achieve the steady state are different between experiment and simulation results.

A diffuse-interface method for two-phase flows with soluble surfactants

PubMed Central

Teigen, Knut Erik; Song, Peng; Lowengrub, John; Voigt, Axel

2010-01-01

A method is presented to solve two-phase problems involving soluble surfactants. The incompressible Navier–Stokes equations are solved along with equations for the bulk and interfacial surfactant concentrations. A non-linear equation of state is used to relate the surface tension to the interfacial surfactant concentration. The method is based on the use of a diffuse interface, which allows a simple implementation using standard finite difference or finite element techniques. Here, finite difference methods on a block-structured adaptive grid are used, and the resulting equations are solved using a non-linear multigrid method. Results are presented for a drop in shear flow in both 2D and 3D, and the effect of solubility is discussed. PMID:21218125

One step linear reconstruction method for continuous wave diffuse optical tomography

NASA Astrophysics Data System (ADS)

Ukhrowiyah, N.; Yasin, M.

2017-09-01

The method one step linear reconstruction method for continuous wave diffuse optical tomography is proposed and demonstrated for polyvinyl chloride based material and breast phantom. Approximation which used in this method is selecting regulation coefficient and evaluating the difference between two states that corresponding to the data acquired without and with a change in optical properties. This method is used to recovery of optical parameters from measured boundary data of light propagation in the object. The research is demonstrated by simulation and experimental data. Numerical object is used to produce simulation data. Chloride based material and breast phantom sample is used to produce experimental data. Comparisons of results between experiment and simulation data are conducted to validate the proposed method. The results of the reconstruction image which is produced by the one step linear reconstruction method show that the image reconstruction almost same as the original object. This approach provides a means of imaging that is sensitive to changes in optical properties, which may be particularly useful for functional imaging used continuous wave diffuse optical tomography of early diagnosis of breast cancer.

[Monitoring of extra- and intra-cellular compartment through total body impedance (author's transl)].

PubMed

Raggueneau, J L; Gambini, D; Levante, A; Riche, F; de Vernejoul, P; Echter, E

1979-01-01

To evaluate the extra-cellular space, we measure the impedance (or resistance) of the extra-cellular electrolyte compartment with an alternating current at a fixed frequency of 5 kHz that can't pass through the cellular membrane. Total water is measured by the impedance to a current of 1 MHz which is conducted by extra and intra cellular hydro-electrolytic space. There is a good correlation between electrical impedance measurements and distribution of isotopic markers. The extra-cellular compartment was evaluated by diffusion of D.T.P.A. marked with 99mTc or with 111In and the total water by the diffusion of Antipyrin marked with 1,311 or 1,231. The findings indicate that there is not a significant difference between the results of the size of extra-cellular water measured by electrical impedance and D.T.P.A. diffusion (r = 0.75). Comparable results have been obtained in the determination of total water by electrical impedance measure and diffusion of Antipyrin (r = 0.90). We have also studied by method of electric impedance:--The state of hydratation in head injured patients and after pituitary surgery.--The lean body mass and hydro-electrolyte compartments in pregnancy. Electrical impedance measure seems to be a simple and reliable method to assess the hydric state of patients.

Diffusion in quasi-one-dimensional channels: A small system n, p, T, transition state theory for hopping times.

PubMed

Ahmadi, Sheida; Bowles, Richard K

2017-04-21

Particles confined to a single file, in a narrow quasi-one-dimensional channel, exhibit a dynamic crossover from single file diffusion to Fickian diffusion as the channel radius increases and the particles begin to pass each other. The long time diffusion coefficient for a system in the crossover regime can be described in terms of a hopping time, which measures the time it takes for a particle to escape the cage formed by its neighbours. In this paper, we develop a transition state theory approach to the calculation of the hopping time, using the small system isobaric-isothermal ensemble to rigorously account for the volume fluctuations associated with the size of the cage. We also describe a Monte Carlo simulation scheme that can be used to calculate the free energy barrier for particle hopping. The theory and simulation method correctly predict the hopping times for a two-dimensional confined ideal gas system and a system of confined hard discs over a range of channel radii, but the method breaks down for wide channels in the hard discs' case, underestimating the height of the hopping barrier due to the neglect of interactions between the small system and its surroundings.

Intensification of the Process of Flame Combustion of a Pulverized Coal Fuel

NASA Astrophysics Data System (ADS)

Popov, V. I.

2017-11-01

Consideration is given to a method of mechanoactivation intensification of the flame combustion of a pulverized coal fuel through the formation of a stressed state for the microstructure of its particles; the method is based on the use of the regularities of their external (diffusion) and internal (relaxation) kinetics. A study has been made of mechanoactivation nonequilibrium processes that occur in fuel particles during the induced relaxation of their stressed state with a resumed mobility of the microstructure of the particles and intensify diffusion-controlled chemical reactions in them under the assumption that the time of these reactions is much shorter than the times of mechanical action on a particle and of stress relaxation in it. The influence of the diffusion and relaxation factors on the burnup time of a fuel particle and on the flame distance has been analyzed. Ranges of variation in the parameters of flame combustion have been singled out in which the flame distance is determined by the mechanisms of combustion of the fuel and of mixing of combustion products.

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

PubMed

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

2016-05-01

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

Morphological inversion of complex diffusion

NASA Astrophysics Data System (ADS)

Nguyen, V. A. T.; Vural, D. C.

2017-09-01

Epidemics, neural cascades, power failures, and many other phenomena can be described by a diffusion process on a network. To identify the causal origins of a spread, it is often necessary to identify the triggering initial node. Here, we define a new morphological operator and use it to detect the origin of a diffusive front, given the final state of a complex network. Our method performs better than algorithms based on distance (closeness) and Jordan centrality. More importantly, our method is applicable regardless of the specifics of the forward model, and therefore can be applied to a wide range of systems such as identifying the patient zero in an epidemic, pinpointing the neuron that triggers a cascade, identifying the original malfunction that causes a catastrophic infrastructure failure, and inferring the ancestral species from which a heterogeneous population evolves.

A Numerical Method for the Simulation of Skew Brownian Motion and its Application to Diffusive Shock Acceleration of Charged Particles

NASA Astrophysics Data System (ADS)

McEvoy, Erica L.

Stochastic differential equations are becoming a popular tool for modeling the transport and acceleration of cosmic rays in the heliosphere. In diffusive shock acceleration, cosmic rays diffuse across a region of discontinuity where the up- stream diffusion coefficient abruptly changes to the downstream value. Because the method of stochastic integration has not yet been developed to handle these types of discontinuities, I utilize methods and ideas from probability theory to develop a conceptual framework for the treatment of such discontinuities. Using this framework, I then produce some simple numerical algorithms that allow one to incorporate and simulate a variety of discontinuities (or boundary conditions) using stochastic integration. These algorithms were then modified to create a new algorithm which incorporates the discontinuous change in diffusion coefficient found in shock acceleration (known as Skew Brownian Motion). The originality of this algorithm lies in the fact that it is the first of its kind to be statistically exact, so that one obtains accuracy without the use of approximations (other than the machine precision error). I then apply this algorithm to model the problem of diffusive shock acceleration, modifying it to incorporate the additional effect of the discontinuous flow speed profile found at the shock. A steady-state solution is obtained that accurately simulates this phenomenon. This result represents a significant improvement over previous approximation algorithms, and will be useful for the simulation of discontinuous diffusion processes in other fields, such as biology and finance.

Probabilistic-driven oriented Speckle reducing anisotropic diffusion with application to cardiac ultrasonic images.

PubMed

Vegas-Sanchez-Ferrero, G; Aja-Fernandez, S; Martin-Fernandez, M; Frangi, A F; Palencia, C

2010-01-01

A novel anisotropic diffusion filter is proposed in this work with application to cardiac ultrasonic images. It includes probabilistic models which describe the probability density function (PDF) of tissues and adapts the diffusion tensor to the image iteratively. For this purpose, a preliminary study is performed in order to select the probability models that best fit the stastitical behavior of each tissue class in cardiac ultrasonic images. Then, the parameters of the diffusion tensor are defined taking into account the statistical properties of the image at each voxel. When the structure tensor of the probability of belonging to each tissue is included in the diffusion tensor definition, a better boundaries estimates can be obtained instead of calculating directly the boundaries from the image. This is the main contribution of this work. Additionally, the proposed method follows the statistical properties of the image in each iteration. This is considered as a second contribution since state-of-the-art methods suppose that noise or statistical properties of the image do not change during the filter process.

Modification of anisotropic plasma diffusion via auxiliary electrons emitted by a carbon nanotubes-based electron gun in an electron cyclotron resonance ion source.

PubMed

Malferrari, L; Odorici, F; Veronese, G P; Rizzoli, R; Mascali, D; Celona, L; Gammino, S; Castro, G; Miracoli, R; Serafino, T

2012-02-01

The diffusion mechanism in magnetized plasmas is a largely debated issue. A short circuit model was proposed by Simon, assuming fluxes of lost particles along the axial (electrons) and radial (ions) directions which can be compensated, to preserve the quasi-neutrality, by currents flowing throughout the conducting plasma chamber walls. We hereby propose a new method to modify Simon's currents via electrons injected by a carbon nanotubes-based electron gun. We found this improves the source performances, increasing the output current for several charge states. The method is especially sensitive to the pumping frequency. Output currents for given charge states, at different auxiliary electron currents, will be reported in the paper and the influence of the frequency tuning on the compensation mechanism will be discussed.

Stochastic modeling of experimental chaotic time series.

PubMed

Stemler, Thomas; Werner, Johannes P; Benner, Hartmut; Just, Wolfram

2007-01-26

Methods developed recently to obtain stochastic models of low-dimensional chaotic systems are tested in electronic circuit experiments. We demonstrate that reliable drift and diffusion coefficients can be obtained even when no excessive time scale separation occurs. Crisis induced intermittent motion can be described in terms of a stochastic model showing tunneling which is dominated by state space dependent diffusion. Analytical solutions of the corresponding Fokker-Planck equation are in excellent agreement with experimental data.

Diffusion of Complete Streets policies Across US communities.

PubMed

Moreland-Russell, Sarah; Eyler, Amy; Barbero, Colleen; Hipp, J Aaron; Walsh, Heidi

2013-01-01

Complete Streets policies guide planning in communities by making the transportation system accommodating to all users including vehicle drivers, pedestrians, and bicyclists, as well as those using public transportation. While the number of Complete Streets policies has increased over the past decade, no research has explored the factors attributing to the widespread diffusion of these policies. The purpose of this study was to apply concepts of the Diffusion of Innovation Theory to data related to Complete Streets policies in order to identify potential patterns and correlates. The main outcome of this study was policy adoption. Using the Diffusion of Innovation Theory and results from previous literature, we identified several factors that had the potential to affect the rate of Complete Streets policy diffusion: rural/urban status, state obesity rate, state funding for transportation, state obesity prevention funding, percentage of people who walk or bike to work in the state, presence of a state Complete Streets policy, and the number of bordering communities with Complete Streets policy. We used event history analysis as the main analysis method. Data from 49 community-level policies were analyzed, with a "community" defined as a city, a county, or a regional/Metropolitan Planning Organization. Three variables were significant predictors of Complete Streets policy adoption: state obesity rate (odds ratio [OR] = 1.465; confidence interval [CI] = 1.10-1.96) percentage of people who bike or walk to work in the state (OR = 1.726; CI = 1.069-2.79), and presence of a border community with a Complete Streets policy (OR = 3.859; CI = 1.084-13.742). Communities with Complete Streets policies varied in geographic and sociodemographic factors. Information about communities that are more likely to adopt a policy can be a tool for advocates and policy makers interested in this topic. Because adoption does not imply implementation, further research is needed to study outcomes of Complete Streets policies.

Large-scale optimization-based non-negative computational framework for diffusion equations: Parallel implementation and performance studies

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

Chang, Justin; Karra, Satish; Nakshatrala, Kalyana B.

It is well-known that the standard Galerkin formulation, which is often the formulation of choice under the finite element method for solving self-adjoint diffusion equations, does not meet maximum principles and the non-negative constraint for anisotropic diffusion equations. Recently, optimization-based methodologies that satisfy maximum principles and the non-negative constraint for steady-state and transient diffusion-type equations have been proposed. To date, these methodologies have been tested only on small-scale academic problems. The purpose of this paper is to systematically study the performance of the non-negative methodology in the context of high performance computing (HPC). PETSc and TAO libraries are, respectively, usedmore » for the parallel environment and optimization solvers. For large-scale problems, it is important for computational scientists to understand the computational performance of current algorithms available in these scientific libraries. The numerical experiments are conducted on the state-of-the-art HPC systems, and a single-core performance model is used to better characterize the efficiency of the solvers. Furthermore, our studies indicate that the proposed non-negative computational framework for diffusion-type equations exhibits excellent strong scaling for real-world large-scale problems.« less

Large-scale optimization-based non-negative computational framework for diffusion equations: Parallel implementation and performance studies

DOE PAGES

Chang, Justin; Karra, Satish; Nakshatrala, Kalyana B.

2016-07-26

It is well-known that the standard Galerkin formulation, which is often the formulation of choice under the finite element method for solving self-adjoint diffusion equations, does not meet maximum principles and the non-negative constraint for anisotropic diffusion equations. Recently, optimization-based methodologies that satisfy maximum principles and the non-negative constraint for steady-state and transient diffusion-type equations have been proposed. To date, these methodologies have been tested only on small-scale academic problems. The purpose of this paper is to systematically study the performance of the non-negative methodology in the context of high performance computing (HPC). PETSc and TAO libraries are, respectively, usedmore » for the parallel environment and optimization solvers. For large-scale problems, it is important for computational scientists to understand the computational performance of current algorithms available in these scientific libraries. The numerical experiments are conducted on the state-of-the-art HPC systems, and a single-core performance model is used to better characterize the efficiency of the solvers. Furthermore, our studies indicate that the proposed non-negative computational framework for diffusion-type equations exhibits excellent strong scaling for real-world large-scale problems.« less

A mathematical modeling method for determination of local vibroacoustic characteristics of structures

NASA Technical Reports Server (NTRS)

Tartakovskiy, B. D.; Dubner, A. B.

1973-01-01

A method is proposed for determining vibroacoustic characteristics from the results of measurements of the distribution of vibrational energy in a structure. The method is based on an energy model of a structure studied earlier. Equations are written to describe the distribution of vibrational energy in a hypothetical diffuse energy state in structural elements.

A comparative analysis of clustering algorithms: O{sub 2} migration in truncated hemoglobin I from transition networks

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

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus, E-mail: m.meuwly@unibas.ch

2015-01-14

The ligand migration network for O{sub 2}–diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k–means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of themore » major differences between k–means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.« less

A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.

PubMed

Cazade, Pierre-André; Zheng, Wenwei; Prada-Gracia, Diego; Berezovska, Ganna; Rao, Francesco; Clementi, Cecilia; Meuwly, Markus

2015-01-14

The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k-means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.

Reduction of numerical diffusion in three-dimensional vortical flows using a coupled Eulerian/Lagrangian solution procedure

NASA Technical Reports Server (NTRS)

Felici, Helene M.; Drela, Mark

1993-01-01

A new approach based on the coupling of an Eulerian and a Lagrangian solver, aimed at reducing the numerical diffusion errors of standard Eulerian time-marching finite-volume solvers, is presented. The approach is applied to the computation of the secondary flow in two bent pipes and the flow around a 3D wing. Using convective point markers the Lagrangian approach provides a correction of the basic Eulerian solution. The Eulerian flow in turn integrates in time the Lagrangian state-vector. A comparison of coarse and fine grid Eulerian solutions makes it possible to identify numerical diffusion. It is shown that the Eulerian/Lagrangian approach is an effective method for reducing numerical diffusion errors.

Comparison of diffusion length measurements from the Flying Spot Technique and the photocarrier grating method in amorphous thin films

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

Vieira, M.; Fantoni, A.; Martins, R.

1994-12-31

Using the Flying Spot Technique (FST) the authors have studied minority carrier transport parallel and perpendicular to the surface of amorphous silicon films (a-Si:H). To reduce slow transients due to charge redistribution in low resistivity regions during the measurement they have applied a strong homogeneously absorbed bias light. The defect density was estimated from Constant Photocurrent Method (CPM) measurements. The steady-state photocarrier grating technique (SSPG) is a 1-dimensional approach. However, the modulation depth of the carrier profile is also dependent on film surface properties, like surface recombination velocity. Both methods yield comparable diffusion lengths when applied to a-Si:H.

The calculation of transport properties in quantum liquids using the maximum entropy numerical analytic continuation method: Application to liquid para-hydrogen

PubMed Central

Rabani, Eran; Reichman, David R.; Krilov, Goran; Berne, Bruce J.

2002-01-01

We present a method based on augmenting an exact relation between a frequency-dependent diffusion constant and the imaginary time velocity autocorrelation function, combined with the maximum entropy numerical analytic continuation approach to study transport properties in quantum liquids. The method is applied to the case of liquid para-hydrogen at two thermodynamic state points: a liquid near the triple point and a high-temperature liquid. Good agreement for the self-diffusion constant and for the real-time velocity autocorrelation function is obtained in comparison to experimental measurements and other theoretical predictions. Improvement of the methodology and future applications are discussed. PMID:11830656

Fast non-overlapping Schwarz domain decomposition methods for solving the neutron diffusion equation

NASA Astrophysics Data System (ADS)

Jamelot, Erell; Ciarlet, Patrick

2013-05-01

Studying numerically the steady state of a nuclear core reactor is expensive, in terms of memory storage and computational time. In order to address both requirements, one can use a domain decomposition method, implemented on a parallel computer. We present here such a method for the mixed neutron diffusion equations, discretized with Raviart-Thomas-Nédélec finite elements. This method is based on the Schwarz iterative algorithm with Robin interface conditions to handle communications. We analyse this method from the continuous point of view to the discrete point of view, and we give some numerical results in a realistic highly heterogeneous 3D configuration. Computations are carried out with the MINOS solver of the APOLLO3® neutronics code. APOLLO3 is a registered trademark in France.

Fast and Accurate Poisson Denoising With Trainable Nonlinear Diffusion.

PubMed

Feng, Wensen; Qiao, Peng; Chen, Yunjin; Wensen Feng; Peng Qiao; Yunjin Chen; Feng, Wensen; Chen, Yunjin; Qiao, Peng

2018-06-01

The degradation of the acquired signal by Poisson noise is a common problem for various imaging applications, such as medical imaging, night vision, and microscopy. Up to now, many state-of-the-art Poisson denoising techniques mainly concentrate on achieving utmost performance, with little consideration for the computation efficiency. Therefore, in this paper we aim to propose an efficient Poisson denoising model with both high computational efficiency and recovery quality. To this end, we exploit the newly developed trainable nonlinear reaction diffusion (TNRD) model which has proven an extremely fast image restoration approach with performance surpassing recent state-of-the-arts. However, the straightforward direct gradient descent employed in the original TNRD-based denoising task is not applicable in this paper. To solve this problem, we resort to the proximal gradient descent method. We retrain the model parameters, including the linear filters and influence functions by taking into account the Poisson noise statistics, and end up with a well-trained nonlinear diffusion model specialized for Poisson denoising. The trained model provides strongly competitive results against state-of-the-art approaches, meanwhile bearing the properties of simple structure and high efficiency. Furthermore, our proposed model comes along with an additional advantage, that the diffusion process is well-suited for parallel computation on graphics processing units (GPUs). For images of size , our GPU implementation takes less than 0.1 s to produce state-of-the-art Poisson denoising performance.

Analysis of a nanocrystalline polymer dispersion of ebselen using solid-state NMR, Raman microscopy, and powder X-ray diffraction.

PubMed

Vogt, Frederick G; Williams, Glenn R

2012-07-01

Nanocrystalline drug-polymer dispersions are of significant interest in pharmaceutical delivery. The purpose of this work is to demonstrate the applicability of methods based on two-dimensional (2D) and multinuclear solid-state NMR (SSNMR) to a novel nanocrystalline pharmaceutical dispersion of ebselen with polyvinylpyrrolidone-vinyl acetate (PVP-VA), after initial characterization with other techniques. A nanocrystalline dispersion of ebselen with PVP-VA was prepared and characterized by powder X-ray diffraction (PXRD), confocal Raman microscopy and mapping, and differential scanning calorimetry (DSC), and then subjected to detailed 1D and 2D SSNMR analysis involving ¹H, ¹³C, and ⁷⁷Se isotopes and ¹H spin diffusion. PXRD was used to show that dispersion contains nanocrystalline ebselen in the 35-60 nm size range. Confocal Raman microscopy and spectral mapping were able to detect regions where short-range interactions may occur between ebselen and PVP-VA. Spin diffusion effects were analyzed using 2D SSNMR experiments and are able to directly detect interactions between ebselen and the surrounding PVP-VA. The methods used here, particularly the 2D SSNMR methods based on spin diffusion, provided detailed structural information about a nanocrystalline polymer dispersion of ebselen, and should be useful in other studies of these types of materials.

Evaluation of glymphatic system activity with the diffusion MR technique: diffusion tensor image analysis along the perivascular space (DTI-ALPS) in Alzheimer's disease cases.

PubMed

Taoka, Toshiaki; Masutani, Yoshitaka; Kawai, Hisashi; Nakane, Toshiki; Matsuoka, Kiwamu; Yasuno, Fumihiko; Kishimoto, Toshifumi; Naganawa, Shinji

2017-04-01

The activity of the glymphatic system is impaired in animal models of Alzheimer's disease (AD). We evaluated the activity of the human glymphatic system in cases of AD with a diffusion-based technique called diffusion tensor image analysis along the perivascular space (DTI-ALPS). Diffusion tensor images were acquired to calculate diffusivities in the x, y, and z axes of the plane of the lateral ventricle body in 31 patients. We evaluated the diffusivity along the perivascular spaces as well as projection fibers and association fibers separately, to acquire an index for diffusivity along the perivascular space (ALPS-index) and correlated them with the mini mental state examinations (MMSE) score. We found a significant negative correlation between diffusivity along the projection fibers and association fibers. We also observed a significant positive correlation between diffusivity along perivascular spaces shown as ALPS-index and the MMSE score, indicating lower water diffusivity along the perivascular space in relation to AD severity. Activity of the glymphatic system may be evaluated with diffusion images. Lower diffusivity along the perivascular space on DTI-APLS seems to reflect impairment of the glymphatic system. This method may be useful for evaluating the activity of the glymphatic system.

Isolation and characterization of potential antibiotic producing actinomycetes from water and sediments of Lake Tana, Ethiopia

PubMed Central

Gebreyohannes, Gebreselema; Moges, Feleke; Sahile, Samuel; Raja, Nagappan

2013-01-01

Objective To isolate, evaluate and characterize potential antibiotic producing actinomycetes from water and sediments of Lake Tana, Ethiopia. Methods A total of 31 strains of actinomycetes were isolated and tested against Gram positive and Gram negative bacterial strains by primary screening. In the primary screening, 11 promising isolates were identified and subjected to solid state and submerged state fermentation methods to produce crude extracts. The fermented biomass was extracted by organic solvent extraction method and tested against bacterial strains by disc and agar well diffusion methods. The isolates were characterized by using morphological, physiological and biochemical methods. Results The result obtained from agar well diffusion method was better than disc diffusion method. The crude extract showed higher inhibition zone against Gram positive bacteria than Gram negative bacteria. One-way analysis of variance confirmed most of the crude extracts were statistically significant at 95% confidence interval. The minimum inhibitory concentration and minimum bactericidal concentration of crude extracts were 1.65 mg/mL and 3.30 mg/mL against Staphylococcus aureus, and 1.84 mg/mL and 3.80 mg/mL against Escherichia coli respectively. The growth of aerial and substrate mycelium varied in different culture media used. Most of the isolates were able to hydrolysis starch and urea; able to survive at 5% concentration of sodium chloride; optimum temperature for their growth was 30 °C. Conclusions The results of the present study revealed that freshwater actinomycetes of Lake Tana appear to have immense potential as a source of antibacterial compounds. PMID:23730554

Accurate, meshless methods for magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.; Raives, Matthias J.

2016-01-01

Recently, we explored new meshless finite-volume Lagrangian methods for hydrodynamics: the `meshless finite mass' (MFM) and `meshless finite volume' (MFV) methods; these capture advantages of both smoothed particle hydrodynamics (SPH) and adaptive mesh refinement (AMR) schemes. We extend these to include ideal magnetohydrodynamics (MHD). The MHD equations are second-order consistent and conservative. We augment these with a divergence-cleaning scheme, which maintains nabla \\cdot B≈ 0. We implement these in the code GIZMO, together with state-of-the-art SPH MHD. We consider a large test suite, and show that on all problems the new methods are competitive with AMR using constrained transport (CT) to ensure nabla \\cdot B=0. They correctly capture the growth/structure of the magnetorotational instability, MHD turbulence, and launching of magnetic jets, in some cases converging more rapidly than state-of-the-art AMR. Compared to SPH, the MFM/MFV methods exhibit convergence at fixed neighbour number, sharp shock-capturing, and dramatically reduced noise, divergence errors, and diffusion. Still, `modern' SPH can handle most test problems, at the cost of larger kernels and `by hand' adjustment of artificial diffusion. Compared to non-moving meshes, the new methods exhibit enhanced `grid noise' but reduced advection errors and diffusion, easily include self-gravity, and feature velocity-independent errors and superior angular momentum conservation. They converge more slowly on some problems (smooth, slow-moving flows), but more rapidly on others (involving advection/rotation). In all cases, we show divergence control beyond the Powell 8-wave approach is necessary, or all methods can converge to unphysical answers even at high resolution.

Distribution of randomly diffusing particles in inhomogeneous media

NASA Astrophysics Data System (ADS)

Li, Yiwei; Kahraman, Osman; Haselwandter, Christoph A.

2017-09-01

Diffusion can be conceptualized, at microscopic scales, as the random hopping of particles between neighboring lattice sites. In the case of diffusion in inhomogeneous media, distinct spatial domains in the system may yield distinct particle hopping rates. Starting from the master equations (MEs) governing diffusion in inhomogeneous media we derive here, for arbitrary spatial dimensions, the deterministic lattice equations (DLEs) specifying the average particle number at each lattice site for randomly diffusing particles in inhomogeneous media. We consider the case of free (Fickian) diffusion with no steric constraints on the maximum particle number per lattice site as well as the case of diffusion under steric constraints imposing a maximum particle concentration. We find, for both transient and asymptotic regimes, excellent agreement between the DLEs and kinetic Monte Carlo simulations of the MEs. The DLEs provide a computationally efficient method for predicting the (average) distribution of randomly diffusing particles in inhomogeneous media, with the number of DLEs associated with a given system being independent of the number of particles in the system. From the DLEs we obtain general analytic expressions for the steady-state particle distributions for free diffusion and, in special cases, diffusion under steric constraints in inhomogeneous media. We find that, in the steady state of the system, the average fraction of particles in a given domain is independent of most system properties, such as the arrangement and shape of domains, and only depends on the number of lattice sites in each domain, the particle hopping rates, the number of distinct particle species in the system, and the total number of particles of each particle species in the system. Our results provide general insights into the role of spatially inhomogeneous particle hopping rates in setting the particle distributions in inhomogeneous media.

Nonlinear optical susceptibilities in the diffusion modified AlxGa1-xN/GaN single quantum well

NASA Astrophysics Data System (ADS)

Das, T.; Panda, S.; Panda, B. K.

2018-05-01

Under thermal treatment of the post growth AlGaN/GaN single quantum well, the diffusion of Al and Ga atoms across the interface is expected to form the diffusion modified quantum well with diffusion length as a quantitative parameter for diffusion. The modification of confining potential and position-dependent effective mass in the quantum well due to diffusion is calculated taking the Fick's law. The built-in electric field which arises from spontaneous and piezoelectric polarizations in the wurtzite structure is included in the effective mass equation. The electronic states are calculated from the effective mass equation using the finite difference method for several diffusion lengths. Since the effective well width decreases with increasing diffusion length, the energy levels increase with it. The intersubband energy spacing in the conduction band decreases with diffusion length due to built-in electric field and reduction of effective well width. The linear susceptibility for first-order and the nonlinear second-order and third-order susceptibilities are calculated using the compact density matrix approach taking only two levels. The calculated susceptibilities are red shifted with increase in diffusion lengths due to decrease in intersubband energy spacing.

Information filtering via preferential diffusion.

PubMed

Lü, Linyuan; Liu, Weiping

2011-06-01

Recommender systems have shown great potential in addressing the information overload problem, namely helping users in finding interesting and relevant objects within a huge information space. Some physical dynamics, including the heat conduction process and mass or energy diffusion on networks, have recently found applications in personalized recommendation. Most of the previous studies focus overwhelmingly on recommendation accuracy as the only important factor, while overlooking the significance of diversity and novelty that indeed provide the vitality of the system. In this paper, we propose a recommendation algorithm based on the preferential diffusion process on a user-object bipartite network. Numerical analyses on two benchmark data sets, MovieLens and Netflix, indicate that our method outperforms the state-of-the-art methods. Specifically, it can not only provide more accurate recommendations, but also generate more diverse and novel recommendations by accurately recommending unpopular objects.

Information filtering via preferential diffusion

NASA Astrophysics Data System (ADS)

Lü, Linyuan; Liu, Weiping

2011-06-01

Recommender systems have shown great potential in addressing the information overload problem, namely helping users in finding interesting and relevant objects within a huge information space. Some physical dynamics, including the heat conduction process and mass or energy diffusion on networks, have recently found applications in personalized recommendation. Most of the previous studies focus overwhelmingly on recommendation accuracy as the only important factor, while overlooking the significance of diversity and novelty that indeed provide the vitality of the system. In this paper, we propose a recommendation algorithm based on the preferential diffusion process on a user-object bipartite network. Numerical analyses on two benchmark data sets, MovieLens and Netflix, indicate that our method outperforms the state-of-the-art methods. Specifically, it can not only provide more accurate recommendations, but also generate more diverse and novel recommendations by accurately recommending unpopular objects.

Analysis of charge transport in gels containing polyoxometallates using methods of different sensitivity to migration.

PubMed

Caban, Karolina; Lewera, Adam; Zukowska, Grazyna Z; Kulesza, Pawel J; Stojek, Zbigniew; Jeffrey, Kenneth R

2006-08-04

Two methods have been used for examination of transport of charge in gels soaked with DMF and containing dissolved polyoxometallates. The first method is based on the analysis of both Cottrellian and steady-state currents and therefore is capable of giving the concentration of the electroactive redox centres and their transport (diffusion-type) coefficient. The second method provides the real diffusion coefficients, i.e. transport coefficients free of migrational influence, for both the substrate and the product of the electrode reaction. Several gels based on poly(methyl methacrylate), with charged (addition of 1-acrylamido-2-methyl-2-propanesulphonic acid to the polymerization mixture) and uncharged chains, have been used in the investigation. The ratio obtained for the diffusion coefficient (second method) and transport coefficient (first method) was smaller for the gels containing charged polymer chains than for the gels with uncharged chains. In part these changes could be explained by the contribution of migration to the transport of polyoxomatallates in the gels. However, the impact of the changes in the polymer-channel capacity at the electrode surface while the electrode process proceeds was also considered. These structural changes should affect differently the methods based on different time domains.

Systematic derivation of reaction-diffusion equations with distributed delays and relations to fractional reaction-diffusion equations and hyperbolic transport equations: application to the theory of Neolithic transition.

PubMed

Vlad, Marcel Ovidiu; Ross, John

2002-12-01

We introduce a general method for the systematic derivation of nonlinear reaction-diffusion equations with distributed delays. We study the interactions among different types of moving individuals (atoms, molecules, quasiparticles, biological organisms, etc). The motion of each species is described by the continuous time random walk theory, analyzed in the literature for transport problems, whereas the interactions among the species are described by a set of transformation rates, which are nonlinear functions of the local concentrations of the different types of individuals. We use the time interval between two jumps (the transition time) as an additional state variable and obtain a set of evolution equations, which are local in time. In order to make a connection with the transport models used in the literature, we make transformations which eliminate the transition time and derive a set of nonlocal equations which are nonlinear generalizations of the so-called generalized master equations. The method leads under different specified conditions to various types of nonlocal transport equations including a nonlinear generalization of fractional diffusion equations, hyperbolic reaction-diffusion equations, and delay-differential reaction-diffusion equations. Thus in the analysis of a given problem we can fit to the data the type of reaction-diffusion equation and the corresponding physical and kinetic parameters. The method is illustrated, as a test case, by the study of the neolithic transition. We introduce a set of assumptions which makes it possible to describe the transition from hunting and gathering to agriculture economics by a differential delay reaction-diffusion equation for the population density. We derive a delay evolution equation for the rate of advance of agriculture, which illustrates an application of our analysis.

A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton

PubMed Central

Das, Raibatak; Cairo, Christopher W.; Coombs, Daniel

2009-01-01

The extraction of hidden information from complex trajectories is a continuing problem in single-particle and single-molecule experiments. Particle trajectories are the result of multiple phenomena, and new methods for revealing changes in molecular processes are needed. We have developed a practical technique that is capable of identifying multiple states of diffusion within experimental trajectories. We model single particle tracks for a membrane-associated protein interacting with a homogeneously distributed binding partner and show that, with certain simplifying assumptions, particle trajectories can be regarded as the outcome of a two-state hidden Markov model. Using simulated trajectories, we demonstrate that this model can be used to identify the key biophysical parameters for such a system, namely the diffusion coefficients of the underlying states, and the rates of transition between them. We use a stochastic optimization scheme to compute maximum likelihood estimates of these parameters. We have applied this analysis to single-particle trajectories of the integrin receptor lymphocyte function-associated antigen-1 (LFA-1) on live T cells. Our analysis reveals that the diffusion of LFA-1 is indeed approximately two-state, and is characterized by large changes in cytoskeletal interactions upon cellular activation. PMID:19893741

A robust and accurate numerical method for transcritical turbulent flows at supercritical pressure with an arbitrary equation of state

NASA Astrophysics Data System (ADS)

Kawai, Soshi; Terashima, Hiroshi; Negishi, Hideyo

2015-11-01

This paper addresses issues in high-fidelity numerical simulations of transcritical turbulent flows at supercritical pressure. The proposed strategy builds on a tabulated look-up table method based on REFPROP database for an accurate estimation of non-linear behaviors of thermodynamic and fluid transport properties at the transcritical conditions. Based on the look-up table method we propose a numerical method that satisfies high-order spatial accuracy, spurious-oscillation-free property, and capability of capturing the abrupt variation in thermodynamic properties across the transcritical contact surface. The method introduces artificial mass diffusivity to the continuity and momentum equations in a physically-consistent manner in order to capture the steep transcritical thermodynamic variations robustly while maintaining spurious-oscillation-free property in the velocity field. The pressure evolution equation is derived from the full compressible Navier-Stokes equations and solved instead of solving the total energy equation to achieve the spurious pressure oscillation free property with an arbitrary equation of state including the present look-up table method. Flow problems with and without physical diffusion are employed for the numerical tests to validate the robustness, accuracy, and consistency of the proposed approach.

A robust and accurate numerical method for transcritical turbulent flows at supercritical pressure with an arbitrary equation of state

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

Kawai, Soshi, E-mail: kawai@cfd.mech.tohoku.ac.jp; Terashima, Hiroshi; Negishi, Hideyo

2015-11-01

This paper addresses issues in high-fidelity numerical simulations of transcritical turbulent flows at supercritical pressure. The proposed strategy builds on a tabulated look-up table method based on REFPROP database for an accurate estimation of non-linear behaviors of thermodynamic and fluid transport properties at the transcritical conditions. Based on the look-up table method we propose a numerical method that satisfies high-order spatial accuracy, spurious-oscillation-free property, and capability of capturing the abrupt variation in thermodynamic properties across the transcritical contact surface. The method introduces artificial mass diffusivity to the continuity and momentum equations in a physically-consistent manner in order to capture themore » steep transcritical thermodynamic variations robustly while maintaining spurious-oscillation-free property in the velocity field. The pressure evolution equation is derived from the full compressible Navier–Stokes equations and solved instead of solving the total energy equation to achieve the spurious pressure oscillation free property with an arbitrary equation of state including the present look-up table method. Flow problems with and without physical diffusion are employed for the numerical tests to validate the robustness, accuracy, and consistency of the proposed approach.« less

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.

LABORATORY AND FIELD EVALUATION OF CRYSTALLIZED DOW 704 OIL ON THE PERFORMANCE OF THE WINS PM2.5 FRACTIONATOR

EPA Science Inventory

Subsequent to the 1997 promulgation of the Federal Reference Method (FRM) for monitoring PM2.5 in ambient air, the United States Environmental Protection Agency (USEPA) received reports that the Dow 704 diffusion oil used in the method's WINS fractionator would occasionally cry...

Practical Bayesian tomography

NASA Astrophysics Data System (ADS)

Granade, Christopher; Combes, Joshua; Cory, D. G.

2016-03-01

In recent years, Bayesian methods have been proposed as a solution to a wide range of issues in quantum state and process tomography. State-of-the-art Bayesian tomography solutions suffer from three problems: numerical intractability, a lack of informative prior distributions, and an inability to track time-dependent processes. Here, we address all three problems. First, we use modern statistical methods, as pioneered by Huszár and Houlsby (2012 Phys. Rev. A 85 052120) and by Ferrie (2014 New J. Phys. 16 093035), to make Bayesian tomography numerically tractable. Our approach allows for practical computation of Bayesian point and region estimators for quantum states and channels. Second, we propose the first priors on quantum states and channels that allow for including useful experimental insight. Finally, we develop a method that allows tracking of time-dependent states and estimates the drift and diffusion processes affecting a state. We provide source code and animated visual examples for our methods.

A transformed path integral approach for solution of the Fokker-Planck equation

NASA Astrophysics Data System (ADS)

Subramaniam, Gnana M.; Vedula, Prakash

2017-10-01

A novel path integral (PI) based method for solution of the Fokker-Planck equation is presented. The proposed method, termed the transformed path integral (TPI) method, utilizes a new formulation for the underlying short-time propagator to perform the evolution of the probability density function (PDF) in a transformed computational domain where a more accurate representation of the PDF can be ensured. The new formulation, based on a dynamic transformation of the original state space with the statistics of the PDF as parameters, preserves the non-negativity of the PDF and incorporates short-time properties of the underlying stochastic process. New update equations for the state PDF in a transformed space and the parameters of the transformation (including mean and covariance) that better accommodate nonlinearities in drift and non-Gaussian behavior in distributions are proposed (based on properties of the SDE). Owing to the choice of transformation considered, the proposed method maps a fixed grid in transformed space to a dynamically adaptive grid in the original state space. The TPI method, in contrast to conventional methods such as Monte Carlo simulations and fixed grid approaches, is able to better represent the distributions (especially the tail information) and better address challenges in processes with large diffusion, large drift and large concentration of PDF. Additionally, in the proposed TPI method, error bounds on the probability in the computational domain can be obtained using the Chebyshev's inequality. The benefits of the TPI method over conventional methods are illustrated through simulations of linear and nonlinear drift processes in one-dimensional and multidimensional state spaces. The effects of spatial and temporal grid resolutions as well as that of the diffusion coefficient on the error in the PDF are also characterized.

Application of the Hilbert space average method on heat conduction models.

PubMed

Michel, Mathias; Gemmer, Jochen; Mahler, Günter

2006-01-01

We analyze closed one-dimensional chains of weakly coupled many level systems, by means of the so-called Hilbert space average method (HAM). Subject to some concrete conditions on the Hamiltonian of the system, our theory predicts energy diffusion with respect to a coarse-grained description for almost all initial states. Close to the respective equilibrium, we investigate this behavior in terms of heat transport and derive the heat conduction coefficient. Thus, we are able to show that both heat (energy) diffusive behavior as well as Fourier's law follows from and is compatible with a reversible Schrödinger dynamics on the complete level of description.

Diffusion coefficients of phenylbutazone in supercritical CO2 and in ethanol.

PubMed

Kong, Chang Yi; Watanabe, Kou; Funazukuri, Toshitaka

2013-03-01

The diffusion coefficients D(12) of phenylbutazone at infinite dilution in supercritical CO(2) were measured by the chromatographic impulse response (CIR) method. The measurements were carried out over the temperature range from 308.2 to 343.2 K at pressures up to 40.0 MPa. In addition, the D(12) data of phenylbutazone at infinite dilution in ethanol were also measured by the Taylor dispersion method at 298.2-333.2K and at atmospheric pressure. The D(12) value of phenylbutazone increased from 4.45×10(-10) m(2) s(-1) at 298.2 K and 0.1 MPa in ethanol to about 1.43×10(-8) m(2) s(-1) at 343.2 K and 14.0 MPa in supercritical CO(2). It was found that all diffusion data of phenylbutazone measured in this study in supercritical CO(2) and in ethanol can be satisfactorily represented by the hydrodynamic equation over a wide range of fluid viscosity from supercritical state to liquid state with average absolute relative deviation of 5.4% for 112 data points. Copyright © 2013 Elsevier B.V. All rights reserved.

Expanding Downward: Innovation, Diffusion, and State Policy Adoptions of Universal Preschool

ERIC Educational Resources Information Center

Curran, F. Chris

2015-01-01

Framed within the theoretical framework of policy innovation and diffusion, this study explores both interstate (diffusion) and intrastate predictors of adoption of state universal preschool policies. Event history analysis methodology is applied to a state level dataset drawn from the Census, the NCES Common Core, the Book of the States, and…

Fractional domain varying-order differential denoising method

NASA Astrophysics Data System (ADS)

Zhang, Yan-Shan; Zhang, Feng; Li, Bing-Zhao; Tao, Ran

2014-10-01

Removal of noise is an important step in the image restoration process, and it remains a challenging problem in image processing. Denoising is a process used to remove the noise from the corrupted image, while retaining the edges and other detailed features as much as possible. Recently, denoising in the fractional domain is a hot research topic. The fractional-order anisotropic diffusion method can bring a less blocky effect and preserve edges in image denoising, a method that has received much interest in the literature. Based on this method, we propose a new method for image denoising, in which fractional-varying-order differential, rather than constant-order differential, is used. The theoretical analysis and experimental results show that compared with the state-of-the-art fractional-order anisotropic diffusion method, the proposed fractional-varying-order differential denoising model can preserve structure and texture well, while quickly removing noise, and yields good visual effects and better peak signal-to-noise ratio.

Self-diffusion in MgO--a density functional study.

PubMed

Runevall, Odd; Sandberg, Nils

2011-08-31

Density functional theory calculations have been performed to study self-diffusion in magnesium oxide, a model material for a wide range of ionic compounds. Formation energies and entropies of Schottky defects and divacancies were obtained by means of total energy and phonon calculations in supercell configurations. Transition state theory was used to estimate defect migration rates, with migration energies taken from static calculations, and the corresponding frequency factors estimated from the phonon spectrum. In all static calculations we corrected for image effects using either a multipole expansion or an extrapolation to the low concentration limit. It is shown that both methods give similar results. The results for self-diffusion of Mg and O confirm the previously established picture, namely that in materials of nominal purity, Mg diffuses extrinsically by a single vacancy mechanism, while O diffuses intrinsically by a divacancy mechanism. Quantitatively, the current results are in very good agreement with experiments concerning O diffusion, while for Mg the absolute diffusion rate is generally underestimated by a factor of 5-10. The reason for this discrepancy is discussed.

A minimally-resolved immersed boundary model for reaction-diffusion problems

NASA Astrophysics Data System (ADS)

Pal Singh Bhalla, Amneet; Griffith, Boyce E.; Patankar, Neelesh A.; Donev, Aleksandar

2013-12-01

We develop an immersed boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a minimally-resolved "blob" using many fewer degrees of freedom per particle than standard discretization approaches. More complicated or more highly resolved particle shapes can be built out of a collection of reactive blobs. We demonstrate numerically that the blob model can provide an accurate representation at low to moderate packing densities of the reactive particles, at a cost not much larger than solving a Poisson equation in the same domain. Unlike multipole expansion methods, our method does not require analytically computed Green's functions, but rather, computes regularized discrete Green's functions on the fly by using a standard grid-based discretization of the Poisson equation. This allows for great flexibility in implementing different boundary conditions, coupling to fluid flow or thermal transport, and the inclusion of other effects such as temporal evolution and even nonlinearities. We develop multigrid-based preconditioners for solving the linear systems that arise when using implicit temporal discretizations or studying steady states. In the diffusion-limited case the resulting linear system is a saddle-point problem, the efficient solution of which remains a challenge for suspensions of many particles. We validate our method by comparing to published results on reaction-diffusion in ordered and disordered suspensions of reactive spheres.

Solid-state diffusion in amorphous zirconolite

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

Yang, C.; Dove, M. T.; Trachenko, K.

2014-11-14

We discuss how structural disorder and amorphization affect solid-state diffusion, and consider zirconolite as a currently important case study. By performing extensive molecular dynamics simulations, we disentangle the effects of amorphization and density, and show that a profound increase of solid-state diffusion takes place as a result of amorphization. Importantly, this can take place at the same density as in the crystal, representing an interesting general insight regarding solid-state diffusion. We find that decreasing the density in the amorphous system increases pre-factors of diffusion constants, but does not change the activation energy in the density range considered. We also findmore » that atomic species in zirconolite are affected differently by amorphization and density change. Our microscopic insights are relevant for understanding how solid-state diffusion changes due to disorder and for building predictive models of operation of materials to be used to encapsulate nuclear waste.« less

A coupling strategy for nonlocal and local diffusion models with mixed volume constraints and boundary conditions

DOE PAGES

D'Elia, Marta; Perego, Mauro; Bochev, Pavel B.; ...

2015-12-21

We develop and analyze an optimization-based method for the coupling of nonlocal and local diffusion problems with mixed volume constraints and boundary conditions. The approach formulates the coupling as a control problem where the states are the solutions of the nonlocal and local equations, the objective is to minimize their mismatch on the overlap of the nonlocal and local domains, and the controls are virtual volume constraints and boundary conditions. When some assumptions on the kernel functions hold, we prove that the resulting optimization problem is well-posed and discuss its implementation using Sandia’s agile software components toolkit. As a result,more » the latter provides the groundwork for the development of engineering analysis tools, while numerical results for nonlocal diffusion in three-dimensions illustrate key properties of the optimization-based coupling method.« less

Comptonization of X-rays by low-temperature electrons. [photon wavelength redistribution in cosmic sources

NASA Technical Reports Server (NTRS)

Illarionov, A.; Kallman, T.; Mccray, R.; Ross, R.

1979-01-01

A method is described for calculating the spectrum that results from the Compton scattering of a monochromatic source of X-rays by low-temperature electrons, both for initial-value relaxation problems and for steady-state spatial diffusion problems. The method gives an exact solution of the inital-value problem for evolution of the spectrum in an infinite homogeneous medium if Klein-Nishina corrections to the Thomson cross section are neglected. This, together with approximate solutions for problems in which Klein-Nishina corrections are significant and/or spatial diffusion occurs, shows spectral structure near the original photon wavelength that may be used to infer physical conditions in cosmic X-ray sources. Explicit results, shown for examples of time relaxation in an infinite medium and spatial diffusion through a uniform sphere, are compared with results obtained by Monte Carlo calculations and by solving the appropriate Fokker-Planck equation.

Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA.

PubMed

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

2018-03-16

We reanalyze trajectories of hOGG1 repair proteins diffusing on DNA. A previous analysis of these trajectories with the popular mean-squared-displacement approach revealed only simple diffusion. Here, a new optimal estimator of diffusion coefficients reveals two-state kinetics of the protein. A simple, solvable model, in which the protein randomly switches between a loosely bound, highly mobile state and a tightly bound, less mobile state is the simplest possible dynamic model consistent with the data. It yields accurate estimates of hOGG1's (i) diffusivity in each state, uncorrupted by experimental errors arising from shot noise, motion blur and thermal fluctuations of the DNA; (ii) rates of switching between states and (iii) rate of detachment from the DNA. The protein spends roughly equal time in each state. It detaches only from the loosely bound state, with a rate that depends on pH and the salt concentration in solution, while its rates for switching between states are insensitive to both. The diffusivity in the loosely bound state depends primarily on pH and is three to ten times higher than in the tightly bound state. We propose and discuss some new experiments that take full advantage of the new tools of analysis presented here.

Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution.

PubMed

Lu, Benzhuo; Zhou, Y C; Huber, Gary A; Bond, Stephen D; Holst, Michael J; McCammon, J Andrew

2007-10-07

A computational framework is presented for the continuum modeling of cellular biomolecular diffusion influenced by electrostatic driving forces. This framework is developed from a combination of state-of-the-art numerical methods, geometric meshing, and computer visualization tools. In particular, a hybrid of (adaptive) finite element and boundary element methods is adopted to solve the Smoluchowski equation (SE), the Poisson equation (PE), and the Poisson-Nernst-Planck equation (PNPE) in order to describe electrodiffusion processes. The finite element method is used because of its flexibility in modeling irregular geometries and complex boundary conditions. The boundary element method is used due to the convenience of treating the singularities in the source charge distribution and its accurate solution to electrostatic problems on molecular boundaries. Nonsteady-state diffusion can be studied using this framework, with the electric field computed using the densities of charged small molecules and mobile ions in the solvent. A solution for mesh generation for biomolecular systems is supplied, which is an essential component for the finite element and boundary element computations. The uncoupled Smoluchowski equation and Poisson-Boltzmann equation are considered as special cases of the PNPE in the numerical algorithm, and therefore can be solved in this framework as well. Two types of computations are reported in the results: stationary PNPE and time-dependent SE or Nernst-Planck equations solutions. A biological application of the first type is the ionic density distribution around a fragment of DNA determined by the equilibrium PNPE. The stationary PNPE with nonzero flux is also studied for a simple model system, and leads to an observation that the interference on electrostatic field of the substrate charges strongly affects the reaction rate coefficient. The second is a time-dependent diffusion process: the consumption of the neurotransmitter acetylcholine by acetylcholinesterase, determined by the SE and a single uncoupled solution of the Poisson-Boltzmann equation. The electrostatic effects, counterion compensation, spatiotemporal distribution, and diffusion-controlled reaction kinetics are analyzed and different methods are compared.

Application of solid state NMR for the study of surface bound species and fossil fuels

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

Althaus, Stacey

2014-01-01

In this study, stimulated echo with pulsed field gradients was used to measure the diffusion of two different solvents, water and hexane, in AP-MSN-2.7 and AP-MSN-3.7. The resulting data were then fit using two different methods. Based on these fits, the diffusion of hexane in AP-MSN-2.7 was shown to be slower than in the larger pores. This agrees well with our studies of catalytic activity, which show an increase in the reaction rate with the increase in pore size. Thus, both substrate inhibition and diffusion played a role in the decreased efficiency of the APMSN with small pore sizes.

The Diffusion of Evidence-Based Practice: Reviewing the Evidence-Based Practice Networks in the United States and German-Speaking Countries.

PubMed

Ghanem, Christian; Lawson, Thomas R; Pankofer, Sabine; Maragkos, Markos; Kollar, Ingo

2017-01-01

Evidence-based practice (EBP) has had a major influence on U.S. social work while it has rarely been adapted in German-speaking countries. This study investigates how knowledge about EBP is diffused within and across geographical contexts. Network analysis methods reveals different diffusion patterns and provide reasons for these differences. For example, the U.S. discourse is self-contained and based on a more homogeneous knowledge base, while the German discourse is more heterogeneous and focuses on a notion of reflexive professionalism. The different conceptual influences within the U.S. and German discourses are discussed in light of future directions of disciplinary social work.

Parametric dictionary learning for modeling EAP and ODF in diffusion MRI.

PubMed

Merlet, Sylvain; Caruyer, Emmanuel; Deriche, Rachid

2012-01-01

In this work, we propose an original and efficient approach to exploit the ability of Compressed Sensing (CS) to recover diffusion MRI (dMRI) signals from a limited number of samples while efficiently recovering important diffusion features such as the ensemble average propagator (EAP) and the orientation distribution function (ODF). Some attempts to sparsely represent the diffusion signal have already been performed. However and contrarly to what has been presented in CS dMRI, in this work we propose and advocate the use of a well adapted learned dictionary and show that it leads to a sparser signal estimation as well as to an efficient reconstruction of very important diffusion features. We first propose to learn and design a sparse and parametric dictionary from a set of training diffusion data. Then, we propose a framework to analytically estimate in closed form two important diffusion features: the EAP and the ODF. Various experiments on synthetic, phantom and human brain data have been carried out and promising results with reduced number of atoms have been obtained on diffusion signal reconstruction, thus illustrating the added value of our method over state-of-the-art SHORE and SPF based approaches.

Multi-Objective Memetic Search for Robust Motion and Distortion Correction in Diffusion MRI.

PubMed

Hering, Jan; Wolf, Ivo; Maier-Hein, Klaus H

2016-10-01

Effective image-based artifact correction is an essential step in the analysis of diffusion MR images. Many current approaches are based on retrospective registration, which becomes challenging in the realm of high b -values and low signal-to-noise ratio, rendering the corresponding correction schemes more and more ineffective. We propose a novel registration scheme based on memetic search optimization that allows for simultaneous exploitation of different signal intensity relationships between the images, leading to more robust registration results. We demonstrate the increased robustness and efficacy of our method on simulated as well as in vivo datasets. In contrast to the state-of-art methods, the median target registration error (TRE) stayed below the voxel size even for high b -values (3000 s ·mm -2 and higher) and low SNR conditions. We also demonstrate the increased precision in diffusion-derived quantities by evaluating Neurite Orientation Dispersion and Density Imaging (NODDI) derived measures on a in vivo dataset with severe motion artifacts. These promising results will potentially inspire further studies on metaheuristic optimization in diffusion MRI artifact correction and image registration in general.

New Numerical Approaches To thermal Convection In A Compositionally Stratified Fluid

NASA Astrophysics Data System (ADS)

Puckett, E. G.; Turcotte, D. L.; Kellogg, L. H.; Lokavarapu, H. V.; He, Y.; Robey, J.

2016-12-01

Seismic imaging of the mantle has revealed large and small scale heterogeneities in the lower mantle; specifically structures known as large low shear velocity provinces (LLSVP) below Africa and the South Pacific. Most interpretations propose that the heterogeneities are compositional in nature, differing from the overlying mantle, an interpretation that would be consistent with chemical geodynamic models. The LLSVP's are thought to be very old, meaning they have persisted thoughout much of Earth's history. Numerical modeling of persistent compositional interfaces present challenges to even state-of-the-art numerical methodology. It is extremely difficult to maintain sharp composition boundaries which migrate and distort with time dependent fingering without compositional diffusion and / or artificial diffusion. The compositional boundary must persist indefinitely. In this work we present computations of an initial compositionally stratified fluid that is subject to a thermal gradient ΔT = T1 - T0 across the height D of a rectangular domain over a range of buoyancy numbers B and Rayleigh numbers Ra. In these computations we compare three numerical approaches to modeling the movement of two distinct, thermally driven, compositional fields; namely, a high-order Finte Element Method (FEM) that employs artifical viscosity to preserve the maximum and minimum values of the compositional field, a Discontinous Galerkin (DG) method with a Bound Preserving (BP) limiter, and a Volume-of-Fluid (VOF) interface tracking algorithm. Our computations demonstrate that the FEM approach has far too much numerical diffusion to yield meaningful results, the DGBP method yields much better resuts but with small amounts of each compositional field being (numerically) entrained within the other compositional field, while the VOF method maintains a sharp interface between the two compositions throughout the computation. In the figure we show a comparison of between the three methods for a computation made with B = 1.111 and Ra = 10,000 after the flow has reached 'steady state'. (R) the images computed with the standard FEM method (with artifical viscosity), (C) the images computed with the DGBP method (with no artifical viscosity or diffusion due to discretization errors) and (L) the images computed with the VOF algorithm.

The transient divided bar method for laboratory measurements of thermal properties

NASA Astrophysics Data System (ADS)

Bording, Thue S.; Nielsen, Søren B.; Balling, Niels

2016-12-01

Accurate information on thermal conductivity and thermal diffusivity of materials is of central importance in relation to geoscience and engineering problems involving the transfer of heat. Several methods, including the classical divided bar technique, are available for laboratory measurements of thermal conductivity, but much fewer for thermal diffusivity. We have generalized the divided bar technique to the transient case in which thermal conductivity, volumetric heat capacity and thereby also thermal diffusivity are measured simultaneously. As the density of samples is easily determined independently, specific heat capacity can also be determined. The finite element formulation provides a flexible forward solution for heat transfer across the bar, and thermal properties are estimated by inverse Monte Carlo modelling. This methodology enables a proper quantification of experimental uncertainties on measured thermal properties and information on their origin. The developed methodology was applied to various materials, including a standard ceramic material and different rock samples, and measuring results were compared with results applying traditional steady-state divided bar and an independent line-source method. All measurements show highly consistent results and with excellent reproducibility and high accuracy. For conductivity the obtained uncertainty is typically 1-3 per cent, and for diffusivity uncertainty may be reduced to about 3-5 per cent. The main uncertainty originates from the presence of thermal contact resistance associated with the internal interfaces in the bar. These are not resolved during inversion and it is imperative that they are minimized. The proposed procedure is simple and may quite easily be implemented to the many steady-state divided bar systems in operation. A thermally controlled bath, as applied here, may not be needed. Simpler systems, such as applying temperature-controlled water directly from a tap, may also be applied.

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.

Identifying Obstacles and Research Gaps of Telemedicine Projects: Approach for a State-of-the-Art Analysis.

PubMed

Harst, Lorenz; Timpel, Patrick; Otto, Lena; Wollschlaeger, Bastian; Richter, Peggy; Schlieter, Hannes

2018-01-01

This paper presents an approach for an evaluation of finished telemedicine projects using qualitative methods. Telemedicine applications are said to improve the performance of health care systems. While there are countless telemedicine projects, the vast majority never makes the threshold from testing to implementation and diffusion. Projects were collected from German project databases in the area of telemedicine following systematically developed criteria. In a testing phase, ten projects were subject to a qualitative content analysis to identify limitations, need for further research, and lessons learned. Using Mayring's method of inductive category development, six categories of possible future research were derived. Thus, the proposed method is an important contribution to diffusion and translation research regarding telemedicine, as it is applicable to a systematic research of databases.

Non-focusing optics spectrophotometer, and methods of use

DOEpatents

Kramer, David M.; Sacksteder, Colette A.

2004-11-02

In one aspect, the present invention provides kinetic spectrophotometers that each comprise: (a) a light source; and (b) a compound parabolic concentrator disposed to receive light from the light source and configured to (1) intensify and diffuse the light received from the light source, and (2) direct the intensified and diffused light onto a sample. In other aspects, the present invention provides methods for measuring a photosynthetic parameter, the methods comprising the steps of: (a) illuminating a plant leaf until steady-state photosynthesis is achieved; (b) subjecting the illuminated plant leaf to a period of darkness; (c) using a kinetic spectrophotometer of the invention to collect spectral data from the plant leaf treated in accordance with steps (a) and (b); and (d) determining a value for a photosynthetic parameter from the spectral data.

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.

Transient diffraction grating measurements of molecular diffusion in the undergraduate laboratory

NASA Astrophysics Data System (ADS)

Spiegel, Daniel R.; Tuli, Santona

2011-07-01

Diffusion is a central process in many biological, chemical, and physical systems. We describe an experiment that employs the interference of laser beams to allow the measurement of molecular diffusion on submillimeter length scales. The interference fringes of two intersecting pump beams within a dye solution create a sinusoidal distribution of long-lived molecular excited states. A third probe beam is incident at a wavelength at which the indices of refraction of the ground and excited states are different, so the probe beam diffracts from the spatially periodic excited-state pattern. After the pump beams are switched off, the excited-state periodicity washes out as the system diffuses back to equilibrium. The molecular diffusion constant is obtained from the rate constant of the exponential decay of the diffracted beam. It is also possible to measure the excited-state lifetime.

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

PubMed

Neri, Izaak; Kern, Norbert; Parmeggiani, Andrea

2013-03-01

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

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

PubMed Central

Whitford, Paul C.; Blanchard, Scott C.; Cate, Jamie H. D.; Sanbonmatsu, Karissa Y.

2013-01-01

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states. PMID:23555233

Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

PubMed

Whitford, Paul C; Blanchard, Scott C; Cate, Jamie H D; Sanbonmatsu, Karissa Y

2013-01-01

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

Molecular dynamics study of strain-induced diffusivity of nitrogen in pure iron nanocrystalline

NASA Astrophysics Data System (ADS)

Mohammadzadeh, Roghayeh; Razmara, Naiyer; Razmara, Fereshteh

2016-12-01

In the present study, the self-diffusion process of nitrogen in pure iron nanocrystalline under strain conditions has been investigated by Molecular Dynamics (MD). The interactions between particles are modeled using Modified Embedded Atom Method (MEAM). Mean Square Displacement (MSD) of nitrogen in iron structure under strain is calculated. Strain is applied along [ 11 2 ¯ 0 ] and [ 0001 ] directions in both tensile and compression conditions. The activation energy and pre-exponential diffusion factor for nitrogen diffusion is comparatively high along [ 0001 ] direction of compressed structure of iron. The strain-induced diffusion coefficient at 973 K under the compression rate of 0.001 Å/ps along [ 0001 ] direction is about 6.72E-14 m2/s. The estimated activation energy of nitrogen under compression along [ 0001 ] direction is equal to 12.39 kcal/mol. The higher activation energy might be due to the fact that the system transforms into a more dense state when compressive stress is applied.

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.

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

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

Axial oxygen diffusion in the Krogh model: modifications to account for myocardial oxygen tension in isolated perfused rat hearts measured by EPR oximetry.

PubMed

Grinberg, Oleg; Novozhilov, Boris; Grinberg, Stalina; Friedman, Bruce; Swartz, Harold M

2005-01-01

The cylindrical steady-state model developed by Krogh with Erlang has served as the basis of understanding oxygen supply in living tissue for over eighty years. Due to its simplicity and agreement with some observations, it has been extensively used and successfully extended to new fields, especially for situations such as drug diffusion, water transport, and ice formation in tissues. However, the applicability of the model to make even a qualitative prediction of the oxygen level of specific volumes of the tissue is still controversial. We recently have developed an approximate analytical solution of a steady-state diffusion equation for a Krogh cylinder, including oxygen concentration in the capillary. This model was used to explain our previous experimental data on myocardial pO2 in isolated perfused rat hearts measured by EPR oximetry. An acceptable agreement with the experimental data was obtained by assuming that a known limitation of the existing EPR methods--a tendency to over-weight low pO2 values--had resulted in an under-estimate of the pO2. These results are consistent with recent results of others, which stress the importance of taking into account the details of what is measured by various methods.

Polarized Helium to Image the Lung

NASA Astrophysics Data System (ADS)

Leduc, Michèle; Nacher, Pierre Jean

2005-05-01

The main findings of the european PHIL project (Polarised Helium to Image the Lung) are reported. State of the art optical pumping techniques for polarising 3He gas are described. MRI methodological improvements allow dynamical ventilation images with a good resolution, ultimately limited by gas diffusion. Diffusion imaging appears as a robust method of lung diagnosis. A discussion of the potential advantage of low field MRI is presented. Selected PHIL results for emphysema are given, with the perspectives that this joint work opens up for the future of respiratory medicine.

Aggregation and Disaggregation of Senile Plaques in Alzheimer Disease

NASA Astrophysics Data System (ADS)

Cruz, L.; Urbanc, B.; Buldyrev, S. V.; Christie, R.; Gomez-Isla, T.; Havlin, S.; McNamara, M.; Stanley, H. E.; Hyman, B. T.

1997-07-01

We quantitatively analyzed, using laser scanning confocal microscopy, the three-dimensional structure of individual senile plaques in Alzheimer disease. We carried out the quantitative analysis using statistical methods to gain insights about the processes that govern Aβ peptide deposition. Our results show that plaques are complex porous structures with characteristic pore sizes. We interpret plaque morphology in the context of a new dynamical model based on competing aggregation and disaggregation processes in kinetic steady-state equilibrium with an additional diffusion process allowing Aβ deposits to diffuse over the surface of plaques.

Mutual influence of molecular diffusion in gas and surface phases

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Passive Rocket Diffuser Testing: Reacting Flow Performance of Four Second-Throat Geometries

NASA Technical Reports Server (NTRS)

Jones, Daniel R.; Allgood, Daniel C.; Saunders, Grady P.

2016-01-01

Second-throat diffusers serve to isolate rocket engines from the effects of ambient back pressure. As one of the nation's largest rocket testing facilities, the performance and design limitations of diffusers are of great interest to NASA's Stennis Space Center. This paper describes a series of tests conducted on four diffuser configurations to better understand the effects of inlet geometry and throat area on starting behavior and boundary layer separation. The diffusers were tested for a duration of five seconds with a 1455-pound thrust, LO2/GH2 thruster to ensure they each reached aerodynamic steady state. The effects of a water spray ring at the diffuser exits and a water-cooled deflector plate were also evaluated. Static pressure and temperature measurements were taken at multiple axial locations along the diffusers, and Computational Fluid Dynamics (CFD) simulations were used as a tool to aid in the interpretation of data. The hot combustion products were confirmed to enable the diffuser start condition with tighter second throats than predicted by historical cold-flow data or the theoretical normal shock method. Both aerodynamic performance and heat transfer were found to increase with smaller diffuser throats. Spray ring and deflector cooling water had negligible impacts on diffuser boundary layer separation. CFD was found to accurately capture diffuser shock structures and full-flowing diffuser wall pressures, and the qualitative behavior of heat transfer. However, the ability to predict boundary layer separated flows was not consistent.

Protein Diffusion on Charged Membranes: A Dynamic Mean-Field Model Describes Time Evolution and Lipid Reorganization

PubMed Central

Khelashvili, George; Weinstein, Harel; Harries, Daniel

2008-01-01

As charged macromolecules adsorb and diffuse on cell membranes in a large variety of cell signaling processes, they can attract or repel oppositely charged lipids. This results in lateral membrane rearrangement and affects the dynamics of protein function. To address such processes quantitatively we introduce a dynamic mean-field scheme that allows self-consistent calculations of the equilibrium state of membrane-protein complexes after such lateral reorganization of the membrane components, and serves to probe kinetic details of the process. Applicable to membranes with heterogeneous compositions containing several types of lipids, this comprehensive method accounts for mobile salt ions and charged macromolecules in three dimensions, as well as for lateral demixing of charged and net-neutral lipids in the membrane plane. In our model, the mobility of membrane components is governed by the diffusion-like Cahn-Hilliard equation, while the local electrochemical potential is based on nonlinear Poisson-Boltzmann theory. We illustrate the method by applying it to the adsorption of the anionic polypeptide poly-Lysine on negatively charged lipid membranes composed of binary mixtures of neutral and monovalent lipids, or onto ternary mixtures of neutral, monovalent, and multivalent lipids. Consistent with previous calculations and experiments, our results show that at steady-state multivalent lipids (such as PIP2), but not monovalent lipid (such as phosphatidylserine), will segregate near the adsorbing macromolecules. To address the corresponding diffusion of the adsorbing protein in the membrane plane, we couple lipid mobility with the propagation of the adsorbing protein through a dynamic Monte Carlo scheme. We find that due to their higher mobility dictated by the electrochemical potential, multivalent lipids such as PIP2 more quickly segregate near oppositely charged proteins than do monovalent lipids, even though their diffusion constants may be similar. The segregation, in turn, slows protein diffusion, as lipids introduce an effective drag on the motion of the adsorbate. In contrast, monovalent lipids such as phosphatidylserine only weakly segregate, and the diffusions of protein and lipid remain largely uncorrelated. PMID:18065451

Thirty years since diffuse sound reflection by maximum length

NASA Astrophysics Data System (ADS)

Cox, Trevor J.; D'Antonio, Peter

2005-09-01

This year celebrates the 30th anniversary of Schroeder's seminal paper on sound scattering from maximum length sequences. This paper, along with Schroeder's subsequent publication on quadratic residue diffusers, broke new ground, because they contained simple recipes for designing diffusers with known acoustic performance. So, what has happened in the intervening years? As with most areas of engineering, the room acoustic diffuser has been greatly influenced by the rise of digital computing technologies. Numerical methods have become much more powerful, and this has enabled predictions of surface scattering to greater accuracy and for larger scale surfaces than previously possible. Architecture has also gone through a revolution where the forms of buildings have become more extreme and sculptural. Acoustic diffuser designs have had to keep pace with this to produce shapes and forms that are desirable to architects. To achieve this, design methodologies have moved away from Schroeder's simple equations to brute force optimization algorithms. This paper will look back at the past development of the modern diffuser, explaining how the principles of diffuser design have been devised and revised over the decades. The paper will also look at the present state-of-the art, and dreams for the future.

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

PubMed

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

2016-05-01

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

Oxide Dissolution and Oxygen Diffusion in Solid-State Recycled Ti-6Al-4V: Numerical Modeling, Verification by Nanoindentation, and Effects on Grain Growth and Recrystallization

NASA Astrophysics Data System (ADS)

Lui, E. W.; Palanisamy, S.; Dargusch, M. S.; Xia, K.

2017-12-01

The oxide dissolution and oxygen diffusion during annealing of Ti-6Al-4V solid-state recycled from machining chips by equal-channel angular pressing (ECAP) have been investigated using nanoindentation and numerical modeling. The hardness profile from nanoindentation was converted into the oxygen concentration distribution using the Fleisher and Friedel model. An iterative fitting method was then employed to revise the ideal model proposed previously, leading to correct predictions of the oxide dissolution times and oxygen concentration profiles and verifying nanoindentation as an effective method to measure local oxygen concentrations. Recrystallization started at the prior oxide boundaries where local strains were high from the severe plastic deformation incurred in the ECAP recycling process, forming a band of ultrafine grains whose growth was retarded by solute dragging thanks to high oxygen concentrations. The recrystallized fine-grained region would advance with time to eventually replace the lamellar structure formed during ECAP.

Estimating Arrhenius parameters using temperature programmed molecular dynamics.

PubMed

Imandi, Venkataramana; Chatterjee, Abhijit

2016-07-21

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.

Improved Dot Diffusion For Image Halftoning

DTIC Science & Technology

1999-01-01

The dot diffusion method for digital halftoning has the advantage of parallelism unlike the error diffusion method. The method was recently improved...by optimization of the so-called class matrix so that the resulting halftones are comparable to the error diffused halftones . In this paper we will...first review the dot diffusion method. Previously, 82 class matrices were used for dot diffusion method. A problem with this size of class matrix is

Tracking Water Diffusion Fronts in a Highly Viscous Aerosol Particle

NASA Astrophysics Data System (ADS)

Bastelberger, Sandra; Krieger, Ulrich; Peter, Thomas

2016-04-01

Field measurements indicate that atmospheric secondary aerosol particles can be present in a highly viscous, glassy state [1]. In contrast to liquid state particles, the gas phase equilibration is kinetically limited and governed by condensed phase diffusion. In recent water diffusion experiments on highly viscous single aerosol particles levitated in an electrodynamic balance (EDB) we observed a characteristic shift behavior of the Mie whispering gallery modes (WGM) indicative of the changing radial structure of the particle, thus providing us with an experimental method to track the diffusion process inside the particle. When a highly viscous, homogeneous particle is exposed to an abrupt increase in relative humidity, the rapid gas phase diffusion and strong concentration dependence of the diffusion coefficient in the condensed phase lead to extremely steep water concentration gradients inside the particle, reminiscent of diffusion fronts. The resulting quasi step-like concentration profile motivates the introduction of a simple core-shell model describing the morphology of the non-equilibrium particle during humidification. The subsequent particle growth and reduction of the shell refractive index can be observed as red and blueshift behavior of the WGM, respectively. The shift pattern can be attributed to a core-shell radius ratio and particle radius derived from model calculations [2]. If supplemented with growth information obtained from the WGM redshift and thermodynamic equilibrium data, we can infer a comprehensive picture of the time evolution of the diffusion fronts in the framework of our core-shell model. The measured time dependent concentration profile is then compared with simulations solving the non-linear diffusion equation [3] [1] Virtanen, A., et al., Nature, 467, 824-827, 2010 [2] Kaiser, T., Schweiger, G., Computers in Physics, Vol. 7, No. 6, 682-686, Nov/Dec 1993 [3] Zobrist, B., Soonsin, V., Luo, B.P., Peter, T. et al., Phys. Chem. Chem. Phys., 13,3514-3526, 2011

Electrochemical ion transfer across liquid/liquid interfaces confined within solid-state micropore arrays--simulations and experiments.

PubMed

Strutwolf, Jörg; Scanlon, Micheál D; Arrigan, Damien W M

2009-01-01

Miniaturised liquid/liquid interfaces provide benefits for bioanalytical detection with electrochemical methods. In this work, microporous silicon membranes which can be used for interface miniaturisation were characterized by simulations and experiments. The microporous membranes possessed hexagonal arrays of pores with radii between 10 and 25 microm, a pore depth of 100 microm and pore centre-to-centre separations between 99 and 986 microm. Cyclic voltammetry was used to monitor ion transfer across arrays of micro-interfaces between two immiscible electrolyte solutions (microITIES) formed at these membranes, with the organic phase present as an organogel. The results were compared to computational simulations taking into account mass transport by diffusion and encompassing diffusion to recessed interfaces and overlapped diffusion zones. The simulation and experimental data were both consistent with the situation where the location of the liquid/liquid (l/l) interface was on the aqueous side of the silicon membrane and the pores were filled with the organic phase. While the current for the forward potential scan (transfer of the ion from the aqueous phase to the organic phase) was strongly dependent on the location of the l/l interface, the current peak during the reverse scan (transfer of the ion from the organic phase to the aqueous phase) was influenced by the ratio of the transferring ion's diffusion coefficients in both phases. The diffusion coefficient of the transferring ion in the gelified organic phase was ca. nine times smaller than in the aqueous phase. Asymmetric cyclic voltammogram shapes were caused by the combined effect of non-symmetrical diffusion (spherical and linear) and by the inequality of the diffusion coefficient in both phases. Overlapping diffusion zones were responsible for the observation of current peaks instead of steady-state currents during the forward scan. The characterisation of the diffusion behaviour is an important requirement for application of these silicon membranes in electroanalytical chemistry.

Does Diffusion Sequester Heavy Metals in Old Contamination Soils?

NASA Astrophysics Data System (ADS)

Ma, J.; Jennings, A. A.

2002-12-01

Old soil contamination refers to soil contamination that has aged over a long period of time. For example, at some brownfields, the soil heavy metal contamination can be one hundred or more years old. When contamination is young, the heavy metals are bound relatively weakly to the soil. However, the speciation and/or mechanisms of association evolve with aging into much more stable forms. It also appears that the metals migrate deeper into the bulk soil matrix where they are less available to participate in surface-related phenomena. Previous research showed elevated heavy metal extraction result after the soil was pulverized, with all other experiment conditions remaining unchanged. This indicates the presence of sequestered heavy metal contamination within the large soil particles (aggregate). The mechanisms of sequestering are uncertain, but diffusion appears to be a major factor. There are two possible pathways of diffusion that can account for heavy metal sequestering: solid-state diffusion through the bulk aggregate or liquid-phase diffusion through micro-pores within the aggregate structure. The second diffusion mechanism can be coupled with sorption (or other surface-related phenomena) on the pore walls. The remediation of sequestered heavy metals is also impacted by diffusion. Grinding a soil significantly reduces its average particle size. This exposes more of its internal bulk volume to extraction and results in much shorter diffusion pathway for the sequestered heavy metals to be released. Evidence has illustrated that this both improves remediation efficiency and provides a method by which the degree of sequestering can be quantified. This paper will present the results of ongoing research that is developing methods to identify the mechanisms of, quantify the magnitude of and determine the relative importance of (i.e. risk analysis) heavy metals sequestered in old contamination soils.

Semi-analytical solutions of the Schnakenberg model of a reaction-diffusion cell with feedback

NASA Astrophysics Data System (ADS)

Al Noufaey, K. S.

2018-06-01

This paper considers the application of a semi-analytical method to the Schnakenberg model of a reaction-diffusion cell. The semi-analytical method is based on the Galerkin method which approximates the original governing partial differential equations as a system of ordinary differential equations. Steady-state curves, bifurcation diagrams and the region of parameter space in which Hopf bifurcations occur are presented for semi-analytical solutions and the numerical solution. The effect of feedback control, via altering various concentrations in the boundary reservoirs in response to concentrations in the cell centre, is examined. It is shown that increasing the magnitude of feedback leads to destabilization of the system, whereas decreasing this parameter to negative values of large magnitude stabilizes the system. The semi-analytical solutions agree well with numerical solutions of the governing equations.

Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations.

PubMed

Wu, Hao; Noé, Frank

2011-03-01

Diffusion processes are relevant for a variety of phenomena in the natural sciences, including diffusion of cells or biomolecules within cells, diffusion of molecules on a membrane or surface, and diffusion of a molecular conformation within a complex energy landscape. Many experimental tools exist now to track such diffusive motions in single cells or molecules, including high-resolution light microscopy, optical tweezers, fluorescence quenching, and Förster resonance energy transfer (FRET). Experimental observations are most often indirect and incomplete: (1) They do not directly reveal the potential or diffusion constants that govern the diffusion process, (2) they have limited time and space resolution, and (3) the highest-resolution experiments do not track the motion directly but rather probe it stochastically by recording single events, such as photons, whose properties depend on the state of the system under investigation. Here, we propose a general Bayesian framework to model diffusion processes with nonlinear drift based on incomplete observations as generated by various types of experiments. A maximum penalized likelihood estimator is given as well as a Gibbs sampling method that allows to estimate the trajectories that have caused the measurement, the nonlinear drift or potential function and the noise or diffusion matrices, as well as uncertainty estimates of these properties. The approach is illustrated on numerical simulations of FRET experiments where it is shown that trajectories, potentials, and diffusion constants can be efficiently and reliably estimated even in cases with little statistics or nonequilibrium measurement conditions.

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

PubMed

Paull, Evan O; Carlin, Daniel E; Niepel, Mario; Sorger, Peter K; Haussler, David; Stuart, Joshua M

2013-11-01

Identifying the cellular wiring that connects genomic perturbations to transcriptional changes in cancer is essential to gain a mechanistic understanding of disease initiation, progression and ultimately to predict drug response. We have developed a method called Tied Diffusion Through Interacting Events (TieDIE) that uses a network diffusion approach to connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The method computes a subnetwork of protein-protein interactions, predicted transcription factor-to-target connections and curated interactions from literature that connects genomic and transcriptomic perturbations. Application of TieDIE to The Cancer Genome Atlas and a breast cancer cell line dataset identified key signaling pathways, with examples impinging on MYC activity. Interlinking genes are predicted to correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor character and suggest subtype-specific drug targets. Software is available from the Stuart lab's wiki: https://sysbiowiki.soe.ucsc.edu/tiedie. jstuart@ucsc.edu. Supplementary data are available at Bioinformatics online.

Evaluation of scale invariance in physiological signals by means of balanced estimation of diffusion entropy.

PubMed

Zhang, Wenqing; Qiu, Lu; Xiao, Qin; Yang, Huijie; Zhang, Qingjun; Wang, Jianyong

2012-11-01

By means of the concept of the balanced estimation of diffusion entropy, we evaluate the reliable scale invariance embedded in different sleep stages and stride records. Segments corresponding to waking, light sleep, rapid eye movement (REM) sleep, and deep sleep stages are extracted from long-term electroencephalogram signals. For each stage the scaling exponent value is distributed over a considerably wide range, which tell us that the scaling behavior is subject and sleep cycle dependent. The average of the scaling exponent values for waking segments is almost the same as that for REM segments (∼0.8). The waking and REM stages have a significantly higher value of the average scaling exponent than that for light sleep stages (∼0.7). For the stride series, the original diffusion entropy (DE) and the balanced estimation of diffusion entropy (BEDE) give almost the same results for detrended series. The evolutions of local scaling invariance show that the physiological states change abruptly, although in the experiments great efforts have been made to keep conditions unchanged. The global behavior of a single physiological signal may lose rich information on physiological states. Methodologically, the BEDE can evaluate with considerable precision the scale invariance in very short time series (∼10^{2}), while the original DE method sometimes may underestimate scale-invariance exponents or even fail in detecting scale-invariant behavior. The BEDE method is sensitive to trends in time series. The existence of trends may lead to an unreasonably high value of the scaling exponent and consequent mistaken conclusions.

Evaluation of scale invariance in physiological signals by means of balanced estimation of diffusion entropy

NASA Astrophysics Data System (ADS)

Zhang, Wenqing; Qiu, Lu; Xiao, Qin; Yang, Huijie; Zhang, Qingjun; Wang, Jianyong

2012-11-01

By means of the concept of the balanced estimation of diffusion entropy, we evaluate the reliable scale invariance embedded in different sleep stages and stride records. Segments corresponding to waking, light sleep, rapid eye movement (REM) sleep, and deep sleep stages are extracted from long-term electroencephalogram signals. For each stage the scaling exponent value is distributed over a considerably wide range, which tell us that the scaling behavior is subject and sleep cycle dependent. The average of the scaling exponent values for waking segments is almost the same as that for REM segments (˜0.8). The waking and REM stages have a significantly higher value of the average scaling exponent than that for light sleep stages (˜0.7). For the stride series, the original diffusion entropy (DE) and the balanced estimation of diffusion entropy (BEDE) give almost the same results for detrended series. The evolutions of local scaling invariance show that the physiological states change abruptly, although in the experiments great efforts have been made to keep conditions unchanged. The global behavior of a single physiological signal may lose rich information on physiological states. Methodologically, the BEDE can evaluate with considerable precision the scale invariance in very short time series (˜102), while the original DE method sometimes may underestimate scale-invariance exponents or even fail in detecting scale-invariant behavior. The BEDE method is sensitive to trends in time series. The existence of trends may lead to an unreasonably high value of the scaling exponent and consequent mistaken conclusions.

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.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

In Silico Estimation of Skin Concentration Following the Dermal Exposure to Chemicals.

PubMed

Hatanaka, Tomomi; Yoshida, Shun; Kadhum, Wesam R; Todo, Hiroaki; Sugibayashi, Kenji

2015-12-01

To develop an in silico method based on Fick's law of diffusion to estimate the skin concentration following dermal exposure to chemicals with a wide range of lipophilicity. Permeation experiments of various chemicals were performed through rat and porcine skin. Permeation parameters, namely, permeability coefficient and partition coefficient, were obtained by the fitting of data to two-layered and one-layered diffusion models for whole and stripped skin. The mean skin concentration of chemicals during steady-state permeation was calculated using the permeation parameters and compared with the observed values. All permeation profiles could be described by the diffusion models. The estimated skin concentrations of chemicals using permeation parameters were close to the observed levels and most data fell within the 95% confidence interval for complete prediction. The permeability coefficient and partition coefficient for stripped skin were almost constant, being independent of the permeant's lipophilicity. Skin concentration following dermal exposure to various chemicals can be accurately estimated based on Fick's law of diffusion. This method should become a useful tool to assess the efficacy of topically applied drugs and cosmetic ingredients, as well as the risk of chemicals likely to cause skin disorders and diseases.

Diffusion MRI noise mapping using random matrix theory

PubMed Central

Veraart, Jelle; Fieremans, Els; Novikov, Dmitry S.

2016-01-01

Purpose To estimate the spatially varying noise map using a redundant magnitude MR series. Methods We exploit redundancy in non-Gaussian multi-directional diffusion MRI data by identifying its noise-only principal components, based on the theory of noisy covariance matrices. The bulk of PCA eigenvalues, arising due to noise, is described by the universal Marchenko-Pastur distribution, parameterized by the noise level. This allows us to estimate noise level in a local neighborhood based on the singular value decomposition of a matrix combining neighborhood voxels and diffusion directions. Results We present a model-independent local noise mapping method capable of estimating noise level down to about 1% error. In contrast to current state-of-the art techniques, the resultant noise maps do not show artifactual anatomical features that often reflect physiological noise, the presence of sharp edges, or a lack of adequate a priori knowledge of the expected form of MR signal. Conclusions Simulations and experiments show that typical diffusion MRI data exhibit sufficient redundancy that enables accurate, precise, and robust estimation of the local noise level by interpreting the PCA eigenspectrum in terms of the Marchenko-Pastur distribution. PMID:26599599

Bifurcation analysis of a delay reaction-diffusion malware propagation model with feedback control

NASA Astrophysics Data System (ADS)

Zhu, Linhe; Zhao, Hongyong; Wang, Xiaoming

2015-05-01

With the rapid development of network information technology, information networks security has become a very critical issue in our work and daily life. This paper attempts to develop a delay reaction-diffusion model with a state feedback controller to describe the process of malware propagation in mobile wireless sensor networks (MWSNs). By analyzing the stability and Hopf bifurcation, we show that the state feedback method can successfully be used to control unstable steady states or periodic oscillations. Moreover, formulas for determining the properties of the bifurcating periodic oscillations are derived by applying the normal form method and center manifold theorem. Finally, we conduct extensive simulations on large-scale MWSNs to evaluate the proposed model. Numerical evidences show that the linear term of the controller is enough to delay the onset of the Hopf bifurcation and the properties of the bifurcation can be regulated to achieve some desirable behaviors by choosing the appropriate higher terms of the controller. Furthermore, we obtain that the spatial-temporal dynamic characteristics of malware propagation are closely related to the rate constant for nodes leaving the infective class for recovered class and the mobile behavior of nodes.

Anomalous Surface Diffusion of Protons on Lipid Membranes

PubMed Central

Wolf, Maarten G.; Grubmüller, Helmut; Groenhof, Gerrit

2014-01-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. PMID:24988343

A study of the polyethylene membrane used in diffusion chambers for radon gas concentration measurements

NASA Astrophysics Data System (ADS)

Leung, S. Y. Y.; Nikezic, D.; Leung, J. K. C.; Yu, K. N.

2007-10-01

Solid-state nuclear track detectors (SSNTDs) in diffusion chambers have been routinely used for long-term measurements of radon gas concentrations. In usual practice, a filter is added across the top of the diffusion chamber to stop the progeny from entering. Thoron can also be deterred from entering the diffusion chamber by using a polyethylene (PE) membrane. However, the thickness of the PE membrane is rarely specified in the literature. In this paper, we will present our experimental results for a radon exposure that the number of alpha-particle tracks registered by the LR 115 SSNTD in a Karlsruhe diffusion chamber covered with one layer of PE membrane is actually enhanced. This is explained by enhanced deposition of radon progeny on the outside surface of the PE membrane and the insufficient thickness of the PE membrane to stop the alpha particles emitted from these deposited radon progeny to reach the SSNTD. We will present the PE thickness which can stop the alpha particles emitted from the deposited radon or thoron progeny. For the "twin diffusion chambers method", one of the diffusion chambers is covered with PE membranes. The optimal number of thickness of PE membranes will be determined, which allows the largest amount of radon gas to diffuse into the diffusion chamber while at the same time screening out the largest amount of thoron gas.

Anomalous surface diffusion of protons on lipid membranes.

PubMed

Wolf, Maarten G; Grubmüller, Helmut; Groenhof, Gerrit

2014-07-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Ti diffusion in ion prebombarded MgO(100). I. A model for quantitative analysis

NASA Astrophysics Data System (ADS)

Lu, M.; Lupu, C.; Styve, V. J.; Lee, S. M.; Rabalais, J. W.

2002-01-01

Enhancement of Ti diffusion in MgO(100) prebombarded with 7 keV Ar+ has been observed. Diffusion was induced by annealing to 1000 °C following the prebombardment and Ti evaporation. Such a sample geometry and experimental procedure alleviates the continuous provision of freely mobile defects introduced by ion irradiation during annealing for diffusion, making diffusion proceed in a non-steady-state condition. Diffusion penetration profiles were obtained by using secondary ion mass spectrometry depth profiling techniques. A model that includes a depth-dependent diffusion coefficient was proposed, which successfully explains the observed non-steady-state radiation enhanced diffusion. The diffusion coefficients are of the order of 10-20 m2/s and are enhanced due to the defect structure inflected by the Ar+ prebombardment.

The Seeds of Policy Change: Leveraging Diffusion to Disseminate Policy Innovations.

PubMed

Boehmke, Frederick J; Rury, Abigail Matthews; Desmarais, Bruce A; Harden, Jeffrey J

2017-04-01

We conduct a series of simulations to compare how various strategies for seeding a policy in the American states affect the rate at which that policy spreads. Using empirically derived parameters of the policy diffusion process, we simulate the diffusion of a hypothetical policy after seeding the policy in just a handful of states. We compare these strategies to seeding the ten states the RWJF monitored during the states' implementation of the Affordable Care Act of 2010. We attempt to mimic the choices that policy advocates make when deciding which states to target with their resources. Our results indicate that focusing on innovative states, that is, those that tend to adopt new policies faster, offers a valuable boost in the speed of diffusion. Even better, though, is a strategy that targets policy leaders. Copyright © 2017 by Duke University Press.

Sensitizing solid state nuclear magnetic resonance of dilute nuclei by spin-diffusion assisted polarization transfers.

PubMed

Lupulescu, Adonis; Frydman, Lucio

2011-10-07

Recent years have witnessed efforts geared at increasing the sensitivity of NMR experiments, by relying on the suitable tailoring and exploitation of relaxation phenomena. These efforts have included the use of paramagnetic agents, enhanced (1)H-(1)H incoherent and coherent transfers processes in 2D liquid state spectroscopy, and homonuclear (13)C-(13)C spin diffusion effects in labeled solids. The present study examines some of the opportunities that could open when exploiting spontaneous (1)H-(1)H spin-diffusion processes, to enhance relaxation and to improve the sensitivity of dilute nuclei in solid state NMR measurements. It is shown that polarization transfer experiments executed under sufficiently fast magic-angle-spinning conditions, enable a selective polarization of the dilute low-γ spins by their immediate neighboring protons. Repolarization of the latter can then occur during the time involved in monitoring the signal emitted by the low-γ nuclei. The basic features involved in the resulting approach, and its potential to improve the effective sensitivity of solid state NMR measurements on dilute nuclei, are analyzed. Experimental tests witness the advantages that could reside from utilizing this kind of approach over conventional cross-polarization processes. These measurements also highlight a number of limitations that will have to be overcome for transforming selective polarization transfers of this kind into analytical methods of choice. © 2011 American Institute of Physics

Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions.

PubMed

Bauler, Patricia; Huber, Gary A; McCammon, J Andrew

2012-04-28

Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetric diffusion systems.

Holographic diffuser by use of a silver halide sensitized gelatin process

NASA Astrophysics Data System (ADS)

Kim, Sun Il; Choi, Yoon Sun; Ham, Yong Nam; Park, Chong Yun; Kim, Jong Man

2003-05-01

Diffusers play an important role in liquid-crystal display (LCD) application as a beam-shaping device, a brightness homogenizer, a light-scattering device, and an imaging screen. The transmittance and diffusing angle of the diffusers are the critical aspects for the applications to the LCD. The holographic diffusers by use of various processing methods have been investigated. The diffusing characteristics of different diffusing materials and processing methods have been evaluated and compared. The micro-structures of holographic diffusers have been investigated by use of using scanning electron microscopy. The holographic diffusers by use of the silver halide sensitized gelatin (SHSG) method have the structural merits for the improvement of the quality of diffusers. The features of holographic diffuser were exceptional in terms of transmittance and diffusing angle. The replication method by use of the SHSG process can be directly used for the manufacturing of diffusers for the display application.

Generation of a Kind of Displaced Thermal States in the Diffusion Process and its Statistical Properties

NASA Astrophysics Data System (ADS)

Xiang-Guo, Meng; Hong-Yi, Fan; Ji-Suo, Wang

2018-04-01

This paper proposes a kind of displaced thermal states (DTS) and explores how this kind of optical field emerges using the entangled state representation. The results show that the DTS can be generated by a coherent state passing through a diffusion channel with the diffusion coefficient ϰ only when there exists κ t = (e^{\\hbar ν /kBT} - 1 )^{-1}. Also, its statistical properties, such as mean photon number, Wigner function and entropy, are investigated.

How to Prepare for a Joint Dissemination Review Panel Meeting.

ERIC Educational Resources Information Center

Schmitt, Marshall L.; Rubak, Seymour S.

This guide defines the objectives and procedures of the United States Department of Education's Joint Dissemination Review Panel (JDRP) and the National Diffusion Network (NDN). The authors discuss the JDRP's methods of identifying successful educational programs and informing other schools nationwide about them. The major questions asked about…

Resolving High Amplitude Surface Motion with Diffusing Light

NASA Technical Reports Server (NTRS)

Wright, W.; Budakian, R.; Putterman, Seth J.

1996-01-01

A new technique has been developed for the purpose of imaging high amplitude surface motion. With this method one can quantitatively measure the transition to ripple wave turbulence. In addition, one can measure the phase of the turbulent state. These experiments reveal strong coherent structures in turbulent range of motion.

An in situ method for real-time monitoring of soil gas diffusivity

NASA Astrophysics Data System (ADS)

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

2016-04-01

Soil aeration is an important factor for the biogeochemistry of soils. Generally, gas exchange between soil and atmosphere is assumed to be governed by molecular diffusion and by this way fluxes can be calculated using by Fick's Law. The soil gas diffusion coefficient DS represents the proportional factor between the gas flux and the gas concentration gradient in the soil and reflects the ability of the soil to "transport passively" gas through the soil. One common way to determine DS is taking core samples in the field and measuring DS in the lab. Unfortunately this method is destructive and laborious and it can only reflect a small fraction of the whole soil. As a consequence, uncertainty about the resulting effective diffusivity on the profile scale, i.e. the real aeration status remains. We developed a method to measure and monitor DS in situ. The set-up consists of a custom made gas sampling device, the continuous injection of an inert tracer gas and inverse gas transport modelling in the soil. The gas sampling device has seven sampling depths (from 0 to -43 cm of depth) and can be easily installed into vertical holes drilled by an auger, which allows for fast installation of the system. Helium (He) as inert tracer gas was injected continuously at the lower end of the device. The resulting steady state distribution of He was used to deduce the DS depth distribution of the soil. For Finite Element Modeling of the gas-sampling-device/soil system the program COMSOL was used. We tested our new method both in the lab and in a field study and compared the results with a reference lab method using soil cores. DS profiles obtained by our in-situ method were consistent with DS profiles determined based on soil core analyses. Soil gas profiles could be measured with a temporal resolution of 30 minutes. During the field study, there was an important rain event and we could monitor the decrease in soil gas diffusivity in the top soil due to water infiltration. The effect of soil water infiltration deeper into the soil on soil gas diffusivity could be observed during the following hours. Our new DS determination device can be quickly and easily installed and allows for monitoring continuously soil gas transport over a long time. It allows following modifications of soil gas diffusivity due to rain events. In addition it enables the analysis of non-diffusive soil gas transport processes.

Understanding the effects of diffusion and relaxation in magnetic resonance imaging using computational modeling

NASA Astrophysics Data System (ADS)

Russell, Greg

The work described in this dissertation was motivated by a desire to better understand the cellular pathology of ischemic stroke. Two of the three bodies of research presented herein address and issue directly related to the investigation of ischemic stroke through the use of diffusion weighted magnetic resonance imaging (DWMRI) methods. The first topic concerns the development of a computationally efficient finite difference method, designed to evaluate the impact of microscopic tissue properties on the formation of DWMRI signal. For the second body of work, the effect of changing the intrinsic diffusion coefficient of a restricted sample on clinical DWMRI experiments is explored. The final body of work, while motivated by the desire to understand stroke, addresses the issue of acquiring large amounts of MRI data well suited for quantitative analysis in reduced scan time. In theory, the method could be used to generate quantitative parametric maps, including those depicting information gleaned through the use of DWMRI methods. Chapter 1 provides an introduction to several topics. A description of the use of DWMRI methods in the study of ischemic stroke is covered. An introduction to the fundamental physical principles at work in MRI is also provided. In this section the means by which magnetization is created in MRI experiments, how MRI signal is induced, as well as the influence of spin-spin and spin-lattice relaxation are discussed. Attention is also given to describing how MRI measurements can be sensitized to diffusion through the use of qualitative and quantitative descriptions of the process. Finally, the reader is given a brief introduction to the use of numerical methods for solving partial differential equations. In Chapters 2, 3 and 4, three related bodies of research are presented in terms of research papers. In Chapter 2, a novel computational method is described. The method reduces the computation resources required to simulate DWMRI experiments. In Chapter 3, a detailed study on how changes in the intrinsic intracellular diffusion coefficient may influence clinical DWMRI experiments is described. In Chapter 4, a novel, non-steady state quantitative MRI method is described.

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.

Solid state diffusion bonded damascus steel and its role within custom knifemaking

NASA Astrophysics Data System (ADS)

Horne, Grace

This thesis describes practice-based research that applied new technology to an ancient process of laminating metals for blades and explored the application of the new possibilities to a craft context. This research built on work by Ferguson on solid-state diffusion bonded Mokume Gane by moving from metal combinations suitable for vessel-making to metal combinations suitable for knife-making. Solid-state diffusion bonding1 is well established within industry. This research applied the industrial process to a craft based setting, and explored the bonding of metals with very dissimilar properties; ferrous and non-ferrous metals, hard and soft, high and low melting points. The materials included in this study were stainless and carbon steel, iron, nickel, vanadium and silver. The characteristics of the carbon steel and silver laminates were explored further by knifemakers, including heat-treating, forging, machining, flex and pattern creation. Analysis of the knifemakers feedback showed that the steel/silver metal was of interest to makers who machined or ground their blades rather than relying on forging.The study used a multi-method approach. The two broad researchquestions were; Is it possible to make a damascus steel using solid-state diffusion bonding that would be impossible using traditional techniques? And would the results be worth the work? Although carried out mainly within a craft setting the investigation is highly metallurgical in subject matter. The methodology was developed to reflect this crossing of subject areas and answer the research questions outlined above. The results are communicated through this thesis and a documentation of an exhibition of the work produced by the researcher and other selected knifemakers.The research produced a coherent composite of steel and pure silver and successfully produced a number of knives using the material.

Cellular interface morphologies in directional solidification. III - The effects of heat transfer and solid diffusivity

NASA Technical Reports Server (NTRS)

Ungar, Lyle H.; Bennett, Mark J.; Brown, Robert A.

1985-01-01

The shape and stability of two-dimensional finite-amplitude cellular interfaces arising during directional solidification are compared for several solidification models that account differently for latent heat released at the interface, unequal thermal conductivities of melt and solid, and solute diffusivity in the solid. Finite-element analysis and computer-implemented perturbation methods are used to analyze the families of steadily growing cellular forms that evolve from the planar state. In all models a secondary bifurcation between different families of finite-amplitude cells exists that halves the spatial wavelength of the stable interface. The quantitative location of this transition is very dependent on the details of the model. Large amounts of solute diffusion in the solid retard the growth of large-amplitude cells.

Investigation of Fission Product Transport into Zeolite-A for Pyroprocessing Waste Minimization

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

James R. Allensworth; Michael F. Simpson; Man-Sung Yim

Methods to improve fission product salt sorption into zeolite-A have been investigated in an effort to reduce waste associated with the electrochemical treatment of spent nuclear fuel. It was demonstrated that individual fission product chloride salts were absorbed by zeolite-A in a solid-state process. As a result, recycling of LiCl-KCl appears feasible via adding a zone-freezing technique to the current treatment process. Ternary salt molten-state experiments showed the limiting kinetics of CsCl and SrCl2 sorption into the zeolite. CsCl sorption occurred rapidly relative to SrCl2 with no observed dependence on zeolite particle size, while SrCl2 sorption was highly dependent onmore » particle size. The application of experimental data to a developed reaction-diffusion-based sorption model yielded diffusivities of 8.04 × 10-6 and 4.04 × 10-7 cm2 /s for CsCl and SrCl2, respectively. Additionally, the chemical reaction term in the developed model was found to be insignificant compared to the diffusion term.« less

Markov Chain Monte Carlo in the Analysis of Single-Molecule Experimental Data

NASA Astrophysics Data System (ADS)

Kou, S. C.; Xie, X. Sunney; Liu, Jun S.

2003-11-01

This article provides a Bayesian analysis of the single-molecule fluorescence lifetime experiment designed to probe the conformational dynamics of a single DNA hairpin molecule. The DNA hairpin's conformational change is initially modeled as a two-state Markov chain, which is not observable and has to be indirectly inferred. The Brownian diffusion of the single molecule, in addition to the hidden Markov structure, further complicates the matter. We show that the analytical form of the likelihood function can be obtained in the simplest case and a Metropolis-Hastings algorithm can be designed to sample from the posterior distribution of the parameters of interest and to compute desired estiamtes. To cope with the molecular diffusion process and the potentially oscillating energy barrier between the two states of the DNA hairpin, we introduce a data augmentation technique to handle both the Brownian diffusion and the hidden Ornstein-Uhlenbeck process associated with the fluctuating energy barrier, and design a more sophisticated Metropolis-type algorithm. Our method not only increases the estimating resolution by several folds but also proves to be successful for model discrimination.

Use of dirichlet distributions and orthogonal projection techniques for the fluctuation analysis of steady-state multivariate birth-death systems

NASA Astrophysics Data System (ADS)

Palombi, Filippo; Toti, Simona

2015-05-01

Approximate weak solutions of the Fokker-Planck equation represent a useful tool to analyze the equilibrium fluctuations of birth-death systems, as they provide a quantitative knowledge lying in between numerical simulations and exact analytic arguments. In this paper, we adapt the general mathematical formalism known as the Ritz-Galerkin method for partial differential equations to the Fokker-Planck equation with time-independent polynomial drift and diffusion coefficients on the simplex. Then, we show how the method works in two examples, namely the binary and multi-state voter models with zealots.

Twirling and Whirling: Viscous Dynamics of Rotating Elastica

NASA Astrophysics Data System (ADS)

Powers, Thomas R.; Wolgemuth, Charles W.; Goldstein, Raymond E.

1999-11-01

Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity. The competition between twist diffusion and writhing instabilities is described by a novel pair of coupled PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist-bend coupling and reveal two dynamical regimes separated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. The consequences of these phenomena for self-propulsion are investigated, and experimental tests proposed.

MR diffusion histology and micro-tractography reveal mesoscale features of the human cerebellum.

PubMed

Dell'Acqua, Flavio; Bodi, Istvan; Slater, David; Catani, Marco; Modo, Michel

2013-12-01

After 140 years from the discovery of Golgi's black reaction, the study of connectivity of the cerebellum remains a fascinating yet challenging task. Current histological techniques provide powerful methods for unravelling local axonal architecture, but the relatively low volume of data that can be acquired in a reasonable amount of time limits their application to small samples. State-of-the-art in vivo magnetic resonance imaging (MRI) methods, such as diffusion tractography techniques, can reveal trajectories of the major white matter pathways, but their correspondence with underlying anatomy is yet to be established. Hence, a significant gap exists between these two approaches as neither of them can adequately describe the three-dimensional complexity of fibre architecture at the level of the mesoscale (from a few millimetres to micrometres). In this study, we report the application of MR diffusion histology and micro-tractography methods to reveal the combined cytoarchitectural organisation and connectivity of the human cerebellum at a resolution of 100-μm (2 nl/voxel volume). Results show that the diffusion characteristics for each layer of the cerebellar cortex correctly reflect the known cellular composition and its architectural pattern. Micro-tractography also reveals details of the axonal connectivity of individual cerebellar folia and the intra-cortical organisation of the different cerebellar layers. The direct correspondence between MR diffusion histology and micro-tractography with immunohistochemistry indicates that these approaches have the potential to complement traditional histology techniques by providing a non-destructive, quantitative and three-dimensional description of the microstructural organisation of the healthy and pathological tissue.

An Electrochemical Investigation of the Chemical Diffusivity in Liquid Metal Alloys

NASA Astrophysics Data System (ADS)

Barriga, Salvador A.

The liquid metal battery has been shown to be a viable candidate for grid-scale energy storage, due to its fast kinetics and ability to be constructed from economically feasible materials. Various of the liquid metal couples that form high stable voltages, such as the calcium chemistries, are rate limited because they tend to form solid intermetallic compounds with high melting points. In order to understand and better engineer these batteries, the kinetic properties of these liquid alloys, in particular the chemical diffusivity, must be known accurately so that it can be used as input in computational simulations to avoid the nucleation of any solids. Unfortunately, the dominant experimental methods for measuring diffusion in liquid metals today are unreliable because the measurement timescales are on the order of days, require long capillaries susceptible to buoyancy-driven flow from temperature fluctuations, and composition analysis must be done ex-situ as a solid. To counter all these problems, a new and novel method for measuring the chemical diffusivity of metals in liquid alloys derived from electrochemical principles is presented in this thesis. This new method has the advantage of operating in shorter times scales of minutes rather than days, and requires the use of small capillaries which collectively minimize the effect of convectively-driven flow caused from temperature gradients. This new method was derived by solving the same boundary conditions required by the galvanostatic intermittent titration technique for solid-state electrodes. To verify the validity of the new theoretical derivation, the method was used to measure the chemical diffusivity of calcium in liquid bismuth within the temperature range of 550 - 700 °C using a three-electrode setup with a ternary molten salt electrolyte. Three compositions where studied (5% Ca-Bi, 10% Ca-Bi, and 15% Ca-Bi) for comparison. The chemical diffusion coefficient was found to range between (6.77 +/- 0.21)x10-5 cm2/s - (10.9 +/- 0.21 )x10-5 cm2/s at 5% Ca-Bi, (4.95 +/- 0.65)x10-5 cm2/s - (7.93 +/- 0.37)x10 -5 cm2/s at 10% Ca-Bi, and (6.22 +/- 1.2)x10 -5 cm2/s- (10.2 +/- 0.26)x10-5 cm2/s at 15% Ca-Bi which, to our knowledge, are the first successful measurements of calcium diffusivity in the liquid state. Arrhenius fits with good correlations revealed the activation energy for diffusion to be (21.4+/-1.7) kJ/mol, (23 .0+/-2.4) kJ/mol, and (17.7+/-5.9) kJ/mol as the calcium concentration increased, which are in excellent agreement with literature published values and lie in the same range of 15-30 kJ/mol that is reported for most liquid metals. The chemical diffusivity value was then used as input in finite element simulations to model how convection affects the overall transport inside a 20-Ah liquid bismuth electrode under the influence of different thermal boundary conditions. Also, a phase field model was created to simulate the motion of the two interfaces inside a liquid metal battery during operation, which to our knowledge, is the first time phase field has been extended beyond two phases. Experimental kinetic values can then be used as input in these numerical models to help characterize and optimize the entire battery. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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.

Diffusion doping in quantum dots: bond strength and diffusivity.

PubMed

Saha, Avijit; Makkar, Mahima; Shetty, Amitha; Gahlot, Kushagra; A R, Pavan; Viswanatha, Ranjani

2017-02-23

Semiconducting materials uniformly doped with optical or magnetic impurities have been useful in a number of potential applications. However, clustering or phase separation during synthesis has made this job challenging. Recently the "inside out" diffusion doping was proposed to be successful in obtaining large sized quantum dots (QDs) uniformly doped with a dilute percentage of dopant atoms. Herein, we demonstrate the use of basic physical chemistry of diffusion to control the size and concentration of the dopants within the QDs for a given transition metal ion. We have studied three parameters; the bond strength of the core molecules and the diffusion coefficient of the diffusing metal ion are found to be important while the ease of cation exchange was not highly influential in the control of size and concentration of the single domain dilute magnetic semiconductor quantum dots (DMSQDs) with diverse dopant ions M 2+ (Fe 2+ , Ni 2+ , Co 2+ , Mn 2+ ). Steady state optical emission spectra reveal that the dopants are incorporated inside the semiconducting CdS and the emission can be tuned during shell growth. We have shown that this method enables control over doping percentage and the QDs show a superior ferromagnetic response at room temperature as compared to previously reported systems.

Stress, deformation and diffusion interactions in solids - A simulation study

NASA Astrophysics Data System (ADS)

Fischer, F. D.; Svoboda, J.

2015-05-01

Equations of diffusion treated in the frame of Manning's concept, are completed by equations for generation/annihilation of vacancies at non-ideal sources and sinks, by conservation laws, by equations for generation of an eigenstrain state and by a strain-stress analysis. The stress-deformation-diffusion interactions are demonstrated on the evolution of a diffusion couple consisting of two thin layers of different chemical composition forming a free-standing plate without external loading. The equations are solved for different material parameters represented by the values of diffusion coefficients of individual components and by the intensity of sources and sinks for vacancies. The results of simulations indicate that for low intensity of sources and sinks for vacancies a significant eigenstress state can develop and the interdiffusion process is slowed down. For high intensity of sources and sinks for vacancies a significant eigenstrain state can develop and the eigenstress state quickly relaxes. If the difference in the diffusion coefficients of individual components is high, then the intensity of sources and sinks for vacancies influences the interdiffusion process considerably. For such systems their description only by diffusion coefficients is insufficient and must be completed by a microstructure characterization.

Nanowire membrane-based nanothermite: towards processable and tunable interfacial diffusion for solid state reactions.

PubMed

Yang, Yong; Wang, Peng-peng; Zhang, Zhi-cheng; Liu, Hui-ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-01-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants.

Nanowire Membrane-based Nanothermite: towards Processable and Tunable Interfacial Diffusion for Solid State Reactions

NASA Astrophysics Data System (ADS)

Yang, Yong; Wang, Peng-Peng; Zhang, Zhi-Cheng; Liu, Hui-Ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-04-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants.

Nanocrystal thin film fabrication methods and apparatus

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

Kagan, Cherie R.; Kim, David K.; Choi, Ji-Hyuk

Nanocrystal thin film devices and methods for fabricating nanocrystal thin film devices are disclosed. The nanocrystal thin films are diffused with a dopant such as Indium, Potassium, Tin, etc. to reduce surface states. The thin film devices may be exposed to air during a portion of the fabrication. This enables fabrication of nanocrystal-based devices using a wider range of techniques such as photolithography and photolithographic patterning in an air environment.

Synchronous infrared imaging methods to characterize thermal properties of materials

NASA Astrophysics Data System (ADS)

Ouyang, Zhong

1999-11-01

A fundamental thermal property of a material is its thermal conductivity. The current state-of-the art for measurement of thermal conductivity is inadequate, especially in the case of composite materials. This dissertation addresses the need for a rapid and accurate measurement of thermal conductivity that can provide values for three orthogonal directions in a single measurement. The theoretical approach is based on three-dimensional thermal wave propagation and scattering treatments that have been developed earlier at Wayne State University. The experimental approach makes use of a state-of-the-art focal-plane-array infrared camera, which is used to follow the time- and spatial-progression of the planar heat pulse on both surfaces of the slab. The method has been used to determine the thermal diffusivity of six pure elemental single crystal materials (Cu, Ti, Bi, Al, Ag, Pb). The results are in good agreement (better than 1%) with the diffusivities calculated from the handbook. The diffusivities of some alloys and unidirectional graphite-fiber-reinforced-polymer composite also are determined by this method. As a byproduct of one of the experimental approaches measuring the IR radiation from the heated surface, direct evidence is obtained for the presence of a thermal wave "echo". The theory and confirming measurements in this dissertation represent its first clear confirmation. A second experimental method which is studied in this dissertation, and which may be used to characterize thermal properties of materials, is that of lock-in thermal wave imaging. In this technique, pioneered earlier at Wayne State University, a periodic heat source is applied to the surface of the material, and synchronous, phase-sensitive detection of the IR radiation from that surface is used to determine the effects of thermal wave propagation to subsurface features, and the effects of reflected thermal waves from those features on the observed IR radiation from the surface. The rationale for re-visiting this technique is the availability of the focal-plane-array IR camera, with its "snapshot" capability, its high spatial resolution, and its high pixel rate. A lock-in imaging method is developed for use with this camera, which can be used at frequencies that considerably exceed the maximum frame rate, with illustrative applications to characterize the thermal properties of printed circuits and electronic packages.

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: a path for the optimization of low-energy many-body bases.

PubMed

Reboredo, Fernando A; Kim, Jeongnim

2014-02-21

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspace of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: A path for the optimization of low-energy many-body bases

NASA Astrophysics Data System (ADS)

Reboredo, Fernando A.; Kim, Jeongnim

2014-02-01

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspace of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.

Thermophysical Properties and Temperature of the Start of Titanium Recrystallization in Different Structural States

NASA Astrophysics Data System (ADS)

Pavlenko, D. V.; Tkach, D. V.; Danilova-Tret'yak, S. M.; Evseeva, L. E.

2017-05-01

The results of measurements of the thermal diffusivity, thermal conductivity, and heat capacity of VT1-0-grade titanium samples in as-cast, deformed submicrocrystalline, and sintered states are presented. It has been established that the decrease in the thermal conductivity and thermal diffusivity of titanium in the submicrocrystalline and sintered states is associated with the increase in the quantity of defects in the material volume, whereas the increase in the temperature of polymorphic transformation of titanium is connected with the dissolution of oxygen in its lattice. The results of investigation of the coefficient of thermal linear expansion of titanium in the macrocrystalline and submicrocrystalline states are presented. The decrease in the coefficient of thermal linear expansion of titanium of submicrocrystalline structure has been established, which may point to the decrease in its melting temperature. It is shown that annealing of samples in a submicrocrystalline state leads to the growth of the temperature coefficient of linear expansion, bringing its value closer to the temperature coefficient of linear expansion of titanium in the equilibrium state. Studies by the method of back reflection photography in a KROS chamber made it possible to estimate the temperature of the start of VT1-0-grade titanium recrystallization after intense plastic deformation by the twist extrusion method. The decrease in the temperature of the start of recrystallization for titanium in the deformed submicrocrystalline state has been established. Based on the trends revealed, optimum regimes of thermal treatment of VT1-0-grade titanium for removing internal stresses and preserving the submicrocrystalline structure have been established.

Effective diffusion coefficients of gas mixture in heavy oil under constant-pressure conditions

NASA Astrophysics Data System (ADS)

Li, Huazhou Andy; Sun, Huijuan; Yang, Daoyong

2017-05-01

We develop a method to determine the effective diffusion coefficient for each individual component of a gas mixture in a non-volatile liquid (e.g., heavy oil) at high pressures with compositional analysis. Theoretically, a multi-component one-way diffusion model is coupled with the volume-translated Peng-Robinson equation of state to quantify the mass transfer between gas and liquid (e.g., heavy oil). Experimentally, the diffusion tests have been conducted with a PVT setup for one pure CO2-heavy oil system and one C3H8-CO2-heavy oil system under constant temperature and pressure, respectively. Both the gas-phase volume and liquid-phase swelling effect are simultaneously recorded during the measurement. As for the C3H8-CO2-heavy oil system, the gas chromatography method is employed to measure compositions of the gas phase at the beginning and end of the diffusion measurement, respectively. The effective diffusion coefficients are then determined by minimizing the discrepancy between the measured and calculated gas-phase composition at the end of diffusion measurement. The newly developed technique can quantify the contributions of each component of mixture to the bulk mass transfer from gas into liquid. The effective diffusion coefficient of C3H8 in the C3H8-CO2 mixture at 3945 ± 20 kPa and 293.85 K, i.e., 18.19 × 10^{ - 10} {{m}}^{ 2} / {{s}}, is found to be much higher than CO2 at 3950 ± 18 kPa and 293.85 K, i.e., 8.68 × 10^{ - 10} {{m}}^{ 2} / {{s}}. In comparison with pure CO2, the presence of C3H8 in the C3H8-CO2 mixture contributes to a faster diffusion of CO2 from the gas phase into heavy oil and consequently a larger swelling factor of heavy oil.

The number statistics and optimal history of non-equilibrium steady states of mortal diffusing particles

NASA Astrophysics Data System (ADS)

Meerson, Baruch

2015-05-01

Suppose that a point-like steady source at x = 0 injects particles into a half-infinite line. The particles diffuse and die. At long times a non-equilibrium steady state sets in, and we assume that it involves many particles. If the particles are non-interacting, their total number N in the steady state is Poisson-distributed with mean \\bar{N} predicted from a deterministic reaction-diffusion equation. Here we determine the most likely density history of this driven system conditional on observing a given N. We also consider two prototypical examples of interacting diffusing particles: (i) a family of mortal diffusive lattice gases with constant diffusivity (as illustrated by the simple symmetric exclusion process with mortal particles), and (ii) random walkers that can annihilate in pairs. In both examples we calculate the variances of the (non-Poissonian) stationary distributions of N.

First-Principles Study of Charge Diffusion between Proximate Solid-State Qubits and Its Implications on Sensor Applications

NASA Astrophysics Data System (ADS)

Chou, Jyh-Pin; Bodrog, Zoltán; Gali, Adam

2018-03-01

Solid-state qubits from paramagnetic point defects in solids are promising platforms to realize quantum networks and novel nanoscale sensors. Recent advances in materials engineering make it possible to create proximate qubits in solids that might interact with each other, leading to electron spin or charge fluctuation. Here we develop a method to calculate the tunneling-mediated charge diffusion between point defects from first principles and apply it to nitrogen-vacancy (NV) qubits in diamond. The calculated tunneling rates are in quantitative agreement with previous experimental data. Our results suggest that proximate neutral and negatively charged NV defect pairs can form a NV-NV molecule. A tunneling-mediated model for the source of decoherence of the near-surface NV qubits is developed based on our findings on the interacting qubits in diamond.

Electrochemical characterization of p(+)n and n(+)p diffused InP structures

NASA Technical Reports Server (NTRS)

Wilt, David M.; Faur, Maria; Faur, Mircea; Goradia, M.; Vargas-Aburto, Carlos

1993-01-01

The relatively well documented and widely used electrolytes for characterization and processing of Si and GaAs-related materials and structures by electrochemical methods are of little or no use with InP because the electrolytes presently used either dissolve the surface preferentially at the defect areas or form residual oxides and introduce a large density of surface states. Using an electrolyte which was newly developed for anodic dissolution of InP, and was named the 'FAP' electrolyte, accurate characterization of InP related structures including nature and density of surface states, defect density, and net majority carrier concentration, all as functions of depth was performed. A step-by-step optimization of n(+)p and p(+)n InP structures made by thermal diffusion was done using the electrochemical techniques, and resulted in high performance homojunction InP structures.

Open quantum random walks: Bistability on pure states and ballistically induced diffusion

NASA Astrophysics Data System (ADS)

Bauer, Michel; Bernard, Denis; Tilloy, Antoine

2013-12-01

Open quantum random walks (OQRWs) deal with quantum random motions on a line for systems with internal and orbital degrees of freedom. The internal system behaves as a quantum random gyroscope coding for the direction of the orbital moves. We reveal the existence of a transition, depending on OQRW moduli, in the internal system behaviors from simple oscillations to random flips between two unstable pure states. This induces a transition in the orbital motions from the usual diffusion to ballistically induced diffusion with a large mean free path and large effective diffusion constant at large times. We also show that mixed states of the internal system are converted into random pure states during the process. We touch upon possible experimental realizations.

A numerical method for solving a nonlinear 2-D optimal control problem with the classical diffusion equation

NASA Astrophysics Data System (ADS)

Mamehrashi, K.; Yousefi, S. A.

2017-02-01

This paper presents a numerical solution for solving a nonlinear 2-D optimal control problem (2DOP). The performance index of a nonlinear 2DOP is described with a state and a control function. Furthermore, dynamic constraint of the system is given by a classical diffusion equation. It is preferred to use the Ritz method for finding the numerical solution of the problem. The method is based upon the Legendre polynomial basis. By using this method, the given optimisation nonlinear 2DOP reduces to the problem of solving a system of algebraic equations. The benefit of the method is that it provides greater flexibility in which the given initial and boundary conditions of the problem are imposed. Moreover, compared with the eigenfunction method, the satisfactory results are obtained only in a small number of polynomials order. This numerical approach is applicable and effective for such a kind of nonlinear 2DOP. The convergence of the method is extensively discussed and finally two illustrative examples are included to observe the validity and applicability of the new technique developed in the current work.

Simple diffusion can support the pitchfork, the flip bifurcations, and the chaos

NASA Astrophysics Data System (ADS)

Meng, Lili; Li, Xinfu; Zhang, Guang

2017-12-01

In this paper, a discrete rational fration population model with the Dirichlet boundary conditions will be considered. According to the discrete maximum principle and the sub- and supper-solution method, the necessary and sufficient conditions of uniqueness and existence of positive steady state solutions will be obtained. In addition, the dynamical behavior of a special two patch metapopulation model is investigated by using the bifurcation method, the center manifold theory, the bifurcation diagrams and the largest Lyapunov exponent. The results show that there exist the pitchfork, the flip bifurcations, and the chaos. Clearly, these phenomena are caused by the simple diffusion. The theoretical analysis of chaos is very imortant, unfortunately, there is not any results in this hand. However, some open problems are given.

Edge-Based Image Compression with Homogeneous Diffusion

NASA Astrophysics Data System (ADS)

Mainberger, Markus; Weickert, Joachim

It is well-known that edges contain semantically important image information. In this paper we present a lossy compression method for cartoon-like images that exploits information at image edges. These edges are extracted with the Marr-Hildreth operator followed by hysteresis thresholding. Their locations are stored in a lossless way using JBIG. Moreover, we encode the grey or colour values at both sides of each edge by applying quantisation, subsampling and PAQ coding. In the decoding step, information outside these encoded data is recovered by solving the Laplace equation, i.e. we inpaint with the steady state of a homogeneous diffusion process. Our experiments show that the suggested method outperforms the widely-used JPEG standard and can even beat the advanced JPEG2000 standard for cartoon-like images.

Short-lived K2S Molecules in Superionic Potassium Sulfide

NASA Astrophysics Data System (ADS)

Okeya, Yusuke; Tsumuraya, Kazuo

2015-03-01

The first principles molecular dynamics method allows us to elucidate the formation of short-lived K2S molecular states in superionic potassium sulfide. The covalent and the Coulomb bonds exist between the ionized mobile potassiums and the ionized immobile sulfurs. Both the bonds induces indirect covalent and indirect Coulomb attractions between the di-interstitial potassiums on the mid-sulfurs, which forms the short-lived K2S molecular states. The covalent electron density also exists between short-lived potassium dimers. The three attractions reduce Haven's ratios of the potassiums in the conductor. The molecule formation indicates the electronic state of the conductor is intermediate between the ionic and covalent crystals. The absence of the long-lived potassium dimers implies a failure of the caterpillar diffusion model or the Frenkel-Kontorova chain model for the superionic diffusion of the potassiums in the sulfide. The incompletely ionized cations and anions reduce the Coulomb attractions between them which induces the sublattice melting of smaller size of the potassiums than the sulfurs.

A parametric finite element method for solid-state dewetting problems with anisotropic surface energies

NASA Astrophysics Data System (ADS)

Bao, Weizhu; Jiang, Wei; Wang, Yan; Zhao, Quan

2017-02-01

We propose an efficient and accurate parametric finite element method (PFEM) for solving sharp-interface continuum models for solid-state dewetting of thin films with anisotropic surface energies. The governing equations of the sharp-interface models belong to a new type of high-order (4th- or 6th-order) geometric evolution partial differential equations about open curve/surface interface tracking problems which include anisotropic surface diffusion flow and contact line migration. Compared to the traditional methods (e.g., marker-particle methods), the proposed PFEM not only has very good accuracy, but also poses very mild restrictions on the numerical stability, and thus it has significant advantages for solving this type of open curve evolution problems with applications in the simulation of solid-state dewetting. Extensive numerical results are reported to demonstrate the accuracy and high efficiency of the proposed PFEM.

Comparison of intracellular water content measurements by dark-field imaging and EELS in medium voltage TEM

NASA Astrophysics Data System (ADS)

Terryn, C.; Michel, J.; Kilian, L.; Bonhomme, P.; Balossier, G.

2000-09-01

Knowledge of the water content at the subcellular level is important to evaluate the intracellular concentration of either diffusible or non-diffusible elements in the physiological state measured by the electron microprobe methods. Water content variations in subcellular compartments are directly related to secretion phenomena and to transmembrane exchange processes, which could be attributed to pathophysiological states. In this paper we will describe in details and compare two local water measurement methods using analytical electron microscopy. The first one is based on darkfield imaging. It is applied on freeze-dried biological cryosections; it allows indirect measurement of the water content at the subcellular level from recorded maps of darkfield intensity. The second method uses electron energy loss spectroscopy. It is applied to hydrated biological cryosections. It is based on the differences that appear in the electron energy loss spectra of macromolecular assemblies and vitrified ice in the 0-30 eV range. By a multiple least squares (MLS) fit between an experimental energy loss spectrum and reference spectra of both frozen-hydrated ice and macromolecular assemblies we can deduce directly the local water concentration in biological cryosections at the subcellular level. These two methods are applied to two test specimens: human erythrocytes in plasma, and baker's yeast (Saccharomyses Cerevisiae) cryosections. We compare the water content measurements obtained by these two methods and discuss their advantages and drawbacks.

Super-resolution reconstruction of diffusion parameters from diffusion-weighted images with different slice orientations.

PubMed

Van Steenkiste, Gwendolyn; Jeurissen, Ben; Veraart, Jelle; den Dekker, Arnold J; Parizel, Paul M; Poot, Dirk H J; Sijbers, Jan

2016-01-01

Diffusion MRI is hampered by long acquisition times, low spatial resolution, and a low signal-to-noise ratio. Recently, methods have been proposed to improve the trade-off between spatial resolution, signal-to-noise ratio, and acquisition time of diffusion-weighted images via super-resolution reconstruction (SRR) techniques. However, during the reconstruction, these SRR methods neglect the q-space relation between the different diffusion-weighted images. An SRR method that includes a diffusion model and directly reconstructs high resolution diffusion parameters from a set of low resolution diffusion-weighted images was proposed. Our method allows an arbitrary combination of diffusion gradient directions and slice orientations for the low resolution diffusion-weighted images, optimally samples the q- and k-space, and performs motion correction with b-matrix rotation. Experiments with synthetic data and in vivo human brain data show an increase of spatial resolution of the diffusion parameters, while preserving a high signal-to-noise ratio and low scan time. Moreover, the proposed SRR method outperforms the previous methods in terms of the root-mean-square error. The proposed SRR method substantially increases the spatial resolution of MRI that can be obtained in a clinically feasible scan time. © 2015 Wiley Periodicals, Inc.

Molecular Diffusion in Plasma Membranes of Primary Lymphocytes Measured by Fluorescence Correlation Spectroscopy.

PubMed

Staaf, Elina; Bagawath-Singh, Sunitha; Johansson, Sofia

2017-02-01

Fluorescence correlation spectroscopy (FCS) is a powerful technique for studying the diffusion of molecules within biological membranes with high spatial and temporal resolution. FCS can quantify the molecular concentration and diffusion coefficient of fluorescently labeled molecules in the cell membrane. This technique has the ability to explore the molecular diffusion characteristics of molecules in the plasma membrane of immune cells in steady state (i.e., without processes affecting the result during the actual measurement time). FCS is suitable for studying the diffusion of proteins that are expressed at levels typical for most endogenous proteins. Here, a straightforward and robust method to determine the diffusion rate of cell membrane proteins on primary lymphocytes is demonstrated. An effective way to perform measurements on antibody-stained live cells and commonly occurring observations after acquisition are described. The recent advancements in the development of photo-stable fluorescent dyes can be utilized by conjugating the antibodies of interest to appropriate dyes that do not bleach extensively during the measurements. Additionally, this allows for the detection of slowly diffusing entities, which is a common feature of proteins expressed in cell membranes. The analysis procedure to extract molecular concentration and diffusion parameters from the generated autocorrelation curves is highlighted. In summary, a basic protocol for FCS measurements is provided; it can be followed by immunologists with an understanding of confocal microscopy but with no other previous experience of techniques for measuring dynamic parameters, such as molecular diffusion rates.

Theoretical studies of floating-reference method for NIR blood glucose sensing

NASA Astrophysics Data System (ADS)

Shi, Zhenzhi; Yang, Yue; Zhao, Huijuan; Chen, Wenliang; Liu, Rong; Xu, Kexin

2011-03-01

Non-invasive blood glucose monitoring using NIR light has been suffered from the variety of optical background that is mainly caused by the change of human body, such as the change of temperature, water concentration, and so on. In order to eliminate these internal influence and external interference a so called floating-reference method has been proposed to provide an internal reference. From the analysis of the diffuse reflectance spectrum, a position has been found where diffuse reflection of light is not sensitive to the glucose concentrations. Our previous work has proved the existence of reference position using diffusion equation. However, since glucose monitoring generally use the NIR light in region of 1000-2000nm, diffusion equation is not valid because of the high absorption coefficient and small source-detector separations. In this paper, steady-state high-order approximate model is used to further investigate the existence of the floating reference position in semi-infinite medium. Based on the analysis of different optical parameters on the impact of spatially resolved reflectance of light, we find that the existence of the floating-reference position is the result of the interaction of optical parameters. Comparing to the results of Monte Carlo simulation, the applicable region of diffusion approximation and higher-order approximation for the calculation of floating-reference position is discussed at the wavelength of 1000nm-1800nm, using the intralipid solution of different concentrations. The results indicate that when the reduced albedo is greater than 0.93, diffusion approximation results are more close to simulation results, otherwise the high order approximation is more applicable.

Mixed analytical-stochastic simulation method for the recovery of a Brownian gradient source from probability fluxes to small windows.

PubMed

Dobramysl, U; Holcman, D

2018-02-15

Is it possible to recover the position of a source from the steady-state fluxes of Brownian particles to small absorbing windows located on the boundary of a domain? To address this question, we develop a numerical procedure to avoid tracking Brownian trajectories in the entire infinite space. Instead, we generate particles near the absorbing windows, computed from the analytical expression of the exit probability. When the Brownian particles are generated by a steady-state gradient at a single point, we compute asymptotically the fluxes to small absorbing holes distributed on the boundary of half-space and on a disk in two dimensions, which agree with stochastic simulations. We also derive an expression for the splitting probability between small windows using the matched asymptotic method. Finally, when there are more than two small absorbing windows, we show how to reconstruct the position of the source from the diffusion fluxes. The present approach provides a computational first principle for the mechanism of sensing a gradient of diffusing particles, a ubiquitous problem in cell biology.

Migration mechanisms and diffusion barriers of vacancies in Ga2O3

NASA Astrophysics Data System (ADS)

Kyrtsos, Alexandros; Matsubara, Masahiko; Bellotti, Enrico

2017-06-01

We employ the nudged elastic band and the dimer methods within the standard density functional theory (DFT) formalism to study the migration of the oxygen and gallium vacancies in the monoclinic structure of β -Ga2O3 . We identify all the first nearest neighbor paths and calculate the migration barriers for the diffusion of the oxygen and gallium vacancies. We also identify the metastable sites of the gallium vacancies which are critical for the diffusion of the gallium atoms. The migration barriers for the diffusion of the gallium vacancies are lower than the migration barriers for oxygen vacancies by 1 eV on average, suggesting that the gallium vacancies are mobile at lower temperatures. Using the calculated migration barriers we estimate the annealing temperature of these defects within the harmonic transition state theory formalism, finding excellent agreement with the observed experimental annealing temperatures. Finally, we suggest the existence of percolation paths which enable the migration of the species without utilizing all the migration paths of the crystal.

Perforated cenosphere-supported pH-sensitive spin probes

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

Fomenko, E.V.; Bobko, A.A.; Salanov, A.N.

2008-03-15

Porous supports with an accessible internal volume and a shell providing the diffusive migration of pH-sensitive spin probes were obtained for the first time from hollow aluminosilicate cenospheres isolated from the coal fly ash. Using the methods of scanning electron microscopy and electron spin resonance, the morphology of different porous cenosphere modifications and its influence on the diffusion of spin probes from the internal volume were studied. When supporting aqueous solutions of a radical, the characteristic diffusion time for the mesoporous structure of the support is longer by a factor of 3-5 than that for the macroporous structure. Ferrospinel inmore » a content of 6 wt.% do not virtually affect the diffusion rate of spin probes. A constant rate of radical migration of similar to 1 {mu} mol min{sup -1}, determined by radical solubility in water, is achieved when a radical in the solid aggregate state is supported on the magnetic cenospheres.« less

Noninvasive optical cytochrome c oxidase redox state measurements using diffuse optical spectroscopy

PubMed Central

Lee, Jangwoen; Kim, Jae G.; Mahon, Sari B.; Mukai, David; Yoon, David; Boss, Gerry R.; Patterson, Steven E.; Rockwood, Gary; Isom, Gary; Brenner, Matthew

2014-01-01

Abstract. A major need exists for methods to assess organ oxidative metabolic states in vivo. By contrasting the responses to cyanide (CN) poisoning versus hemorrhage in animal models, we demonstrate that diffuse optical spectroscopy (DOS) can detect cytochrome c oxidase (CcO) redox states. Intermittent decreases in inspired O2 from 100% to 21% were applied before, during, and after CN poisoning, hemorrhage, and resuscitation in rabbits. Continuous DOS measurements of total hemoglobin, oxyhemoglobin, deoxyhemoglobin, and oxidized and reduced CcO from muscle were obtained. Rabbit hemorrhage was accomplished with stepwise removal of blood, followed by blood resuscitation. CN treated rabbits received 0.166  mg/min NaCN infusion. During hemorrhage, CcO redox state became reduced concurrently with decreases in oxyhemoglobin, resulting from reduced tissue oxygen delivery and hypoxia. In contrast, during CN infusion, CcO redox state decreased while oxyhemoglobin concentration increased due to CN binding and reduction of CcO with resultant inhibition of the electron transport chain. Spectral absorption similarities between hemoglobin and CcO make noninvasive spectroscopic distinction of CcO redox states difficult. By contrasting physiological perturbations of CN poisoning versus hemorrhage, we demonstrate that DOS measured CcO redox state changes are decoupled from hemoglobin concentration measurement changes. PMID:24788369

Noninvasive optical cytochrome c oxidase redox state measurements using diffuse optical spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Jangwoen; Kim, Jae G.; Mahon, Sari B.; Mukai, David; Yoon, David; Boss, Gerry R.; Patterson, Steven E.; Rockwood, Gary; Isom, Gary; Brenner, Matthew

2014-05-01

A major need exists for methods to assess organ oxidative metabolic states in vivo. By contrasting the responses to cyanide (CN) poisoning versus hemorrhage in animal models, we demonstrate that diffuse optical spectroscopy (DOS) can detect cytochrome c oxidase (CcO) redox states. Intermittent decreases in inspired O2 from 100% to 21% were applied before, during, and after CN poisoning, hemorrhage, and resuscitation in rabbits. Continuous DOS measurements of total hemoglobin, oxyhemoglobin, deoxyhemoglobin, and oxidized and reduced CcO from muscle were obtained. Rabbit hemorrhage was accomplished with stepwise removal of blood, followed by blood resuscitation. CN treated rabbits received 0.166 mg/min NaCN infusion. During hemorrhage, CcO redox state became reduced concurrently with decreases in oxyhemoglobin, resulting from reduced tissue oxygen delivery and hypoxia. In contrast, during CN infusion, CcO redox state decreased while oxyhemoglobin concentration increased due to CN binding and reduction of CcO with resultant inhibition of the electron transport chain. Spectral absorption similarities between hemoglobin and CcO make noninvasive spectroscopic distinction of CcO redox states difficult. By contrasting physiological perturbations of CN poisoning versus hemorrhage, we demonstrate that DOS measured CcO redox state changes are decoupled from hemoglobin concentration measurement changes.

Estimating Arrhenius parameters using temperature programmed molecular dynamics

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

Imandi, Venkataramana; Chatterjee, Abhijit, E-mail: abhijit@che.iitb.ac.in

2016-07-21

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight variousmore » aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.« less

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

2014-07-01

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

Application of quasi-steady state methods to molecular motor transport on microtubules in fungal hyphae.

PubMed

Dauvergne, Duncan; Edelstein-Keshet, Leah

2015-08-21

We consider bidirectional transport of cargo by molecular motors dynein and kinesin that walk along microtubules, and/or diffuse in the cell. The motors compete to transport cargo in opposite directions with respect to microtubule polarity (towards the plus or minus end of the microtubule). In recent work, Gou et al. (2014) used a hierarchical set of models, each consisting of continuum transport equations to track the evolution of motors and their cargo (early endosomes) in the specific case of the fungus Ustilago maydis. We complement their work using a framework of quasi-steady state analysis developed by Newby and Bressloff (2010) and Bressloff and Newby (2013) to reduce the models to an approximating steady state Fokker-Plank equation. This analysis allows us to find analytic approximations to the steady state solutions in many cases where the full models are not easily solved. Consequently, we can make predictions about parameter dependence of the resulting spatial distributions. We also characterize the overall rates of bulk transport and diffusion, and how these are related to state transition parameters, motor speeds, microtubule polarity distribution, and specific assumptions made. Copyright © 2015 Elsevier Ltd. All rights reserved.

A COMPREHENSIVE EXAMINATION OF WHITE MATTER TRACTS AND CONNECTOMETRY IN MAJOR DEPRESSIVE DISORDER

PubMed Central

Delaparte, Lauren; Yeh, Fang‐Cheng; DeLorenzo, Christine; McGrath, Patrick J.; Weissman, Myrna M.; Adams, Phillip; Fava, Maurizio; Deckersbach, Thilo; McInnis, Melvin G.; Carmody, Thomas J.; Cooper, Crystal M.; Kurian, Benji T.; Lu, Hanzhang; Toups, Marisa S.; Trivedi, Madhukar H.; Parsey, Ramin V.

2015-01-01

Background Major depressive disorder (MDD) is a debilitating disorder characterized by widespread brain abnormalities. The literature is mixed as to whether or not white matter abnormalities are associated with MDD. This study sought to examine fractional anisotropy (FA) in white matter tracts in individuals with MDD using diffusion tensor imaging (DTI). Methods 139 participants with MDD and 39 healthy controls (HC) in a multisite study were included. DTI scans were acquired in 64 directions and FA was determined in the brain using four methods: region of interest (ROI), tract‐based spatial statistics (TBSS), and diffusion tractography. Diffusion connectometry was used to identify white matter pathways associated with MDD. Results There were no significant differences when comparing FA in MDD and HC groups using any method. In the MDD group, there was a significant relationship between depression severity and FA in the right medial orbitofrontal cortex, and between age of onset of MDD and FA in the right caudal anterior cingulate cortex using the ROI method. There was a significant relationship between age of onset and connectivity in the thalamocortical radiation, inferior longitudinal fasciculus, and cerebellar tracts using diffusion connectometry. Conclusions The lack of group differences in FA and connectometry analysis may result from the clinically heterogenous nature of MDD. However, the relationship between FA and depression severity may suggest a state biomarker of depression that should be investigated as a potential indicator of response. Age of onset may also be a significant clinical feature to pursue when studying white matter tracts. PMID:26477532

An accurate computational method for the diffusion regime verification

NASA Astrophysics Data System (ADS)

Zhokh, Alexey A.; Strizhak, Peter E.

2018-04-01

The diffusion regime (sub-diffusive, standard, or super-diffusive) is defined by the order of the derivative in the corresponding transport equation. We develop an accurate computational method for the direct estimation of the diffusion regime. The method is based on the derivative order estimation using the asymptotic analytic solutions of the diffusion equation with the integer order and the time-fractional derivatives. The robustness and the computational cheapness of the proposed method are verified using the experimental methane and methyl alcohol transport kinetics through the catalyst pellet.

Solid-State Reaction Between Fe-Al-Ca Alloy and Al2O3-CaO-FeO Oxide During Heat Treatment at 1473 K (1200 °C)

NASA Astrophysics Data System (ADS)

Liu, Chengsong; Yang, Shufeng; Li, Jingshe; Ni, Hongwei; Zhang, Xueliang

2017-04-01

The aim of this study was to control the physicochemical characteristics of inclusions in steel through appropriate heat treatment. Using a confocal scanning laser microscope (CSLM) and pipe furnace, the solid-state reactions between Fe-Al-Ca alloy and Al2O3-CaO-FeO oxide during heat treatment at 1473 K (1200 °C) and the influence of these reactions on the compositions of and phases in the alloy and oxide were investigated by the diffusion couple method. Suitable pretreatment of the oxide using a CSLM and production of the diffusion couple of Fe-Al-Ca alloy and Al2O3-CaO-FeO oxide gave good contact between the alloy and oxide. The diffusion couple was then sealed in a quartz tube with a piece of Ti foil to lower oxygen partial pressure and a block of Fe-Al-Ca alloy was introduced to conduct heat treatment experiments. Solid-state reactions between the alloy and oxide during heat treatment at 1473 K (1200 °C) were analyzed and discussed. A dynamic model to calculate the width of the particle precipitation zone based on the Wagner model of internal oxidation of metal was proposed. This model was helpful to understand the solid-state reaction mechanism between Fe-Al-Ca alloy and Al2O3-CaO-FeO oxide.

Multi-scale diffuse interface modeling of multi-component two-phase flow with partial miscibility

NASA Astrophysics Data System (ADS)

Kou, Jisheng; Sun, Shuyu

2016-08-01

In this paper, we introduce a diffuse interface model to simulate multi-component two-phase flow with partial miscibility based on a realistic equation of state (e.g. Peng-Robinson equation of state). Because of partial miscibility, thermodynamic relations are used to model not only interfacial properties but also bulk properties, including density, composition, pressure, and realistic viscosity. As far as we know, this effort is the first time to use diffuse interface modeling based on equation of state for modeling of multi-component two-phase flow with partial miscibility. In numerical simulation, the key issue is to resolve the high contrast of scales from the microscopic interface composition to macroscale bulk fluid motion since the interface has a nanoscale thickness only. To efficiently solve this challenging problem, we develop a multi-scale simulation method. At the microscopic scale, we deduce a reduced interfacial equation under reasonable assumptions, and then we propose a formulation of capillary pressure, which is consistent with macroscale flow equations. Moreover, we show that Young-Laplace equation is an approximation of this capillarity formulation, and this formulation is also consistent with the concept of Tolman length, which is a correction of Young-Laplace equation. At the macroscopical scale, the interfaces are treated as discontinuous surfaces separating two phases of fluids. Our approach differs from conventional sharp-interface two-phase flow model in that we use the capillary pressure directly instead of a combination of surface tension and Young-Laplace equation because capillarity can be calculated from our proposed capillarity formulation. A compatible condition is also derived for the pressure in flow equations. Furthermore, based on the proposed capillarity formulation, we design an efficient numerical method for directly computing the capillary pressure between two fluids composed of multiple components. Finally, numerical tests are carried out to verify the effectiveness of the proposed multi-scale method.

Multi-scale diffuse interface modeling of multi-component two-phase flow with partial miscibility

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

Kou, Jisheng; Sun, Shuyu, E-mail: shuyu.sun@kaust.edu.sa; School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an 710049

2016-08-01

In this paper, we introduce a diffuse interface model to simulate multi-component two-phase flow with partial miscibility based on a realistic equation of state (e.g. Peng–Robinson equation of state). Because of partial miscibility, thermodynamic relations are used to model not only interfacial properties but also bulk properties, including density, composition, pressure, and realistic viscosity. As far as we know, this effort is the first time to use diffuse interface modeling based on equation of state for modeling of multi-component two-phase flow with partial miscibility. In numerical simulation, the key issue is to resolve the high contrast of scales from themore » microscopic interface composition to macroscale bulk fluid motion since the interface has a nanoscale thickness only. To efficiently solve this challenging problem, we develop a multi-scale simulation method. At the microscopic scale, we deduce a reduced interfacial equation under reasonable assumptions, and then we propose a formulation of capillary pressure, which is consistent with macroscale flow equations. Moreover, we show that Young–Laplace equation is an approximation of this capillarity formulation, and this formulation is also consistent with the concept of Tolman length, which is a correction of Young–Laplace equation. At the macroscopical scale, the interfaces are treated as discontinuous surfaces separating two phases of fluids. Our approach differs from conventional sharp-interface two-phase flow model in that we use the capillary pressure directly instead of a combination of surface tension and Young–Laplace equation because capillarity can be calculated from our proposed capillarity formulation. A compatible condition is also derived for the pressure in flow equations. Furthermore, based on the proposed capillarity formulation, we design an efficient numerical method for directly computing the capillary pressure between two fluids composed of multiple components. Finally, numerical tests are carried out to verify the effectiveness of the proposed multi-scale method.« less

Nanowire Membrane-based Nanothermite: towards Processable and Tunable Interfacial Diffusion for Solid State Reactions

PubMed Central

Yang, Yong; Wang, Peng-peng; Zhang, Zhi-cheng; Liu, Hui-ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-01-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants. PMID:23603809

Acceleration of metal-atom diffusion in electric field at metal/insulator interfaces: First-principles study

NASA Astrophysics Data System (ADS)

Nagasawa, Riki; Asayama, Yoshihiro; Nakayama, Takashi

2018-04-01

Metal-atom diffusion from metal electrodes into SiO2 in electric fields was studied using first-principles calculations. It was shown in the case without electric field that the diffusion barrier of a metal atom is mainly made of the cohesive energy of bulk metal layers, while the shape of the diffusion potential reflects the hybridization of the metal-atom state with metal-induced gap states (MIGSs) and the electron transfer between the metal atom and the electrode. We found that the metal-atom diffusion is markedly accelerated by the applied electric field, such that the diffusion barrier ϕB(E) decreases almost linearly with increasing electric field strength E. By analyzing the physical origins of the metal-atom diffusion, we derived the universal formula to estimate the diffusion barrier in the electric field, which is closely related to MIGSs.

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

Song, Kai; Song, Linze; Shi, Qiang, E-mail: qshi@iccas.ac.cn

Based on the path integral approach, we derive a new realization of the exact non-Markovian stochastic Schrödinger equation (SSE). The main difference from the previous non-Markovian quantum state diffusion (NMQSD) method is that the complex Gaussian stochastic process used for the forward propagation of the wave function is correlated, which may be used to reduce the amplitude of the non-Markovian memory term at high temperatures. The new SSE is then written into the recently developed hierarchy of pure states scheme, in a form that is more closely related to the hierarchical equation of motion approach. Numerical simulations are then performedmore » to demonstrate the efficiency of the new method.« less

Simulation of a fast diffuse optical tomography system based on radiative transfer equation

NASA Astrophysics Data System (ADS)

Motevalli, S. M.; Payani, A.

2016-12-01

Studies show that near-infrared (NIR) light (light with wavelength between 700nm and 1300nm) undergoes two interactions, absorption and scattering, when it penetrates a tissue. Since scattering is the predominant interaction, the calculation of light distribution in the tissue and the image reconstruction of absorption and scattering coefficients are very complicated. Some analytical and numerical methods, such as radiative transport equation and Monte Carlo method, have been used for the simulation of light penetration in tissue. Recently, some investigators in the world have tried to develop a diffuse optical tomography system. In these systems, NIR light penetrates the tissue and passes through the tissue. Then, light exiting the tissue is measured by NIR detectors placed around the tissue. These data are collected from all the detectors and transferred to the computational parts (including hardware and software), which make a cross-sectional image of the tissue after performing some computational processes. In this paper, the results of the simulation of an optical diffuse tomography system are presented. This simulation involves two stages: a) Simulation of the forward problem (or light penetration in the tissue), which is performed by solving the diffusion approximation equation in the stationary state using FEM. b) Simulation of the inverse problem (or image reconstruction), which is performed by the optimization algorithm called Broyden quasi-Newton. This method of image reconstruction is faster compared to the other Newton-based optimization algorithms, such as the Levenberg-Marquardt one.

Optical luminescence studies of diffusion times at the potassium ethyl xanthate adsorption layer on the surface of sphalerite minerals

NASA Astrophysics Data System (ADS)

Todoran, R.; Todoran, D.; Anitas, E. M.; Szakács, Zs

2016-08-01

We propose reflectance measurements as a method for the evaluation of the kinetics of adsorption processes, to compute the diffusion times of the adsorption products at the thin layers formed at the sphalerite natural mineral-potassium ethyl xanthate solution interface. The method is based on the intensity measurement of the reflected monochromatic radiation obtained from the mineral-xanthate thin layer as a function of time. These determinations were made at the thin layer formed between the sphalerite or activated sphalerite natural minerals with potassium ethyl xanthate, for different solutions concentrations and pH values at constant temperature. Diffusion times of desorbed molecular species into the liquid bring important information about the global kinetics of the ions in this phase during adsorption processes at interfaces. Analysing the time dependence of this parameter one concluded on the diffusion properties of the xanthate molecule in the solution depending on its concentration and pH, knowing that at the initial time these molecules had a uniform spread. This method enabled us to determine that, in time interval of approximately 35 minutes to achieve dynamic equilibrium in the formation of the interface layer, one had three different kinetic behaviours of our systems. In the first 5-8 min one had highly adsorbent character, the state of equilibrium is followed by low adsorbent properties. Gaining information on the adsorption kinetics in the case of xanthate on mineral surface leads to the optimization of the industrial froth flotation process.

Discrete diffusion Lyman α radiative transfer

NASA Astrophysics Data System (ADS)

Smith, Aaron; Tsang, Benny T.-H.; Bromm, Volker; Milosavljević, Miloš

2018-06-01

Due to its accuracy and generality, Monte Carlo radiative transfer (MCRT) has emerged as the prevalent method for Lyα radiative transfer in arbitrary geometries. The standard MCRT encounters a significant efficiency barrier in the high optical depth, diffusion regime. Multiple acceleration schemes have been developed to improve the efficiency of MCRT but the noise from photon packet discretization remains a challenge. The discrete diffusion Monte Carlo (DDMC) scheme has been successfully applied in state-of-the-art radiation hydrodynamics (RHD) simulations. Still, the established framework is not optimal for resonant line transfer. Inspired by the DDMC paradigm, we present a novel extension to resonant DDMC (rDDMC) in which diffusion in space and frequency are treated on equal footing. We explore the robustness of our new method and demonstrate a level of performance that justifies incorporating the method into existing Lyα codes. We present computational speedups of ˜102-106 relative to contemporary MCRT implementations with schemes that skip scattering in the core of the line profile. This is because the rDDMC runtime scales with the spatial and frequency resolution rather than the number of scatterings—the latter is typically ∝τ0 for static media, or ∝(aτ0)2/3 with core-skipping. We anticipate new frontiers in which on-the-fly Lyα radiative transfer calculations are feasible in 3D RHD. More generally, rDDMC is transferable to any computationally demanding problem amenable to a Fokker-Planck approximation of frequency redistribution.

Solid-state diffusion-controlled growth of the phases in the Au-Sn system

NASA Astrophysics Data System (ADS)

Baheti, Varun A.; Kashyap, Sanjay; Kumar, Praveen; Chattopadhyay, Kamanio; Paul, Aloke

2018-01-01

The solid state diffusion-controlled growth of the phases is studied for the Au-Sn system in the range of room temperature to 200 °C using bulk and electroplated diffusion couples. The number of product phases in the interdiffusion zone decreases with the decrease in annealing temperature. These phases grow with significantly high rates even at the room temperature. The growth rate of the AuSn4 phase is observed to be higher in the case of electroplated diffusion couple because of the relatively small grains and hence high contribution of the grain boundary diffusion when compared to the bulk diffusion couple. The diffraction pattern analysis indicates the same equilibrium crystal structure of the phases in these two types of diffusion couples. The analysis in the AuSn4 phase relating the estimated tracer diffusion coefficients with grain size, crystal structure, the homologous temperature of experiments and the concept of the sublattice diffusion mechanism in the intermetallic compounds indicate that Au diffuses mainly via the grain boundaries, whereas Sn diffuses via both the grain boundaries and the lattice.

Solution of non-steady-state substrate concentration in the action of biosensor response at mixed enzyme kinetics

NASA Astrophysics Data System (ADS)

Senthamarai, R.; Jana Ranjani, R.

2018-04-01

In this paper, a mathematical model of an amperometric biosensor at mixed enzyme kinetics and diffusion limitation in the case of substrate inhibition has been developed. The model is based on time dependent reaction diffusion equation containing a non -linear term related to non -Michaelis - Menten kinetics of the enzymatic reaction. Solution for the concentration of the substrate has been derived for all values of parameters using the homotopy perturbation method. All the approximate analytic expressions of substrate concentration are compared with simulation results using Scilab/Matlab program. Finally, we have given a satisfactory agreement between them.

Application of laser ranging and VLBI data to a study of plate tectonic driving forces. [finite element method

NASA Technical Reports Server (NTRS)

Solomon, S. C.

1980-01-01

The measurability of changes in plate driving or resistive forces associated with plate boundary earthquakes by laser rangefinding or VLBI is considered with emphasis on those aspects of plate forces that can be characterized by such measurements. Topics covered include: (1) analytic solutions for two dimensional stress diffusion in a plate following earthquake faulting on a finite fault; (2) two dimensional finite-element solutions for the global state of stress at the Earth's surface for possible plate driving forces; and (3) finite-element solutions for three dimensional stress diffusion in a viscoelastic Earth following earthquake faulting.

Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

NASA Astrophysics Data System (ADS)

Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

2015-03-01

We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

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.

State Relationships of Laminar Permanently-Blue Opposed-Jet Hydrocarbon-Fueled Diffusion Flames. Appendix D

NASA Technical Reports Server (NTRS)

Lin, K.-C.; Faeth, G. M.; Urban, D. L. (Technical Monitor)

2000-01-01

The structure and state relationships of laminar soot-free (permanently-blue) diffusion flames at various strain rates were studied experimentally using an opposed-jet configuration, motivated by the importance of soot-free hydrocarbon-fueled diffusion flames for many practical applications. Measurements of gas velocities, temperatures and compositions were carried out along the stagnation stream line. Flame conditions studied included propylene- and 1,3-butadiene-fueled opposed-jet diffusion flames having a stoichiometric mixture fractions of 0.7 and strain rates of 60-240 s (exp -1) at normal temperature and pressure. It was found that oxygen leakage to fuel-rich conditions and carbon monoxide leakage to fuel-lean conditions both increased as strain rates increased. Furthermore, increased strain rates caused increased fuel concentrations near the flame sheet, decreased peak gas temperatures, and decreased concentrations of carbon dioxide and water vapor throughout the flames. State relationships for major gas species and gas temperatures for these flames were found to exist over broad ranges of strain rates. In addition, current measurements, as well as previous measurements and predictions of ethylene-fueled permanently-blue diffusion flames, all having a stoichiometric mixture fraction of 0.7, were combined to establish generalized state relationships for permanently-blue diffusion flames for this stoichiometric mixture fraction. The combined measurements and predictions support relatively universal generalized state relationships for N2, CO2, H2O and fuel over a broad range of strain rates and fuel types. State relationships for O2 in the fuel-rich region, and for CO in the fuel-lean region, however, are functions of strain rate and fuel type. State relationships for H2 and temperature exhibit less universality, mainly due to the increased experimental uncertainties for these variables. The existence of state relationships for soot-free hydrocarbon-fueled diffusion flames provides potential for significant computational simplifications for modeling purposes in many instances, allowing for effects of finite-rate chemistry while avoiding time-consuming computations of Arrhenius expressions.

Surface photovoltage method extended to silicon solar cell junction

NASA Technical Reports Server (NTRS)

Wang, E. Y.; Baraona, C. R.; Brandhorst, H. W., Jr.

1974-01-01

The conventional surface photovoltage (SPV) method is extended to the measurement of the minority carrier diffusion length in diffused semiconductor junctions of the type used in a silicon solar cell. The minority carrier diffusion values obtained by the SPV method agree well with those obtained by the X-ray method. Agreement within experimental error is also obtained between the minority carrier diffusion lengths in solar cell diffusion junctions and in the same materials with n-regions removed by etching, when the SPV method was used in the measurements.

Phenomenology and energetics of diffusion across cell phase states.

PubMed

Ashrafuzzaman, Md

2015-11-01

Cell based transport properties have been mathematically addressed. Cell contained cross boundary diffusion of materials has been explained using valid formalisms and related analytical expressions have been developed. Various distinguishable physical structures and their properties raise different general structure specific diffusion mechanisms and controlled transport related parameters. Some of these parameters play phenomenological roles and some cause regulatory effects. The cell based compartments may be divided into three major physical phase states namely liquid, plasma and solid phase states. Transport of ions, nutrients, small molecules like proteins, etc. across inter phase states and intraphase states follows general transport related formalisms. Creation of some localized permanent and/or temporary structures e.g., ion channels, clustering of constituents, etc. and the transitions between such structures appear as regulators of the transport mechanisms. In this article, I have developed mainly a theoretical analysis of the commonly observed cell transport phenomena. I have attempted to develop formalisms on general cell based diffusion followed by a few numerical computations to address the analytical expression phenomenologically. I have then extended the analysis to adopting with the local structure originated energetics. Independent or correlated molecular transport naturally relies on some general parameters that define the nature of local cell environment as well as on some occasionally raised or transiently active stochastic resonance due to localized interactions. Short and long range interaction energies play crucial roles in this regard. Physical classification of cellular compartments has led us developing analytical expressions on both biologically observed diffusion mechanisms and the diffusions's occasional stochasticity causing energetics. These analytical expressions help us address the diffusion phenomena generally considering the physical properties of the biostructures across the diffusion pathways. A specific example case of single molecule transport and localized interaction energetics in a specific cell phase has been utilized to address the diffusion quite clearly. This article helps to address the mechanisms of cell based diffusion and nutrient movements and thus helps develop strategic templates to manipulate the diffusion mechanisms. Application of the theoretical knowledge into designing or discovering drugs or small molecule inhibitors targeting cell based structures may open up new avenues in biomedical sciences.

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: a path for the optimization of low-energy many-body basis expansions

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

Kim, Jeongnim; Reboredo, Fernando A.

The self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo J. Chem. Phys. {\\bf 136}, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. {\\bf 89}, 6316 (1988)] are blended to obtain a method for the calculation of thermodynamic properties of many-body systems at low temperatures. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric trial wave functions. A statistical method is derived for the calculation of finite temperature properties of many-body systemsmore » near the ground state. In the process we also obtain a parallel algorithm that optimizes the many-body basis of a small subspace of the many-body Hilbert space. This small subspace is optimized to have maximum overlap with the one expanded by the lower energy eigenstates of a many-body Hamiltonian. We show in a model system that the Helmholtz free energy is minimized within this subspace as the iteration number increases. We show that the subspace expanded by the small basis systematically converges towards the subspace expanded by the lowest energy eigenstates. Possible applications of this method to calculate the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can be also used to accelerate the calculation of the ground or excited states with Quantum Monte Carlo.« less

Mouse Experimental Myopia Has Features of Primate Myopia

PubMed Central

Tkatchenko, Tatiana V.; Shen, Yimin

2010-01-01

Purpose. Several recent studies have suggested that experimental myopia can be induced in mice. However, it is not clear what role the photopic visual input plays in this process and whether mouse myopia is similar to human myopia. The purpose of this study was to carry out an in vivo high-resolution analysis of changes in ocular components and refractive state of the eye upon induction of experimental myopia in mice. Methods. A high-resolution small animal MRI system and a high-resolution automated eccentric infrared photorefractor were used to analyze changes of the refractive state and ocular components in C57BL/6J mice associated with experimental myopia induced by diffusers and −25 D lenses under photopic conditions. Results. The authors found that both diffusers and −25 D lenses induce myopia in C57BL/6J mice under photopic conditions (continuous light, 200 ± 15 lux). The extent of myopic shift induced by −25 D lenses was greater than the shift induced by diffusers (−15.2 ± 0.7 D, lenses; −12.0 ± 1.4 D, diffusers). Myopia in mice is attributed to an increase in size of the postequatorial segment of the eye. Experimental myopia in mice can be induced only during the susceptible period in postnatal development, which ends around postnatal day 67. Conclusions. Both diffusers and spectacle lenses induce myopia in mice under photopic conditions, during the susceptible period in postnatal development. Myopia in mice is associated with elongation of the vitreous chamber of the eye, as in humans and nonhuman primates. PMID:19875658

High-order finite-volume solutions of the steady-state advection-diffusion equation with nonlinear Robin boundary conditions

NASA Astrophysics Data System (ADS)

Lin, Zhi; Zhang, Qinghai

2017-09-01

We propose high-order finite-volume schemes for numerically solving the steady-state advection-diffusion equation with nonlinear Robin boundary conditions. Although the original motivation comes from a mathematical model of blood clotting, the nonlinear boundary conditions may also apply to other scientific problems. The main contribution of this work is a generic algorithm for generating third-order, fourth-order, and even higher-order explicit ghost-filling formulas to enforce nonlinear Robin boundary conditions in multiple dimensions. Under the framework of finite volume methods, this appears to be the first algorithm of its kind. Numerical experiments on boundary value problems show that the proposed fourth-order formula can be much more accurate and efficient than a simple second-order formula. Furthermore, the proposed ghost-filling formulas may also be useful for solving other partial differential equations.

Gas storage materials, including hydrogen storage materials

DOEpatents

Mohtadi, Rana F; Wicks, George G; Heung, Leung K; Nakamura, Kenji

2013-02-19

A material for the storage and release of gases comprises a plurality of hollow elements, each hollow element comprising a porous wall enclosing an interior cavity, the interior cavity including structures of a solid-state storage material. In particular examples, the storage material is a hydrogen storage material such as a solid state hydride. An improved method for forming such materials includes the solution diffusion of a storage material solution through a porous wall of a hollow element into an interior cavity.

Gas storage materials, including hydrogen storage materials

DOEpatents

Mohtadi, Rana F; Wicks, George G; Heung, Leung K; Nakamura, Kenji

2014-11-25

A material for the storage and release of gases comprises a plurality of hollow elements, each hollow element comprising a porous wall enclosing an interior cavity, the interior cavity including structures of a solid-state storage material. In particular examples, the storage material is a hydrogen storage material, such as a solid state hydride. An improved method for forming such materials includes the solution diffusion of a storage material solution through a porous wall of a hollow element into an interior cavity.

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.

Local discretization method for overdamped Brownian motion on a potential with multiple deep wells.

PubMed

Nguyen, P T T; Challis, K J; Jack, M W

2016-11-01

We present a general method for transforming the continuous diffusion equation describing overdamped Brownian motion on a time-independent potential with multiple deep wells to a discrete master equation. The method is based on an expansion in localized basis states of local metastable potentials that match the full potential in the region of each potential well. Unlike previous basis methods for discretizing Brownian motion on a potential, this approach is valid for periodic potentials with varying multiple deep wells per period and can also be applied to nonperiodic systems. We apply the method to a range of potentials and find that potential wells that are deep compared to five times the thermal energy can be associated with a discrete localized state while shallower wells are better incorporated into the local metastable potentials of neighboring deep potential wells.

Local discretization method for overdamped Brownian motion on a potential with multiple deep wells

NASA Astrophysics Data System (ADS)

Nguyen, P. T. T.; Challis, K. J.; Jack, M. W.

2016-11-01

We present a general method for transforming the continuous diffusion equation describing overdamped Brownian motion on a time-independent potential with multiple deep wells to a discrete master equation. The method is based on an expansion in localized basis states of local metastable potentials that match the full potential in the region of each potential well. Unlike previous basis methods for discretizing Brownian motion on a potential, this approach is valid for periodic potentials with varying multiple deep wells per period and can also be applied to nonperiodic systems. We apply the method to a range of potentials and find that potential wells that are deep compared to five times the thermal energy can be associated with a discrete localized state while shallower wells are better incorporated into the local metastable potentials of neighboring deep potential wells.

Heterostructures with diffused interfaces: Luminescent technique for ascertainment of band alignment type

NASA Astrophysics Data System (ADS)

Abramkin, D. S.; Gutakovskii, A. K.; Shamirzaev, T. S.

2018-03-01

The experimental ascertainment of band alignment type for semiconductor heterostructures with diffused interfaces is discussed. A method based on the analysis of the spectral shift of photoluminescence (PL) band with excitation density (Pex) that takes into account state filling and band bending effects on the PL band shift is developed. It is shown that the shift of PL band maximum position is proportional to ℏωmax ˜ (Ue + Uh).ln(Pex) + b.Pex1/3, where Ue (Uh) are electron (hole) Urbach energy tail, and parameter b characterizes the effect of band bending or is equal to zero for heterostructures with type-II or type-I band alignment, respectively. The method was approved with InAs/AlAs, GaAs/AlAs, GaSb/AlAs, and AlSb/AlAs heterostructures containing quantum wells.

A solid-state NMR method to determine domain sizes in multi-component polymer formulations

NASA Astrophysics Data System (ADS)

Schlagnitweit, Judith; Tang, Mingxue; Baias, Maria; Richardson, Sara; Schantz, Staffan; Emsley, Lyndon

2015-12-01

Polymer domain sizes are related to many of the physical properties of polymers. Here we present a solid-state NMR experiment that is capable of measuring domain sizes in multi-component mixtures. The method combines selective excitation of carbon magnetization to isolate a specific component with proton spin diffusion to report on domain size. We demonstrate the method in the context of controlled release formulations, which represents one of today's challenges in pharmaceutical science. We show that we can measure domain sizes of interest in the different components of industrial pharmaceutical formulations at natural isotopic abundance containing various (modified) cellulose derivatives, such as microcrystalline cellulose matrixes that are film-coated with a mixture of ethyl cellulose (EC) and hydroxypropyl cellulose (HPC).

A review of double-diffusion wood preservation suitable for Alaska.

Treesearch

K. Josephine Pavia

2006-01-01

Currently, all treated lumber used in Alaska is imported from the 48 contiguous states and Canada because there are no wood-treating facilities in Alaska. This report explores conventional and alternative wood-treating methods and reviews previous studies and laboratory tests on treated wood. In investigating wood treatment as a possible processing option for Alaska...

Transport coefficients and heat fluxes in non-equilibrium high-temperature flows with electronic excitation

NASA Astrophysics Data System (ADS)

Istomin, V. A.; Kustova, E. V.

2017-02-01

The influence of electronic excitation on transport processes in non-equilibrium high-temperature ionized mixture flows is studied. Two five-component mixtures, N 2 / N2 + / N / N + / e - and O 2 / O2 + / O / O + / e - , are considered taking into account the electronic degrees of freedom for atomic species as well as the rotational-vibrational-electronic degrees of freedom for molecular species, both neutral and ionized. Using the modified Chapman-Enskog method, the transport coefficients (thermal conductivity, shear viscosity and bulk viscosity, diffusion and thermal diffusion) are calculated in the temperature range 500-50 000 K. Thermal conductivity and bulk viscosity coefficients are strongly affected by electronic states, especially for neutral atomic species. Shear viscosity, diffusion, and thermal diffusion coefficients are not sensible to electronic excitation if the size of excited states is assumed to be constant. The limits of applicability for the Stokes relation are discussed; at high temperatures, this relation is violated not only for molecular species but also for electronically excited atomic gases. Two test cases of strongly non-equilibrium flows behind plane shock waves corresponding to the spacecraft re-entry (Hermes and Fire II) are simulated numerically. Fluid-dynamic variables and heat fluxes are evaluated in gases with electronic excitation. In inviscid flows without chemical-radiative coupling, the flow-field is weakly affected by electronic states; however, in viscous flows, their influence can be more important, in particular, on the convective heat flux. The contribution of different dissipative processes to the heat transfer is evaluated as well as the effect of reaction rate coefficients. The competition of diffusion and heat conduction processes reduces the overall effect of electronic excitation on the convective heating, especially for the Fire II test case. It is shown that reliable models of chemical reaction rates are of great importance for accurate predictions of the fluid dynamic variables and heat fluxes.

Non-equilibrium steady-state distributions of colloids in a tilted periodic potential

NASA Astrophysics Data System (ADS)

Ma, Xiaoguang; Lai, Pik-Yin; Ackerson, Bruce; Tong, Penger

A two-layer colloidal system is constructed to study the effects of the external force F on the non-equilibrium steady-state (NESS) dynamics of the diffusing particles over a tilted periodic potential, in which detailed balance is broken due to the presence of a steady particle flux. The periodic potential is provided by the bottom layer colloidal spheres forming a fixed crystalline pattern on a glass substrate. The corrugated surface of the bottom colloidal crystal provides a gravitational potential field for the top layer diffusing particles. By tilting the sample with respect to gravity, a tangential component F is applied to the diffusing particles. The measured NESS probability density function Pss (x , y) of the particles is found to deviate from the equilibrium distribution depending on the driving or distance from equilibrium. The experimental results are compared with the exact solution of the 1D Smoluchowski equation and the numerical results of the 2D Smoluchowski equation. Moreover, from the obtained exact 1D solution, we develop an analytical method to accurately extract the 1D potential U0 (x) from the measured Pss (x) . Work supported in part by the Research Grants Council of Hong Kong SAR.

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: A path for the optimization of low-energy many-body bases

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

Reboredo, Fernando A.; Kim, Jeongnim

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspacemore » of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.« less

When Do States Respond to Low Fertility? Contexts of State Concern in Wealthier Countries, 1976-2011.

PubMed

Marshall, Emily A

2015-06-01

Since the 1970s, expressions of state concern over low fertility have greatly increased among wealthier countries. This study asks to what extent this increase is explained by demographic factors, national-level economic and political factors, and processes of international diffusion and changing international norms. Analyses integrate the world polity literature on global policy diffusion with a social problems approach to examine international diffusion of state concern among more powerful members of the world polity, a process that can produce changes in international policy consensus. Comparisons of the characteristics of states that do and do not express concern over low fertility find that among wealthier "first-world" countries, state concern has become more responsive to fertility rates: fertility rates are not significantly associated with concern early in the study period, but are strongly associated with concern later in the study period. There is no evidence that integration into the world polity is associated with concern in these countries, and some evidence that less integrated countries are more likely to express concern, suggesting that processes shaping the diffusion of state concern may differ from those identified as shaping policy diffusion in the existing literature. Among "second-world" former Eastern bloc countries, different patterns of associations reflect different political histories: concern is associated only with demographic factors, with no significant change in this association over time.

When Do States Respond to Low Fertility? Contexts of State Concern in Wealthier Countries, 1976–2011

PubMed Central

Marshall, Emily A.

2015-01-01

Since the 1970s, expressions of state concern over low fertility have greatly increased among wealthier countries. This study asks to what extent this increase is explained by demographic factors, national-level economic and political factors, and processes of international diffusion and changing international norms. Analyses integrate the world polity literature on global policy diffusion with a social problems approach to examine international diffusion of state concern among more powerful members of the world polity, a process that can produce changes in international policy consensus. Comparisons of the characteristics of states that do and do not express concern over low fertility find that among wealthier “first-world” countries, state concern has become more responsive to fertility rates: fertility rates are not significantly associated with concern early in the study period, but are strongly associated with concern later in the study period. There is no evidence that integration into the world polity is associated with concern in these countries, and some evidence that less integrated countries are more likely to express concern, suggesting that processes shaping the diffusion of state concern may differ from those identified as shaping policy diffusion in the existing literature. Among “second-world” former Eastern bloc countries, different patterns of associations reflect different political histories: concern is associated only with demographic factors, with no significant change in this association over time. PMID:26213421

A novel content-based active contour model for brain tumor segmentation.

PubMed

Sachdeva, Jainy; Kumar, Vinod; Gupta, Indra; Khandelwal, Niranjan; Ahuja, Chirag Kamal

2012-06-01

Brain tumor segmentation is a crucial step in surgical and treatment planning. Intensity-based active contour models such as gradient vector flow (GVF), magneto static active contour (MAC) and fluid vector flow (FVF) have been proposed to segment homogeneous objects/tumors in medical images. In this study, extensive experiments are done to analyze the performance of intensity-based techniques for homogeneous tumors on brain magnetic resonance (MR) images. The analysis shows that the state-of-art methods fail to segment homogeneous tumors against similar background or when these tumors show partial diversity toward the background. They also have preconvergence problem in case of false edges/saddle points. However, the presence of weak edges and diffused edges (due to edema around the tumor) leads to oversegmentation by intensity-based techniques. Therefore, the proposed method content-based active contour (CBAC) uses both intensity and texture information present within the active contour to overcome above-stated problems capturing large range in an image. It also proposes a novel use of Gray-Level Co-occurrence Matrix to define texture space for tumor segmentation. The effectiveness of this method is tested on two different real data sets (55 patients - more than 600 images) containing five different types of homogeneous, heterogeneous, diffused tumors and synthetic images (non-MR benchmark images). Remarkable results are obtained in segmenting homogeneous tumors of uniform intensity, complex content heterogeneous, diffused tumors on MR images (T1-weighted, postcontrast T1-weighted and T2-weighted) and synthetic images (non-MR benchmark images of varying intensity, texture, noise content and false edges). Further, tumor volume is efficiently extracted from 2-dimensional slices and is named as 2.5-dimensional segmentation. Copyright © 2012 Elsevier Inc. All rights reserved.

Stochastic Optimal Control via Bellman's Principle

NASA Technical Reports Server (NTRS)

Crespo, Luis G.; Sun, Jian Q.

2003-01-01

This paper presents a method for finding optimal controls of nonlinear systems subject to random excitations. The method is capable to generate global control solutions when state and control constraints are present. The solution is global in the sense that controls for all initial conditions in a region of the state space are obtained. The approach is based on Bellman's Principle of optimality, the Gaussian closure and the Short-time Gaussian approximation. Examples include a system with a state-dependent diffusion term, a system in which the infinite hierarchy of moment equations cannot be analytically closed, and an impact system with a elastic boundary. The uncontrolled and controlled dynamics are studied by creating a Markov chain with a control dependent transition probability matrix via the Generalized Cell Mapping method. In this fashion, both the transient and stationary controlled responses are evaluated. The results show excellent control performances.

Convergence to equilibrium of renormalised solutions to nonlinear chemical reaction–diffusion systems

NASA Astrophysics Data System (ADS)

Fellner, Klemens; Tang, Bao Quoc

2018-06-01

The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex balanced condition. By applying the so-called entropy method, we show that if the system does not have boundary equilibria, i.e. equilibrium states lying on the boundary of R_+^N, then any renormalised solution converges exponentially to the complex balanced equilibrium with a rate, which can be computed explicitly up to a finite-dimensional inequality. This inequality is proven via a contradiction argument and thus not explicitly. An explicit method of proof, however, is provided for a specific application modelling a reversible enzyme reaction by exploiting the specific structure of the conservation laws. Our approach is also useful to study the trend to equilibrium for systems possessing boundary equilibria. More precisely, to show the convergence to equilibrium for systems with boundary equilibria, we establish a sufficient condition in terms of a modified finite-dimensional inequality along trajectories of the system. By assuming this condition, which roughly means that the system produces too much entropy to stay close to a boundary equilibrium for infinite time, the entropy method shows exponential convergence to equilibrium for renormalised solutions to complex balanced systems with boundary equilibria.

Comparison of diffusion- and pumped-sampling methods to monitor volatile organic compounds in ground water, Massachusetts Military Reservation, Cape Cod, Massachusetts, July 1999-December 2002

USGS Publications Warehouse

Archfield, Stacey A.; LeBlanc, Denis R.

2005-01-01

To evaluate diffusion sampling as an alternative method to monitor volatile organic compound (VOC) concentrations in ground water, concentrations in samples collected by traditional pumped-sampling methods were compared to concentrations in samples collected by diffusion-sampling methods for 89 monitoring wells at or near the Massachusetts Military Reservation, Cape Cod. Samples were analyzed for 36 VOCs. There was no substantial difference between the utility of diffusion and pumped samples to detect the presence or absence of a VOC. In wells where VOCs were detected, diffusion-sample concentrations of tetrachloroethene (PCE) and trichloroethene (TCE) were significantly lower than pumped-sample concentrations. Because PCE and TCE concentrations detected in the wells dominated the calculation of many of the total VOC concentrations, when VOC concentrations were summed and compared by sampling method, visual inspection also showed a downward concentration bias in the diffusion-sample concentration. The degree to which pumped- and diffusion-sample concentrations agreed was not a result of variability inherent within the sampling methods or the diffusion process itself. A comparison of the degree of agreement in the results from the two methods to 13 quantifiable characteristics external to the sampling methods offered only well-screen length as being related to the degree of agreement between the methods; however, there is also evidence to indicate that the flushing rate of water through the well screen affected the agreement between the sampling methods. Despite poor agreement between the concentrations obtained by the two methods at some wells, the degree to which the concentrations agree at a given well is repeatable. A one-time, well-bywell comparison between diffusion- and pumped-sampling methods could determine which wells are good candidates for the use of diffusion samplers. For wells with good method agreement, the diffusion-sampling method is a time-saving and cost-effective alternative to pumped-sampling methods in a long-term monitoring program, such as at the Massachusetts Military Reservation.

Importance of hydrophobic traps for proton diffusion in lyotropic liquid crystals

DOE PAGES

McDaniel, Jesse G.; Yethiraj, Arun

2016-03-04

The diffusion of protons in self-assembled systems is potentially important for the design of efficient proton exchange membranes. In this work, we study proton dynamics in a low-water content, lamellar phase of an sodium-carboxylate gemini surfactant/water system using computer simulations. The hopping of protons via the Grotthuss mechanism is explicity allowed through the multi-state empirical valence bond (MS-EVB) method. We find that the hydronium ion is trapped on the hydrophobic side of the surfactant-water interface, and proton diffusion then proceeds by hopping between surface sites. The importance of hydrophobic traps is surprising, because one would expect the hydronium ions tomore » be trapped at the charged head-groups. Finally, the physics illustrated in this system should be relevant to the proton dynamics in other amphiphilic membrane systems, whenever there exists exposed hydrophobic surface regions.« less

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Catalytic conversion reactions mediated by single-file diffusion in linear nanopores: hydrodynamic versus stochastic behavior.

PubMed

Ackerman, David M; Wang, Jing; Wendel, Joseph H; Liu, Da-Jiang; Pruski, Marek; Evans, James W

2011-03-21

We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. Diffusion within the pores is subject to a strict single-file (no passing) constraint. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice-gas model for this reaction-diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction-diffusion type equations (mf-RDE). For slowly varying concentrations, we further develop coarse-grained continuum hydrodynamic reaction-diffusion equations (h-RDE) incorporating a precise treatment of single-file diffusion in this multispecies system. The h-RDE successfully describe nontrivial aspects of transient behavior, in contrast to the mf-RDE, and also correctly capture unreactive steady-state behavior in the pore interior. However, steady-state reactivity, which is localized near the pore ends when those regions are catalytic, is controlled by fluctuations not incorporated into the hydrodynamic treatment. The mf-RDE partly capture these fluctuation effects, but cannot describe scaling behavior of the reactivity.

The "Spread" of Merit-Based College Aid: Politics, Policy Consortia, and Interstate Competition

ERIC Educational Resources Information Center

Cohen-Vogel, Lora; Ingle, William Kyle; Levine, Amy Albee; Spence, Matthew

2008-01-01

Many political scientists maintain that public policies diffuse across states and that proximate states, in particular, influence one another's policy activities. Using state-funded merit aid for college as its case, this article takes a new approach to the study of the diffusion phenomenon, leaving behind conventional techniques used by…

Analytical approach to impurity transport studies: Charge state dynamics in tokamak plasmas

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

Shurygin, V. A.

2006-08-15

Ionization and recombination of plasma impurities govern their charge state kinetics, which is imposed upon the dynamics of ions that implies a superposition of the appropriate probabilities and causes an impurity charge state dynamics. The latter is considered in terms of a vector field of conditional probabilities and presented by a vector charge state distribution function with coupled equations of the Kolmogorov type. Analytical solutions of a diffusion problem are derived with the basic spatial and temporal dimensionless parameters. Analysis shows that the empirical scaling D{sub A}{proportional_to}n{sub e}{sup -1} [K. Krieger, G. Fussmann, and the ASDEX Upgrade Team, Nucl. Fusionmore » 30, 2392 (1990)] can be explained by the ratio of the diffusive and kinetic terms, D{sub A}/(n{sub e}a{sup 2}), being used instead of diffusivity, D{sub A}. The derived time scales of charge state dynamics are given by a sum of the diffusive and kinetic times. Detailed simulations of charge state dynamics are performed for argon impurity and compared with the reference modeling.« less

Benchmarking FEniCS for mantle convection simulations

NASA Astrophysics Data System (ADS)

Vynnytska, L.; Rognes, M. E.; Clark, S. R.

2013-01-01

This paper evaluates the usability of the FEniCS Project for mantle convection simulations by numerical comparison to three established benchmarks. The benchmark problems all concern convection processes in an incompressible fluid induced by temperature or composition variations, and cover three cases: (i) steady-state convection with depth- and temperature-dependent viscosity, (ii) time-dependent convection with constant viscosity and internal heating, and (iii) a Rayleigh-Taylor instability. These problems are modeled by the Stokes equations for the fluid and advection-diffusion equations for the temperature and composition. The FEniCS Project provides a novel platform for the automated solution of differential equations by finite element methods. In particular, it offers a significant flexibility with regard to modeling and numerical discretization choices; we have here used a discontinuous Galerkin method for the numerical solution of the advection-diffusion equations. Our numerical results are in agreement with the benchmarks, and demonstrate the applicability of both the discontinuous Galerkin method and FEniCS for such applications.

Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation.

PubMed

Boitard, Simon; Loisel, Patrice

2007-05-01

The probability distribution of haplotype frequencies in a population, and the way it is influenced by genetical forces such as recombination, selection, random drift ...is a question of fundamental interest in population genetics. For large populations, the distribution of haplotype frequencies for two linked loci under the classical Wright-Fisher model is almost impossible to compute because of numerical reasons. However the Wright-Fisher process can in such cases be approximated by a diffusion process and the transition density can then be deduced from the Kolmogorov equations. As no exact solution has been found for these equations, we developed a numerical method based on finite differences to solve them. It applies to transient states and models including selection or mutations. We show by several tests that this method is accurate for computing the conditional joint density of haplotype frequencies given that no haplotype has been lost. We also prove that it is far less time consuming than other methods such as Monte Carlo simulations.

Some basic mathematical methods of diffusion theory. [emphasis on atmospheric applications

NASA Technical Reports Server (NTRS)

Giere, A. C.

1977-01-01

An introductory treatment of the fundamentals of diffusion theory is presented, starting with molecular diffusion and leading up to the statistical methods of turbulent diffusion. A multilayer diffusion model, designed to permit concentration and dosage calculations downwind of toxic clouds from rocket vehicles, is described. The concepts and equations of diffusion are developed on an elementary level, with emphasis on atmospheric applications.

Part-2: Analytical Expressions of Concentrations of Glucose, Oxygen, and Gluconic Acid in a Composite Membrane for Closed-Loop Insulin Delivery for the Non-steady State Conditions.

PubMed

Mehala, N; Rajendran, L; Meena, V

2017-02-01

A mathematical model developed by Abdekhodaie and Wu (J Membr Sci 335:21-31, 2009), which describes a dynamic process involving an enzymatic reaction and diffusion of reactants and product inside glucose-sensitive composite membrane has been discussed. This theoretical model depicts a system of non-linear non-steady state reaction diffusion equations. These equations have been solved using new approach of homotopy perturbation method and analytical solutions pertaining to the concentrations of glucose, oxygen, and gluconic acid are derived. These analytical results are compared with the numerical results, and limiting case results for steady state conditions and a good agreement is observed. The influence of various kinetic parameters involved in the model has been presented graphically. Theoretical evaluation of the kinetic parameters like the maximal reaction velocity (V max ) and Michaelis-Menten constants for glucose and oxygen (K g and K ox ) is also reported. This predicted model is very much useful for designing the glucose-responsive composite membranes for closed-loop insulin delivery.

Measurement of radon diffusion in polyethylene based on alpha detection

NASA Astrophysics Data System (ADS)

Rau, Wolfgang

2012-02-01

Radon diffusion in different materials has been measured in the past. Usually the diffusion measurements are based on a direct determination of the amount of radon that diffuses through a thin layer of material. Here we present a method based on the measurement of the radon daughter products which are deposited inside the material. Looking at the decay of 210Po allows us to directly measure the exponential diffusion profile characterized by the diffusion length. In addition we can determine the solubility of radon in PE. We also describe a second method to determine the diffusion constant based on the short-lived radon daughter products 218Po and 214Po, using the identical experimental setup. Measurements for regular polyethylene (PE) and High Molecular Weight Polyethylene (HMWPE) yielded diffusion lengths of (1.3±0.3) mm and (0.8±0.2) mm and solubilities of 0.5±0.1 and 0.7±0.2, respectively, for the first method; the diffusion lengths extracted from the second method are noticeably larger which may be caused by different experimental conditions during diffusion.

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.

Minimum uncertainty and squeezing in diffusion processes and stochastic quantization

NASA Technical Reports Server (NTRS)

Demartino, S.; Desiena, S.; Illuminati, Fabrizo; Vitiello, Giuseppe

1994-01-01

We show that uncertainty relations, as well as minimum uncertainty coherent and squeezed states, are structural properties for diffusion processes. Through Nelson stochastic quantization we derive the stochastic image of the quantum mechanical coherent and squeezed states.

An accurate two-dimensional LBIC solution for bipolar transistors

NASA Astrophysics Data System (ADS)

Benarab, A.; Baudrand, H.; Lescure, M.; Boucher, J.

1988-05-01

A complete solution of the diffusion problem of carriers generated by a located light beam in the emitter and base region of a bipolar structure is presented. Green's function method and moment method are used to solve the 2-D diffusion equation in these regions. From the Green's functions solution of these equations, the light beam induced currents (LBIC) in the different junctions of the structure due to an extended generation represented by a rectangular light spot; are thus decided. The equations of these currents depend both on the parameters which characterise the structure, surface states, dimensions of the emitter and the base region, and the characteristics of the light spot, that is to say, the width and the wavelength. Curves illustrating the variation of the various LBIC in the base region junctions as a function of the impact point of the light beam ( x0) for different values of these parameters are discussed. In particular, the study of the base-emitter currents when the light beam is swept right across the sample illustrates clearly a good geometrical definition of the emitter region up to base end of the emitter-base space-charge areas and a "whirl" lateral diffusion beneath this region, (i.e. the diffusion of the generated carriers near the surface towards the horizontal base-emitter junction and those created beneath this junction towards the lateral (B-E) junctions).

Diffusion Monte Carlo studies of MB-pol (H2O)2-6 and (D2O)2-6 clusters: Structures and binding energies

NASA Astrophysics Data System (ADS)

Mallory, Joel D.; Mandelshtam, Vladimir A.

2016-08-01

We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H2O)2-6 clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitive to the isotope substitution. Most remarkably, the ground state of the (H2O)6 hexamer is represented by four distinct cage structures, while that of (D2O)6 is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H2O)6 and (D2O)6, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F.

Hylleraas-Configuration Interaction study of the 1S ground state of the negative Li ion.

PubMed

Sims, James S

2017-12-28

In a previous work Sims and Hagstrom [J. Chem. Phys. 140, 224312 (2014)] reported Hylleraas-Configuration Interaction (Hy-CI) method variational calculations for the neutral atom and positive ion 1 S ground states of the beryllium isoelectronic sequence. The Li - ion, nominally the first member of this series, has a decidedly different electronic structure. This paper reports the results of a large, comparable calculation for the Li - ground state to explore how well the Hy-CI method can represent the more diffuse L shell of Li - which is representative of the Be(2sns) excited states as well. The best non-relativistic energy obtained was -7.500 776 596 hartree, indicating that 10 - 20 nh accuracy is attainable in Hy-CI and that convergence of the r 12 r 34 double cusp is fast and that this correlation type can be accurately represented within the Hy-CI model.

A framework to analyze cerebral mean diffusivity using surface guided diffusion mapping in diffusion tensor imaging

PubMed Central

Kwon, Oh-Hun; Park, Hyunjin; Seo, Sang-Won; Na, Duk L.; Lee, Jong-Min

2015-01-01

The mean diffusivity (MD) value has been used to describe microstructural properties in Diffusion Tensor Imaging (DTI) in cortical gray matter (GM). Recently, researchers have applied a cortical surface generated from the T1-weighted volume. When the DTI data are analyzed using the cortical surface, it is important to assign an accurate MD value from the volume space to the vertex of the cortical surface, considering the anatomical correspondence between the DTI and the T1-weighted image. Previous studies usually sampled the MD value using the nearest-neighbor (NN) method or Linear method, even though there are geometric distortions in diffusion-weighted volumes. Here we introduce a Surface Guided Diffusion Mapping (SGDM) method to compensate for such geometric distortions. We compared our SGDM method with results using NN and Linear methods by investigating differences in the sampled MD value. We also projected the tissue classification results of non-diffusion-weighted volumes to the cortical midsurface. The CSF probability values provided by the SGDM method were lower than those produced by the NN and Linear methods. The MD values provided by the NN and Linear methods were significantly greater than those of the SGDM method in regions suffering from geometric distortion. These results indicate that the NN and Linear methods assigned the MD value in the CSF region to the cortical midsurface (GM region). Our results suggest that the SGDM method is an effective way to correct such mapping errors. PMID:26236180

A physics-based fractional order model and state of energy estimation for lithium ion batteries. Part II: Parameter identification and state of energy estimation for LiFePO4 battery

NASA Astrophysics Data System (ADS)

Li, Xiaoyu; Pan, Ke; Fan, Guodong; Lu, Rengui; Zhu, Chunbo; Rizzoni, Giorgio; Canova, Marcello

2017-11-01

State of energy (SOE) is an important index for the electrochemical energy storage system in electric vehicles. In this paper, a robust state of energy estimation method in combination with a physical model parameter identification method is proposed to achieve accurate battery state estimation at different operating conditions and different aging stages. A physics-based fractional order model with variable solid-state diffusivity (FOM-VSSD) is used to characterize the dynamic performance of a LiFePO4/graphite battery. In order to update the model parameter automatically at different aging stages, a multi-step model parameter identification method based on the lexicographic optimization is especially designed for the electric vehicle operating conditions. As the battery available energy changes with different applied load current profiles, the relationship between the remaining energy loss and the state of charge, the average current as well as the average squared current is modeled. The SOE with different operating conditions and different aging stages are estimated based on an adaptive fractional order extended Kalman filter (AFEKF). Validation results show that the overall SOE estimation error is within ±5%. The proposed method is suitable for the electric vehicle online applications.

Mathematical model for the Bridgman-Stockbarger crystal growing system

NASA Technical Reports Server (NTRS)

Roberts, G. O.

1986-01-01

In a major technical breakthrough, a computer model for Bridgman-Stockbarger crystal growth was developed. The model includes melt convection, solute effects, thermal conduction in the ampule, melt, and crystal, and the determination of the curved moving crystal-melt interface. The key to the numerical method is the use of a nonuniform computational mesh which moves with the interface, so that the interface is a mesh surface. In addition, implicit methods are used for advection and diffusion of heat, concentration, and vorticity, for interface movement, and for internal gracity waves. This allows large time-steps without loss of stability or accuracy. Numerical results are presented for the interface shape, temperature distribution, and concentration distribution, in steady-state crystl growth. Solutions are presented for two test cases using water, with two different salts in solution. The two diffusivities differ by a factor of ten, and the concentrations differ by a factor of twenty.

A Reconstruction Approach to High-Order Schemes Including Discontinuous Galerkin for Diffusion

NASA Technical Reports Server (NTRS)

Huynh, H. T.

2009-01-01

We introduce a new approach to high-order accuracy for the numerical solution of diffusion problems by solving the equations in differential form using a reconstruction technique. The approach has the advantages of simplicity and economy. It results in several new high-order methods including a simplified version of discontinuous Galerkin (DG). It also leads to new definitions of common value and common gradient quantities at each interface shared by the two adjacent cells. In addition, the new approach clarifies the relations among the various choices of new and existing common quantities. Fourier stability and accuracy analyses are carried out for the resulting schemes. Extensions to the case of quadrilateral meshes are obtained via tensor products. For the two-point boundary value problem (steady state), it is shown that these schemes, which include most popular DG methods, yield exact common interface quantities as well as exact cell average solutions for nearly all cases.

An Eulerian/Lagrangian coupling procedure for three-dimensional vortical flows

NASA Technical Reports Server (NTRS)

Felici, Helene M.; Drela, Mark

1993-01-01

A coupled Eulerian/Lagrangian method is presented for the reduction of numerical diffusion observed in solutions of 3D vortical flows using standard Eulerian finite-volume time-marching procedures. A Lagrangian particle tracking method, added to the Eulerian time-marching procedure, provides a correction of the Eulerian solution. In turn, the Eulerian solution is used to integrate the Lagrangian state-vector along the particles trajectories. While the Eulerian solution ensures the conservation of mass and sets the pressure field, the particle markers describe accurately the convection properties and enhance the vorticity and entropy capturing capabilities of the Eulerian solver. The Eulerian/Lagrangian coupling strategies are discussed and the combined scheme is tested on a constant stagnation pressure flow in a 90 deg bend and on a swirling pipe flow. As the numerical diffusion is reduced when using the Lagrangian correction, a vorticity gradient augmentation is identified as a basic problem of this inviscid calculation.

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.

The C4H radical and the diffuse interstellar bands. An ab initio study

NASA Technical Reports Server (NTRS)

Kolbuszewski, Marcin

1994-01-01

An ab initio study of the low-lying electronic states of C4H has been presented where the species studied has a chi(2)sigma(+) ground state and two low lying pi states. Based on the vertical and adiabatic excitation energies between those states it is suggested that the 4428 A diffuse interstellar band is not carried by C4H. The application of the particle in a box model shows strong coincidences between the strong DIB's and predicted wavelengths of pi-pi transitions in C(2n)H series. Based on those coincidences, it is suggested the C(2n)H species as good candidates for carriers of diffuse interstellar bands.

Cross-diffusive effects on the onset of double-diffusive convection in a horizontal saturated porous fluid layer heated and salted from above

NASA Astrophysics Data System (ADS)

Rajib, Basu; C. Layek, G.

2013-05-01

Double-diffusive stationary and oscillatory instabilities at the marginal state in a saturated porous horizontal fluid layer heated and salted from above are investigated theoretically under the Darcy's framework for a porous medium. The contributions of Soret and Dufour coefficients are taken into account in the analysis. Linear stability analysis shows that the critical value of the Darcy—Rayleigh number depends on cross-diffusive parameters at marginally stationary convection, while the marginal state characterized by oscillatory convection does not depend on the cross-diffusion terms even if the condition and frequency of oscillatory convection depends on the cross-diffusive parameters. The critical value of the Darcy—Rayleigh number increases with increasing value of the solutal Darcy—Rayleigh number in the absence of cross-diffusive parameters. The critical Darcy—Rayleigh number decreases with increasing Soret number, resulting in destabilization of the system, while its value increases with increasing Dufour number, resulting in stabilization of the system at the marginal state characterized by stationary convection. The analysis reveals that the Dufour and Soret parameters as well as the porosity parameter play an important role in deciding the type of instability at the onset. This analysis also indicates that the stationary convection is followed by the oscillatory convection for certain fluid mixtures. It is interesting to note that the roles of cross-diffusive parameters on the double-diffusive system heated and salted from above are reciprocal to the double-diffusive system heated and salted from below.

Compositional and Ionic-Size Controls on the Diffusion of Divalent Cations in Garnet: Insights from Atomistic Simulations

NASA Astrophysics Data System (ADS)

Carlson, W. D.

2012-12-01

Divalent cations in garnet (Mg, Fe, Mn, Ca) diffuse at rates that depend strongly on the host-crystal composition and on the ionic radius of the diffusant. Understanding of the nanoscale basis for these behaviors comes from atomistic simulations that calculate energies in the static limit for the defects and transition-state configurations associated with each diffusive step. Diffusion of divalent cations requires (a) creation of a cation-vacancy defect in a dodecahedral site and of a charge-compensating oxygen-vacancy defect that may or may not be in close spatial association; (b) except in the case of self-diffusion, creation of an impurity defect in which a foreign atom replaces the normal atom in a dodecahedral site adjacent to the vacancy; and (c) during the diffusive process, motion of the diffusing atom to a 'saddlepoint' position that represents the transition-state configuration. Comparisons of the system's energy in these various states, in structures of different composition and for ions of different ionic size, allows assessment of the nanoscale controls on diffusion kinetics. Molecular-statics calculations quantify defect energies and identify the transition-state configuration: the maximum energy along the diffusion path between two adjacent dodecahedral sites results when the diffusing ion is surrounded symmetrically by the six oxygen atoms that lie between the two sites. Across the range of end-member compositions, self-diffusion coefficients measured at identical conditions, and the tracer diffusivity of a single ion measured at identical conditions, can each vary by five orders of magnitude or more. Measured activation energies for these motions, however, are all equivalent to within ±6%. Calculated activation energies are in agreement with observations, in that they vary by only ±10%. Calculated vacancy-formation energies, on the other hand, are significantly larger in expanded structures; for example, that energy is greater for Prp than for Grs by ~ 470 kJ/mol. Thus in expanded structures, much higher vacancy concentrations can be produced at the same energetic cost, greatly enhancing rates of diffusion. The primary explanation for the more rapid diffusion of divalent cations in structures with larger cell dimensions therefore comes not from reduced saddlepoint strain energies in more compliant structures, but instead from the smaller energy required to create vacancy defects. Diffusivities of divalent cations exhibit a curious parabolic dependence on ionic size: for each structure, an optimally-sized ion exists, close in size to the dominant ion, that exhibits the fastest diffusion. Larger ions — and enigmatically, smaller ions — both diffuse more slowly. Calculated impurity-defect energies show that undersized impurity ions are bound more tightly in their sites, but the effects are too small in comparison to corresponding reductions in strain energy for the transition-state configuration to account for observed rate differences. Calculated vacancy-association energies reveal a slight tendency for vacancies to associate preferentially with larger impurity ions, but again the effect appears to be too small to provide a full explanation for observed behaviors.

LiFePO4/C nanocomposites for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Eftekhari, Ali

2017-03-01

LiFePO4, as the most famous member of the family of olivine-type lithium transition metal phosphates, is one of the promising candidates for the cathodes of lithium-ion batteries. However, its battery performance is limited by its low electrical conductivity and slow Li solid-state diffusion. Various methods have been attempted to improve the battery performance of lithium iron phosphate. Among them, compositing the LiFePO4 with carbon nanomaterials seems to be the most promising, as it is facile and efficient. Carbon nanomaterials usually serve as a conductive agent to improve the electrical conductivity while increasing the material porosity in which the solid-state diffusion distances are significantly shortened. Owing to the popularity of various carbonaceous nanomaterials, there is no straightforward line of research for comparing the LiFePO4/C nanocomposites. This review aims to provide a general perspective based on the research achievements reported in the literature. While surveying the research findings reported in the literature, controversial issues are also discussed. The possible contribution of pseudocapacitance as a result of functionalized carbon or LiFePO4 lattice defects is described, since from a practical perspective, a LiFePO4/C electrode can be considered as a supercapacitor at high C rates (with a specific capacitance as large as 200 F g-1). The Li diffusion in LiFePO4 has not been well understood yet; while the Li diffusion within the LiFePO4 lattice seems to be quite fast, the peculiar interfacial electrochemistry of LiFePO4 slows down the diffusion within the entire electrode by a few orders of magnitude.

Diffusion parameter mapping with the combined intravoxel incoherent motion and kurtosis model using artificial neural networks at 3 T.

PubMed

Bertleff, Marco; Domsch, Sebastian; Weingärtner, Sebastian; Zapp, Jascha; O'Brien, Kieran; Barth, Markus; Schad, Lothar R

2017-12-01

Artificial neural networks (ANNs) were used for voxel-wise parameter estimation with the combined intravoxel incoherent motion (IVIM) and kurtosis model facilitating robust diffusion parameter mapping in the human brain. The proposed ANN approach was compared with conventional least-squares regression (LSR) and state-of-the-art multi-step fitting (LSR-MS) in Monte-Carlo simulations and in vivo in terms of estimation accuracy and precision, number of outliers and sensitivity in the distinction between grey (GM) and white (WM) matter. Both the proposed ANN approach and LSR-MS yielded visually increased parameter map quality. Estimations of all parameters (perfusion fraction f, diffusion coefficient D, pseudo-diffusion coefficient D*, kurtosis K) were in good agreement with the literature using ANN, whereas LSR-MS resulted in D* overestimation and LSR yielded increased values for f and D*, as well as decreased values for K. Using ANN, outliers were reduced for the parameters f (ANN, 1%; LSR-MS, 19%; LSR, 8%), D* (ANN, 21%; LSR-MS, 25%; LSR, 23%) and K (ANN, 0%; LSR-MS, 0%; LSR, 15%). Moreover, ANN enabled significant distinction between GM and WM based on all parameters, whereas LSR facilitated this distinction only based on D and LSR-MS on f, D and K. Overall, the proposed ANN approach was found to be superior to conventional LSR, posing a powerful alternative to the state-of-the-art method LSR-MS with several advantages in the estimation of IVIM-kurtosis parameters, which might facilitate increased applicability of enhanced diffusion models at clinical scan times. Copyright © 2017 John Wiley & Sons, Ltd.

[Analyze nanofiltration separation rule of chlorogenic acid from low concentration ethanol by Donnan effect and solution-diffusion effect].

PubMed

Li, Cun-Yu; Liu, Li-Cheng; Jin, Li-Yang; Li, Hong-Yang; Peng, Guo-Ping

2017-07-01

To separate chlorogenic acid from low concentration ethanol and explore the influence of Donnan effect and solution-diffusion effect on the nanofiltration separation rule. The experiment showed that solution pH and ethanol volume percent had influences on the separation of chlorogenic acid. Within the pH values from 3 to 7 for chlorogenic acid in 30% ethanol, the rejection rate of chlorogenic acid was changed by 70.27%. Through the response surface method for quadratic regression model, an interaction had been found in molecule weight cut-off, pH and ethanol volume percent. In fixed nanofiltration apparatus, the existence states of chlorogenic acid determinedits separation rules. With the increase of ethanol concentration, the free form chlorogenic acid was easily adsorbed, dissolved on membrane surface and then caused high transmittance due to the solution-diffusion effect. However, at the same time, due to the double effects of Donnan effect and solution-diffusion effect, the ionic state of chlorogenic acid was hard to be adsorbed in membrane surface and thus caused high rejection rate. The combination of Box-Behnken design and response surface analysis can well optimize the concentrate process by nanofiltration, and the results showed that nanofiltration had several big advantages over the traditional vacuum concentrate technology, meanwhile, and solved the problems of low efficiency and serious component lossesin the Chinese medicines separation process for low concentration organic solvent-water solution. Copyright© by the Chinese Pharmaceutical Association.

Study of fluorescence quenching due to 2, 3, 5, 6-tetrafluoro-7, 7', 8, 8'-tetracyano quinodimethane and its solid state diffusion analysis using photoluminescence spectroscopy.

PubMed

Tyagi, Priyanka; Tuli, Suneet; Srivastava, Ritu

2015-02-07

In this work, we have studied the fluorescence quenching and solid state diffusion of 2, 3, 5, 6-tetrafluoro-7,  7',  8,  8'-tetracyano quinodimethane (F4-TCNQ) using photoluminescence (PL) spectroscopy. Quenching studies were performed with tris (8-hydroxyquinolinato) aluminum (Alq3) in solid state samples. Thickness of F4-TCNQ was varied in order to realize different concentrations and study the effect of concentration. PL intensity has reduced with the increase in F4-TCNQ thicknesses. Stern-Volmer and bimolecular quenching constants were evaluated to be 13.8 M(-1) and 8.7 × 10(8) M(-1) s(-1), respectively. The quenching mechanism was found to be of static type, which was inferred by the independent nature of excited state life time from the F4-TCNQ thickness. Further, solid state diffusion of F4-TCNQ was studied by placing a spacing layer of α-NPD between F4-TCNQ and Alq3, and its thickness was varied to probe the diffusion length. PL intensity was found to increase with the increase in this thickness. Quenching efficiency was evaluated as a function of distance between F4-TCNQ and Alq3. These studies were performed for the samples having 1, 2.5, and 5.5 nm thicknesses of F4-TCNQ to study the thickness dependence of diffusion length. Diffusion lengths were evaluated to be 12.5, 15, and 20 nm for 1, 2.5, and 5.5 nm thicknesses of F4-TCNQ. These diffusion lengths were found to be very close to that of determined by secondary ion mass spectroscopy technique.

Polymeric hydrogen diffusion barrier, high-pressure storage tank so equipped, method of fabricating a storage tank and method of preventing hydrogen diffusion

DOEpatents

Lessing, Paul A [Idaho Falls, ID

2008-07-22

An electrochemically active hydrogen diffusion barrier which comprises an anode layer, a cathode layer, and an intermediate electrolyte layer, which is conductive to protons and substantially impermeable to hydrogen. A catalytic metal present in or adjacent to the anode layer catalyzes an electrochemical reaction that converts any hydrogen that diffuses through the electrolyte layer to protons and electrons. The protons and electrons are transported to the cathode layer and reacted to form hydrogen. The hydrogen diffusion barrier is applied to a polymeric substrate used in a storage tank to store hydrogen under high pressure. A storage tank equipped with the electrochemically active hydrogen diffusion barrier, a method of fabricating the storage tank, and a method of preventing hydrogen from diffusing out of a storage tank are also disclosed.

Polymeric hydrogen diffusion barrier, high-pressure storage tank so equipped, method of fabricating a storage tank and method of preventing hydrogen diffusion

DOEpatents

Lessing, Paul A.

2004-09-07

An electrochemically active hydrogen diffusion barrier which comprises an anode layer, a cathode layer, and an intermediate electrolyte layer, which is conductive to protons and substantially impermeable to hydrogen. A catalytic metal present in or adjacent to the anode layer catalyzes an electrochemical reaction that converts any hydrogen that diffuses through the electrolyte layer to protons and electrons. The protons and electrons are transported to the cathode layer and reacted to form hydrogen. The hydrogen diffusion barrier is applied to a polymeric substrate used in a storage tank to store hydrogen under high pressure. A storage tank equipped with the electrochemically active hydrogen diffusion barrier, a method of fabricating the storage tank, and a method of preventing hydrogen from diffusing out of a storage tank are also disclosed.

Picosecond dynamics of excited singlet states in organic microcrystals: Diffuse reflectance laser photolysis study

NASA Astrophysics Data System (ADS)

Ikeda, Noriaki; Koshioka, Masanori; Masuhara, Hiroshi; Yoshihara, Keitaro

1988-09-01

Absorption spectra and picosecond dynamics of the singlet exciton states of benzil and p-terphenyl in a microcrystal have been measured for the first time by analyzing the diffuse reflected spectra of the picosecond continuum.

Resonant Acoustic Measurement of Vapor Phase Transport Phenomenon

NASA Astrophysics Data System (ADS)

Schuhmann, R. J.; Garrett, S. L.; Matson, J. V.

2002-12-01

A major impediment to accurate non steady-state diffusion measurements is the ability to accurately measure and track a rapidly changing gas concentration without disturbing the system. Non-destructive methods that do not interfere with system dynamics have been developed in the past. These methods, however, have tended to be cumbersome or inaccurate at low concentrations. A new experimental approach has been developed to measure gaseous diffusion in free air and through porous materials. The method combines the traditional non steady-state laboratory methodology with resonant acoustic gas analysis. A phase-locked-loop (PLL) resonance frequency tracker is combined with a thermally insulated copper resonator. A piston sealed with a metal bellows excites the fundamental standing wave resonance of the resonator. The PLL maintains a constant phase difference (typically 90§) between the accelerometer mounted on the piston and a microphone near the piston to track the resonance frequency in real time. A capillary or glass bead filled core is fitted into an o-ring sealed opening at the end of the resonator opposite the bellows. The rate at which the tracer gas is replaced by air within the resonator is controlled by the diffusion coefficient of the gas in free air through the capillary (DA) or by the effective diffusion coefficient of the gas through the core (De). The mean molecular weight of the gas mixture in the resonator is directly determined six times each minute from the ratio of the absolute temperature to the square of the fundamental acoustic resonance frequency. Average system stability (temperature divided by frequency squared) is better than 350 ppm. DA values for a 0.3-inch diameter capillary were in excellent agreement with published values. De values for porous media samples (0.5 mm glass beads) of four different lengths (1 through 4 inches) using three different tracer gases (He, CH4, Kr) will be reported. Comments will be offered regarding tracer gas selection and device orientation and their effect on experimental results. [Work supported by the Office of Naval Research.

A flexible nonlinear diffusion acceleration method for the S N transport equations discretized with discontinuous finite elements

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

Schunert, Sebastian; Wang, Yaqi; Gleicher, Frederick

This paper presents a flexible nonlinear diffusion acceleration (NDA) method that discretizes both the S N transport equation and the diffusion equation using the discontinuous finite element method (DFEM). The method is flexible in that the diffusion equation can be discretized on a coarser mesh with the only restriction that it is nested within the transport mesh and the FEM shape function orders of the two equations can be different. The consistency of the transport and diffusion solutions at convergence is defined by using a projection operator mapping the transport into the diffusion FEM space. The diffusion weak form ismore » based on the modified incomplete interior penalty (MIP) diffusion DFEM discretization that is extended by volumetric drift, interior face, and boundary closure terms. In contrast to commonly used coarse mesh finite difference (CMFD) methods, the presented NDA method uses a full FEM discretized diffusion equation for acceleration. Suitable projection and prolongation operators arise naturally from the FEM framework. Via Fourier analysis and numerical experiments for a one-group, fixed source problem the following properties of the NDA method are established for structured quadrilateral meshes: (1) the presented method is unconditionally stable and effective in the presence of mild material heterogeneities if the same mesh and identical shape functions either of the bilinear or biquadratic type are used, (2) the NDA method remains unconditionally stable in the presence of strong heterogeneities, (3) the NDA method with bilinear elements extends the range of effectiveness and stability by a factor of two when compared to CMFD if a coarser diffusion mesh is selected. In addition, the method is tested for solving the C5G7 multigroup, eigenvalue problem using coarse and fine mesh acceleration. Finally, while NDA does not offer an advantage over CMFD for fine mesh acceleration, it reduces the iteration count required for convergence by almost a factor of two in the case of coarse mesh acceleration.« less

A flexible nonlinear diffusion acceleration method for the S N transport equations discretized with discontinuous finite elements

DOE PAGES

Schunert, Sebastian; Wang, Yaqi; Gleicher, Frederick; ...

2017-02-21

This paper presents a flexible nonlinear diffusion acceleration (NDA) method that discretizes both the S N transport equation and the diffusion equation using the discontinuous finite element method (DFEM). The method is flexible in that the diffusion equation can be discretized on a coarser mesh with the only restriction that it is nested within the transport mesh and the FEM shape function orders of the two equations can be different. The consistency of the transport and diffusion solutions at convergence is defined by using a projection operator mapping the transport into the diffusion FEM space. The diffusion weak form ismore » based on the modified incomplete interior penalty (MIP) diffusion DFEM discretization that is extended by volumetric drift, interior face, and boundary closure terms. In contrast to commonly used coarse mesh finite difference (CMFD) methods, the presented NDA method uses a full FEM discretized diffusion equation for acceleration. Suitable projection and prolongation operators arise naturally from the FEM framework. Via Fourier analysis and numerical experiments for a one-group, fixed source problem the following properties of the NDA method are established for structured quadrilateral meshes: (1) the presented method is unconditionally stable and effective in the presence of mild material heterogeneities if the same mesh and identical shape functions either of the bilinear or biquadratic type are used, (2) the NDA method remains unconditionally stable in the presence of strong heterogeneities, (3) the NDA method with bilinear elements extends the range of effectiveness and stability by a factor of two when compared to CMFD if a coarser diffusion mesh is selected. In addition, the method is tested for solving the C5G7 multigroup, eigenvalue problem using coarse and fine mesh acceleration. Finally, while NDA does not offer an advantage over CMFD for fine mesh acceleration, it reduces the iteration count required for convergence by almost a factor of two in the case of coarse mesh acceleration.« less

Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis-Menten kinetics and assessment of numerical methods.

PubMed

Pereira, Félix Monteiro; Oliveira, Samuel Conceição

2016-11-01

In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.

Real-Time Nonlocal Means-Based Despeckling.

PubMed

Breivik, Lars Hofsoy; Snare, Sten Roar; Steen, Erik Normann; Solberg, Anne H Schistad

2017-06-01

In this paper, we propose a multiscale nonlocal means-based despeckling method for medical ultrasound. The multiscale approach leads to large computational savings and improves despeckling results over single-scale iterative approaches. We present two variants of the method. The first, denoted multiscale nonlocal means (MNLM), yields uniform robust filtering of speckle both in structured and homogeneous regions. The second, denoted unnormalized MNLM (UMNLM), is more conservative in regions of structure assuring minimal disruption of salient image details. Due to the popularity of anisotropic diffusion-based methods in the despeckling literature, we review the connection between anisotropic diffusion and iterative variants of NLM. These iterative variants in turn relate to our multiscale variant. As part of our evaluation, we conduct a simulation study making use of ground truth phantoms generated from clinical B-mode ultrasound images. We evaluate our method against a set of popular methods from the despeckling literature on both fine and coarse speckle noise. In terms of computational efficiency, our method outperforms the other considered methods. Quantitatively on simulations and on a tissue-mimicking phantom, our method is found to be competitive with the state-of-the-art. On clinical B-mode images, our method is found to effectively smooth speckle while preserving low-contrast and highly localized salient image detail.

The role of boundary variability in polycrystalline grain-boundary diffusion

NASA Astrophysics Data System (ADS)

Moghadam, M. M.; Rickman, J. M.; Harmer, M. P.; Chan, H. M.

2015-01-01

We investigate the impact of grain-boundary variability on mass transport in a polycrystal. More specifically, we perform both numerical and analytical studies of steady-state diffusion in prototypical microstructures in which there is either a discrete spectrum of grain-boundary activation energies or else a complex distribution of grain-boundary character, and hence a continuous spectrum of boundary activation energies. An effective diffusivity is calculated for these structures using simplified multi-state models and, for the case of a continuous spectrum, employing experimentally obtained grain-boundary energy data. We identify different diffusive regimes for these cases and quantify deviations from Arrhenius behavior using effective medium theory. Finally, we examine the diffusion kinetics of a simplified model of an interfacial layering (i.e., complexion) transition.

Anisotropic diffusion of oxygen on a few layers of black phosphorous

NASA Astrophysics Data System (ADS)

Fernández-Escamilla, Hector Noe; González-Chávez, Víctor Hugo; Martínez-Guerra, Eduardo; Garay-Tapia, Andrés; Martínez-Guerra, Edgar

Recently, phosporene has also been scored well as a functional material for two-dimensional electronic and optoelectronic devices. That is, because in contrast to graphene, black phosphorous has an inherent, direct and appreciable band gap that can be modulated with the numbers of layes. However, the presence of exposed lone pairs at the surface makes phosphorous very reactive to air and humidity and consequently, degradation of its properties. No such fundamental explanation have been made, thus corresponding first principle predictions to evaluate diffusion of O over and along a mono- and a few layers are indispensable. Energy barriers and the mechanisms of oxygen diffusion on mono- and a few layer of black phosphorous were calculated using the NEB(Nudge Elastic band) method as implemented in Quantum Espresso. The electronic states are expanded in plane waves with kinetic-energy cutoffs of 25 and 200 Ry for the wave function and charge density, respectively. Also, as the H2O and O2 are polar molecules, spin-polarized calculations have been carried out. We evaluated the diffusion barriers for O2 and H2O on phosphorene along zigzag, armchair and intermediated directions. Our calculations show that diffusion of O is preferred on zigzag directions and dissociation of O2 is favored as a result of energy gains of about 2 eV. Also, apparently diffusion pathways are blocked along layers.

A Method for Medical Diagnosis Based on Optical Fluence Rate Distribution at Tissue Surface

PubMed Central

Hamdy, Omnia; El-Azab, Jala; Al-Saeed, Tarek A.; Hassan, Mahmoud F.

2017-01-01

Optical differentiation is a promising tool in biomedical diagnosis mainly because of its safety. The optical parameters’ values of biological tissues differ according to the histopathology of the tissue and hence could be used for differentiation. The optical fluence rate distribution on tissue boundaries depends on the optical parameters. So, providing image displays of such distributions can provide a visual means of biomedical diagnosis. In this work, an experimental setup was implemented to measure the spatially-resolved steady state diffuse reflectance and transmittance of native and coagulated chicken liver and native and boiled breast chicken skin at 635 and 808 nm wavelengths laser irradiation. With the measured values, the optical parameters of the samples were calculated in vitro using a combination of modified Kubelka-Munk model and Bouguer-Beer-Lambert law. The estimated optical parameters values were substituted in the diffusion equation to simulate the fluence rate at the tissue surface using the finite element method. Results were verified with Monte-Carlo simulation. The results obtained showed that the diffuse reflectance curves and fluence rate distribution images can provide discrimination tools between different tissue types and hence can be used for biomedical diagnosis. PMID:28930158

Correlation between Photoluminescence and Carrier Transport and a Simple In Situ Passivation Method for High-Bandgap Hybrid Perovskites

DOE PAGES

Stoddard, Ryan J.; Eickemeyer, Felix T.; Katahara, John K.; ...

2017-06-21

High-bandgap mixed-halide hybrid perovskites have higher open-circuit voltage deficits and lower carrier diffusion lengths than their lower-bandgap counterparts. We have developed a ligand-assisted crystallization (LAC) technique that introduces additives in situ during the solvent wash and developed a new method to dynamically measure the absolute intensity steady-state photoluminescence and the mean carrier diffusion length simultaneously. The measurements reveal four distinct regimes of material changes and show that photoluminescence brightening often coincides with losses in carrier transport, such as in degradation or phase segregation. Further, the measurements enabled optimization of LAC on the 1.75 eV bandgap FA 0.83Cs 0.17Pb(I 0.66Br 0.34)more » 3, resulting in an enhancement of the photoluminescence quantum yield (PLQY) of over an order of magnitude, an increase of 80 meV in the quasi-Fermi level splitting (to 1.29 eV), an increase in diffusion length by a factor of 3.5 (to over 1 μm), and enhanced open-circuit voltage and short-circuit current from photovoltaics fabricated from the LAC-treated films.« less

Correlation between Photoluminescence and Carrier Transport and a Simple In Situ Passivation Method for High-Bandgap Hybrid Perovskites.

PubMed

Stoddard, Ryan J; Eickemeyer, Felix T; Katahara, John K; Hillhouse, Hugh W

2017-07-20

High-bandgap mixed-halide hybrid perovskites have higher open-circuit voltage deficits and lower carrier diffusion lengths than their lower-bandgap counterparts. We have developed a ligand-assisted crystallization (LAC) technique that introduces additives in situ during the solvent wash and developed a new method to dynamically measure the absolute intensity steady-state photoluminescence and the mean carrier diffusion length simultaneously. The measurements reveal four distinct regimes of material changes and show that photoluminescence brightening often coincides with losses in carrier transport, such as in degradation or phase segregation. Further, the measurements enabled optimization of LAC on the 1.75 eV bandgap FA 0.83 Cs 0.17 Pb(I 0.66 Br 0.34 ) 3 , resulting in an enhancement of the photoluminescence quantum yield (PLQY) of over an order of magnitude, an increase of 80 meV in the quasi-Fermi level splitting (to 1.29 eV), an increase in diffusion length by a factor of 3.5 (to over 1 μm), and enhanced open-circuit voltage and short-circuit current from photovoltaics fabricated from the LAC-treated films.

A Method for Medical Diagnosis Based on Optical Fluence Rate Distribution at Tissue Surface.

PubMed

Hamdy, Omnia; El-Azab, Jala; Al-Saeed, Tarek A; Hassan, Mahmoud F; Solouma, Nahed H

2017-09-20

Optical differentiation is a promising tool in biomedical diagnosis mainly because of its safety. The optical parameters' values of biological tissues differ according to the histopathology of the tissue and hence could be used for differentiation. The optical fluence rate distribution on tissue boundaries depends on the optical parameters. So, providing image displays of such distributions can provide a visual means of biomedical diagnosis. In this work, an experimental setup was implemented to measure the spatially-resolved steady state diffuse reflectance and transmittance of native and coagulated chicken liver and native and boiled breast chicken skin at 635 and 808 nm wavelengths laser irradiation. With the measured values, the optical parameters of the samples were calculated in vitro using a combination of modified Kubelka-Munk model and Bouguer-Beer-Lambert law. The estimated optical parameters values were substituted in the diffusion equation to simulate the fluence rate at the tissue surface using the finite element method. Results were verified with Monte-Carlo simulation. The results obtained showed that the diffuse reflectance curves and fluence rate distribution images can provide discrimination tools between different tissue types and hence can be used for biomedical diagnosis.

A new class of accelerated kinetic Monte Carlo algorithms

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

Bulatov, V V; Oppelstrup, T; Athenes, M

2011-11-30

Kinetic (aka dynamic) Monte Carlo (KMC) is a powerful method for numerical simulations of time dependent evolution applied in a wide range of contexts including biology, chemistry, physics, nuclear sciences, financial engineering, etc. Generally, in a KMC the time evolution takes place one event at a time, where the sequence of events and the time intervals between them are selected (or sampled) using random numbers. While details of the method implementation vary depending on the model and context, there exist certain common issues that limit KMC applicability in almost all applications. Among such is the notorious 'flicker problem' where themore » same states of the systems are repeatedly visited but otherwise no essential evolution is observed. In its simplest form the flicker problem arises when two states are connected to each other by transitions whose rates far exceed the rates of all other transitions out of the same two states. In such cases, the model will endlessly hop between the two states otherwise producing no meaningful evolution. In most situation of practical interest, the trapping cluster includes more than two states making the flicker somewhat more difficult to detect and to deal with. Several methods have been proposed to overcome or mitigate the flicker problem, exactly [1-3] or approximately [4,5]. Of the exact methods, the one proposed by Novotny [1] is perhaps most relevant to our research. Novotny formulates the problem of escaping from a trapping cluster as a Markov system with absorbing states. Given an initial state inside the cluster, it is in principle possible to solve the Master Equation for the time dependent probabilities to find the walker in a given state (transient or absorbing) of the cluster at any time in the future. Novotny then proceeds to demonstrate implementation of his general method to trapping clusters containing the initial state plus one or two transient states and all of their absorbing states. Similar methods have been subsequently proposed in [refs] but applied in a different context. The most serious deficiency of the earlier methods is that size of the trapping cluster size is fixed and often too small to bring substantial simulation speedup. Furthermore, the overhead associated with solving for the probability distribution on the trapping cluster sometimes makes such simulations less efficient than the standard KMC. Here we report on a general and exact accelerated kinetic Monte Carlo algorithm generally applicable to arbitrary Markov models1. Two different implementations are attempted both based on incremental expansion of trapping sub-set of Markov states: (1) numerical solution of the Master Equation with absorbing states and (2) incremental graph reduction followed by randomization. Of the two implementations, the 2nd one performs better allowing, for the first time, to overcome trapping basins spanning several million Markov states. The new method is used for simulations of anomalous diffusion on a 2D substrate and of the kinetics of diffusive 1st order phase transformations in binary alloys. Depending on temperature and (alloy) super-saturation conditions, speedups of 3 to 7 orders of magnitude are demonstrated, with no compromise of simulation accuracy.« less

On common noise-induced synchronization in complex networks with state-dependent noise diffusion processes

NASA Astrophysics Data System (ADS)

Russo, Giovanni; Shorten, Robert

2018-04-01

This paper is concerned with the study of common noise-induced synchronization phenomena in complex networks of diffusively coupled nonlinear systems. We consider the case where common noise propagation depends on the network state and, as a result, the noise diffusion process at the nodes depends on the state of the network. For such networks, we present an algebraic sufficient condition for the onset of synchronization, which depends on the network topology, the dynamics at the nodes, the coupling strength and the noise diffusion. Our result explicitly shows that certain noise diffusion processes can drive an unsynchronized network towards synchronization. In order to illustrate the effectiveness of our result, we consider two applications: collective decision processes and synchronization of chaotic systems. We explicitly show that, in the former application, a sufficiently large noise can drive a population towards a common decision, while, in the latter, we show how common noise can synchronize a network of Lorentz chaotic systems.

Determination of diffusion coefficient in disordered organic semiconductors

NASA Astrophysics Data System (ADS)

Rani, Varsha; Sharma, Akanksha; Ghosh, Subhasis

2016-05-01

Charge carrier transport in organic semiconductors is dominated by positional and energetic disorder in Gaussian density of states (GDOS) and is characterized by hopping through localized states. Due to the immobilization of charge carriers in these localized states, significant non-uniform carrier distribution exists, resulting diffusive transport. A simple, nevertheless powerful technique to determine diffusion coefficient D in disordered organic semiconductors has been presented. Diffusion coefficients of charge carriers in two technologically important organic molecular semiconductors, Pentacene and copper phthalocyanine (CuPc) have been measured from current-voltage (J-V) characteristics of Al/Pentacene/Au and Al/CuPc/Au based Schottky diodes. Ideality factor g and carrier mobility μ have been calculated from the exponential and space charge limited region respectively of J-V characteristics. Classical Einstein relation is not valid in organic semiconductors due to energetic disorders in DOS. Using generalized Einstein relation, diffusion coefficients have been obtained to be 1.31×10-6 and 1.73×10-7 cm2/s for Pentacene and CuPc respectively.

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

PubMed Central

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

2014-01-01

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

NMR diffusion simulation based on conditional random walk.

PubMed

Gudbjartsson, H; Patz, S

1995-01-01

The authors introduce here a new, very fast, simulation method for free diffusion in a linear magnetic field gradient, which is an extension of the conventional Monte Carlo (MC) method or the convolution method described by Wong et al. (in 12th SMRM, New York, 1993, p.10). In earlier NMR-diffusion simulation methods, such as the finite difference method (FD), the Monte Carlo method, and the deterministic convolution method, the outcome of the calculations depends on the simulation time step. In the authors' method, however, the results are independent of the time step, although, in the convolution method the step size has to be adequate for spins to diffuse to adjacent grid points. By always selecting the largest possible time step the computation time can therefore be reduced. Finally the authors point out that in simple geometric configurations their simulation algorithm can be used to reduce computation time in the simulation of restricted diffusion.

Correlation between information diffusion and opinion evolution on social media

NASA Astrophysics Data System (ADS)

Xiong, Fei; Liu, Yun; Zhang, Zhenjiang

2014-12-01

Information diffusion and opinion evolution are often treated as two independent processes. Opinion models assume the topic reaches each agent and agents initially have their own ideas. In fact, the processes of information diffusion and opinion evolution often intertwine with each other. Whether the influence between these two processes plays a role in the system state is unclear. In this paper, we collected more than one million real data from a well-known social platform, and analysed large-scale user diffusion behaviour and opinion formation. We found that user inter-event time follows a two-scaling power-law distribution with two different power exponents. Public opinion stabilizes quickly and evolves toward the direction of convergence, but the consensus state is prevented by a few opponents. We propose a three-state opinion model accompanied by information diffusion. Agents form and exchange their opinions during information diffusion. Conversely, agents' opinions also influence their diffusion actions. Simulations show that the model with a correlation of the two processes produces similar statistical characteristics as empirical results. A fast epidemic process drives individual opinions to converge more obviously. Unlike previous epidemic models, the number of infected agents does not always increase with the update rate, but has a peak with an intermediate value of the rate.

Mapping Ionic Currents and Reactivity on the Nanoscale: Electrochemical Strain Microscopy

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

Kalinin, S.V.

2010-10-19

Solid-state electrochemical processes in oxides underpin a broad spectrum of energy and information storage devices, ranging from Li-ion and Li-air batteries, to solid oxide fuel cells (SOFC) to electroresistive and memristive systems. These functionalities are controlled by the bias-driven diffusive and electromigration transport of mobile ionic species, as well as intricate a set of electrochemical and defect-controlled reactions at interfaces and in bulk. Despite the wealth of device-level and atomistic studies, little is known on the mesoscopic mechanisms of ion diffusion and electronic transport on the level of grain clusters, individual grains, and extended defects. The development of the capabilitymore » for probing ion transport on the nanometer scale is a key to deciphering complex interplay between structure, functionality, and performance in these systems. Here we introduce Electrochemical Strain Microscopy, a scanning probe microscopy technique based on strong strain-bias coupling in the systems in which local ion concentrations are changed by electrical fields. The imaging capability, as well as time- and voltage spectroscopies analogous to traditional current based electrochemical characterization methods are developed. The reversible intercalation of Li and mapping electrochemical activity in LiCoO2 is demonstrated, illustrating higher Li diffusivity at non-basal planes and grain boundaries. In Si-anode device structure, the direct mapping of Li diffusion at extended defects and evolution of Li-activity with charge state is explored. The electrical field-dependence of Li mobility is studied to determine the critical bias required for the onset of electrochemical transformation, allowing reaction and diffusion processes in the battery system to be separated at each location. Finally, the applicability of ESM for probing oxygen vacancy diffusion and oxygen reduction/evolution reactions is illustrated, and the high resolution ESM maps are correlated with aberration corrected scanning transmission electron microscopy imaging. The future potential for deciphering mechanisms of electrochemical transformations on an atomically-defined single-defect level is discussed.« less

Analytic Models of Oxygen and Nutrient Diffusion, Metabolism Dynamics, and Architecture Optimization in Three-Dimensional Tissue Constructs with Applications and Insights in Cerebral Organoids

PubMed Central

2016-01-01

Diffusion models are important in tissue engineering as they enable an understanding of gas, nutrient, and signaling molecule delivery to cells in cell cultures and tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically applicable, it will be essential to understand internal dynamics and signaling molecule concentrations throughout the tissue and whether cells are receiving appropriate nutrient delivery. Diffusion characteristics present a significant limitation in many engineered tissues, particularly for avascular tissues and for cells whose viability, differentiation, or function are affected by concentrations of oxygen and nutrients. This article seeks to provide novel analytic solutions for certain cases of steady-state and nonsteady-state diffusion and metabolism in basic 3D construct designs (planar, cylindrical, and spherical forms), solutions that would otherwise require mathematical approximations achieved through numerical methods. This model is applied to cerebral organoids, where it is shown that limitations in diffusion and organoid size can be partially overcome by localizing metabolically active cells to an outer layer in a sphere, a regionalization process that is known to occur through neuroglial precursor migration both in organoids and in early brain development. The given prototypical solutions include a review of metabolic information for many cell types and can be broadly applied to many forms of tissue constructs. This work enables researchers to model oxygen and nutrient delivery to cells, predict cell viability, study dynamics of mass transport in 3D tissue constructs, design constructs with improved diffusion capabilities, and accurately control molecular concentrations in tissue constructs that may be used in studying models of development and disease or for conditioning cells to enhance survival after insults like ischemia or implantation into the body, thereby providing a framework for better understanding and exploring the characteristics and behaviors of engineered tissue constructs. PMID:26650970

Impact of Moisture Content and Grain Size on Hydrocarbon Diffusion in Porous Media

NASA Astrophysics Data System (ADS)

McLain, A. A.; Ho, C. K.

2001-12-01

Diffusion of hydrocarbon vapors in porous media can play an important role in our ability to characterize subsurface contaminants such as trichloroethylene (TCE). For example, traditional monitoring methods often rely on direct sampling of contaminated soils or vapor. These samples may be influenced by the diffusion of vapors away from the contaminant source term, such as non-aqueous-phase TCE liquid. In addition, diffusion of hydrocarbon vapors can also impact the migration and dispersion of the contaminant in the subsurface. Therefore, understanding the diffusion rates and vapor transport processes of hydrocarbons in variably-saturated, heterogeneous porous media will assist in the characterization and detection of these subsurface contaminants. The purpose of this study was to investigate the impact of soil heterogeneity and water-moisture content on the diffusion processes for TCE. A one-dimensional column experiment was used to monitor the rates of vapor diffusion through sand. Experiments were performed with different average water-moisture contents and different grain sizes. On one end of the column, a reservoir cap is used to encase the TCE, providing a constant vapor boundary condition while sealing the end. The other end of the column contains a novel microchemical sensor. The sensor employs a polymer-absorption resistor (chemiresistor) that reversibly swells and increases in resistance when exposed to hydrocarbons. Once calibrated, the chemiresistors can be used to passively monitor vapor concentrations. This unique method allows the detection of in-situ vapor concentrations without disturbing the local environment. Results are presented in the form of vapor-concentration breakthrough curves as detected by the sensor. The shape of the breakthrough curve is dependent on several key parameters, including the length of the column and parameters (e.g., water-moisture content and grain-size) that affect the effective diffusion coefficient of TCE in air. Comparisons are made between theoretical and observed breakthrough curves to evaluate the diffusion of TCE and other relevant physical processes (e.g., air-water partitioning of TCE). The relative impact of water-moisture content and grain size on the diffusion of TCE vapor in porous media is also addressed. The authors thank Bob Hughes, who developed the chemiresistor sensors, and Chad Davis, who assisted with the calibrations. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL85000.

Molten salt synthesis of nanocrystalline phase of high dielectric constant material CaCu3Ti4O12.

PubMed

Prakash, B Shri; Varma, K B R

2008-11-01

Nanocrystalline powders of giant dielectric constant material, CaCu3Ti4O12 (CCTO), have been prepared successfully by the molten salt synthesis (MSS) using KCl at 750 degrees C/10 h, which is significantly lower than the calcination temperature (approximately 1000 degrees C) that is employed to obtain phase pure CCTO in the conventional solid-state reaction route. The water washed molten salt synthesized powder, characterized by X-ray powder diffraction (XRD), Scanning electron microscopy (SEM), and Transmission electron microscopy (TEM) confirmed to be a phase pure CCTO associated with approximately 150 nm sized crystallites of nearly spherical shape. The decrease in the formation temperature/duration of CCTO in MSS method was attributed to an increase in the diffusion rate or a decrease in the diffusion length of reacting ions in the molten salt medium. As a consequence of liquid phase sintering, pellets of as-synthesized KCl containing CCTO powder exhibited higher sinterability and grain size than that of KCl free CCTO samples prepared by both MSS method and conventional solid-state reaction route. The grain size and the dielectric constant of KCl containing CCTO ceramics increased with increasing sintering temperature (900 degrees C-1050 degrees C). Indeed the dielectric constants of these ceramics were higher than that of KCl free CCTO samples prepared by both MSS method and those obtained via the solid-state reaction route and sintered at the same temperature. Internal barrier layer capacitance (IBLC) model was invoked to correlate the observed dielectric constant with the grain size in these samples.

Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels.

PubMed

Tahat, Amani; Martí, Jordi

2016-07-01

Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 Å(-3) have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Development of a restricted state space stochastic differential equation model for bacterial growth in rich media.

PubMed

Møller, Jan Kloppenborg; Bergmann, Kirsten Riber; Christiansen, Lasse Engbo; Madsen, Henrik

2012-07-21

In the present study, bacterial growth in a rich media is analysed in a Stochastic Differential Equation (SDE) framework. It is demonstrated that the SDE formulation and smoothened state estimates provide a systematic framework for data driven model improvements, using random walk hidden states. Bacterial growth is limited by the available substrate and the inclusion of diffusion must obey this natural restriction. By inclusion of a modified logistic diffusion term it is possible to introduce a diffusion term flexible enough to capture both the growth phase and the stationary phase, while concentration is restricted to the natural state space (substrate and bacteria non-negative). The case considered is the growth of Salmonella and Enterococcus in a rich media. It is found that a hidden state is necessary to capture the lag phase of growth, and that a flexible logistic diffusion term is needed to capture the random behaviour of the growth model. Further, it is concluded that the Monod effect is not needed to capture the dynamics of bacterial growth in the data presented. Copyright © 2012 Elsevier Ltd. All rights reserved.

Upscaling the diffusion equations in particulate media made of highly conductive particles. I. Theoretical aspects.

PubMed

Vassal, J-P; Orgéas, L; Favier, D; Auriault, J-L; Le Corre, S

2008-01-01

Many analytical and numerical works have been devoted to the prediction of macroscopic effective transport properties in particulate media. Usually, structure and properties of macroscopic balance and constitutive equations are stated a priori. In this paper, the upscaling of the transient diffusion equations in concentrated particulate media with possible particle-particle interfacial barriers, highly conductive particles, poorly conductive matrix, and temperature-dependent physical properties is revisited using the homogenization method based on multiple scale asymptotic expansions. This method uses no a priori assumptions on the physics at the macroscale. For the considered physics and microstructures and depending on the order of magnitude of dimensionless Biot and Fourier numbers, it is shown that some situations cannot be homogenized. For other situations, three different macroscopic models are identified, depending on the quality of particle-particle contacts. They are one-phase media, following the standard heat equation and Fourier's law. Calculations of the effective conductivity tensor and heat capacity are proved to be uncoupled. Linear and steady state continuous localization problems must be solved on representative elementary volumes to compute the effective conductivity tensors for the two first models. For the third model, i.e., for highly resistive contacts, the localization problem becomes simpler and discrete whatever the shape of particles. In paper II [Vassal, Phys. Rev. E 77, 011303 (2008)], diffusion through networks of slender, wavy, entangled, and oriented fibers is considered. Discrete localization problems can then be obtained for all models, as well as semianalytical or fully analytical expressions of the corresponding effective conductivity tensors.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure.

PubMed

Chang, Wendi; Akselrod, Gleb M; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole-dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopant molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole-dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole-dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure

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

Chang, Wendi; Akselrod, Gleb M.; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole–dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopantmore » molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole–dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole–dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.« less

On the Maxwell-Stefan approach to diffusion: a general resolution in the transient regime for one-dimensional systems.

PubMed

Leonardi, Erminia; Angeli, Celestino

2010-01-14

The diffusion process in a multicomponent system can be formulated in a general form by the generalized Maxwell-Stefan equations. This formulation is able to describe the diffusion process in different systems, such as, for instance, bulk diffusion (in the gas, liquid, and solid phase) and diffusion in microporous materials (membranes, zeolites, nanotubes, etc.). The Maxwell-Stefan equations can be solved analytically (only in special cases) or by numerical approaches. Different numerical strategies have been previously presented, but the number of diffusing species is normally restricted, with only few exceptions, to three in bulk diffusion and to two in microporous systems, unless simplifications of the Maxwell-Stefan equations are considered. In the literature, a large effort has been devoted to the derivation of the analytic expression of the elements of the Fick-like diffusion matrix and therefore to the symbolic inversion of a square matrix with dimensions n x n (n being the number of independent components). This step, which can be easily performed for n = 2 and remains reasonable for n = 3, becomes rapidly very complex in problems with a large number of components. This paper addresses the problem of the numerical resolution of the Maxwell-Stefan equations in the transient regime for a one-dimensional system with a generic number of components, avoiding the definition of the analytic expression of the elements of the Fick-like diffusion matrix. To this aim, two approaches have been implemented in a computational code; the first is the simple finite difference second-order accurate in time Crank-Nicolson scheme for which the full mathematical derivation and the relevant final equations are reported. The second is based on the more accurate backward differentiation formulas, BDF, or Gear's method (Shampine, L. F. ; Gear, C. W. SIAM Rev. 1979, 21, 1.), as implemented in the Livermore solver for ordinary differential equations, LSODE (Hindmarsh, A. C. Serial Fortran Solvers for ODE Initial Value Problems, Technical Report; https://computation.llnl.gov/casc/odepack/odepack_ home.html (2006).). Both methods have been applied to a series of specific problems, such as bulk diffusion of acetone and methanol through stagnant air, uptake of two components on a microporous material in a model system, and permeation across a microporous membrane in model systems, both with the aim to validate the method and to add new information to the comprehension of the peculiar behavior of these systems. The approach is validated by comparison with different published results and with analytic expressions for the steady-state concentration profiles or fluxes in particular systems. The possibility to treat a generic number of components (the limitation being essentially the computational power) is also tested, and results are reported on the permeation of a five component mixture through a membrane in a model system. It is worth noticing that the algorithm here reported can be applied also to the Fick formulation of the diffusion problem with concentration-dependent diffusion coefficients.

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

When Neighbours Matter Most: Innovation, Diffusion and State Policy Adoption in Tertiary Education

ERIC Educational Resources Information Center

Cohen-Vogel, Lora; Ingle, William Kyle

2007-01-01

We now have ample evidence that public policies diffuse across the American states; that is, policy adoption is due at least in part to the emulation of policies enacted in nearby states. But, policy adoption is the result of a complex process, a process that often takes years and sometimes decades to complete. According to the "stage"…

Molecular diffusion of stable water isotopes in polar firn as a proxy for past temperatures

NASA Astrophysics Data System (ADS)

Holme, Christian; Gkinis, Vasileios; Vinther, Bo M.

2018-03-01

Polar precipitation archived in ice caps contains information on past temperature conditions. Such information can be retrieved by measuring the water isotopic signals of δ18O and δD in ice cores. These signals have been attenuated during densification due to molecular diffusion in the firn column, where the magnitude of the diffusion is isotopologue specific and temperature dependent. By utilizing the differential diffusion signal, dual isotope measurements of δ18O and δD enable multiple temperature reconstruction techniques. This study assesses how well six different methods can be used to reconstruct past surface temperatures from the diffusion-based temperature proxies. Two of the methods are based on the single diffusion lengths of δ18O and δD , three of the methods employ the differential diffusion signal, while the last uses the ratio between the single diffusion lengths. All techniques are tested on synthetic data in order to evaluate their accuracy and precision. We perform a benchmark test to thirteen high resolution Holocene data sets from Greenland and Antarctica, which represent a broad range of mean annual surface temperatures and accumulation rates. Based on the benchmark test, we comment on the accuracy and precision of the methods. Both the benchmark test and the synthetic data test demonstrate that the most precise reconstructions are obtained when using the single isotope diffusion lengths, with precisions of approximately 1.0 °C . In the benchmark test, the single isotope diffusion lengths are also found to reconstruct consistent temperatures with a root-mean-square-deviation of 0.7 °C . The techniques employing the differential diffusion signals are more uncertain, where the most precise method has a precision of 1.9 °C . The diffusion length ratio method is the least precise with a precision of 13.7 °C . The absolute temperature estimates from this method are also shown to be highly sensitive to the choice of fractionation factor parameterization.

Investigation of diffusion length distribution on polycrystalline silicon wafers via photoluminescence methods

PubMed Central

Lou, Shishu; Zhu, Huishi; Hu, Shaoxu; Zhao, Chunhua; Han, Peide

2015-01-01

Characterization of the diffusion length of solar cells in space has been widely studied using various methods, but few studies have focused on a fast, simple way to obtain the quantified diffusion length distribution on a silicon wafer. In this work, we present two different facile methods of doing this by fitting photoluminescence images taken in two different wavelength ranges or from different sides. These methods, which are based on measuring the ratio of two photoluminescence images, yield absolute values of the diffusion length and are less sensitive to the inhomogeneity of the incident laser beam. A theoretical simulation and experimental demonstration of this method are presented. The diffusion length distributions on a polycrystalline silicon wafer obtained by the two methods show good agreement. PMID:26364565

Roles of Diffusion Dynamics in Stem Cell Signaling and Three-Dimensional Tissue Development.

PubMed

McMurtrey, Richard J

2017-09-15

Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have ignited investigation into important aspects of molecular diffusion in 3D cellular architectures. This article describes fundamental mechanics of diffusion with equations for modeling these dynamic processes under a variety of scenarios in 3D cellular tissue constructs. The effects of these diffusion processes and resultant concentration gradients are described in the context of the major molecular signaling pathways in stem cells that both mediate and are influenced by gas and nutrient concentrations, including how diffusion phenomena can affect stem cell state, cell differentiation, and metabolic states of the cell. The application of these diffusion models and pathways is of vital importance for future studies of developmental processes, disease modeling, and tissue regeneration.

Diffusion and interactions of interstitials in hard-sphere interstitial solid solutions

NASA Astrophysics Data System (ADS)

van der Meer, Berend; Lathouwers, Emma; Smallenburg, Frank; Filion, Laura

2017-12-01

Using computer simulations, we study the dynamics and interactions of interstitial particles in hard-sphere interstitial solid solutions. We calculate the free-energy barriers associated with their diffusion for a range of size ratios and densities. By applying classical transition state theory to these free-energy barriers, we predict the diffusion coefficients, which we find to be in good agreement with diffusion coefficients as measured using event-driven molecular dynamics simulations. These results highlight that transition state theory can capture the interstitial dynamics in the hard-sphere model system. Additionally, we quantify the interactions between the interstitials. We find that, apart from excluded volume interactions, the interstitial-interstitial interactions are almost ideal in our system. Lastly, we show that the interstitial diffusivity can be inferred from the large-particle fluctuations alone, thus providing an empirical relationship between the large-particle fluctuations and the interstitial diffusivity.

Sparse and Adaptive Diffusion Dictionary (SADD) for recovering intra-voxel white matter structure.

PubMed

Aranda, Ramon; Ramirez-Manzanares, Alonso; Rivera, Mariano

2015-12-01

On the analysis of the Diffusion-Weighted Magnetic Resonance Images, multi-compartment models overcome the limitations of the well-known Diffusion Tensor model for fitting in vivo brain axonal orientations at voxels with fiber crossings, branching, kissing or bifurcations. Some successful multi-compartment methods are based on diffusion dictionaries. The diffusion dictionary-based methods assume that the observed Magnetic Resonance signal at each voxel is a linear combination of the fixed dictionary elements (dictionary atoms). The atoms are fixed along different orientations and diffusivity profiles. In this work, we present a sparse and adaptive diffusion dictionary method based on the Diffusion Basis Functions Model to estimate in vivo brain axonal fiber populations. Our proposal overcomes the following limitations of the diffusion dictionary-based methods: the limited angular resolution and the fixed shapes for the atom set. We propose to iteratively re-estimate the orientations and the diffusivity profile of the atoms independently at each voxel by using a simplified and easier-to-solve mathematical approach. As a result, we improve the fitting of the Diffusion-Weighted Magnetic Resonance signal. The advantages with respect to the former Diffusion Basis Functions method are demonstrated on the synthetic data-set used on the 2012 HARDI Reconstruction Challenge and in vivo human data. We demonstrate that improvements obtained in the intra-voxel fiber structure estimations benefit brain research allowing to obtain better tractography estimations. Hence, these improvements result in an accurate computation of the brain connectivity patterns. Copyright © 2015 Elsevier B.V. All rights reserved.

An Analysis of a Finite Element Method for Convection-Diffusion Problems. Part II. A Posteriori Error Estimates and Adaptivity.

DTIC Science & Technology

1983-03-01

AN ANALYSIS OF A FINITE ELEMENT METHOD FOR CONVECTION- DIFFUSION PROBLEMS PART II: A POSTERIORI ERROR ESTIMATES AND ADAPTIVITY by W. G. Szymczak Y 6a...PERIOD COVERED AN ANALYSIS OF A FINITE ELEMENT METHOD FOR final life of the contract CONVECTION- DIFFUSION PROBLEM S. Part II: A POSTERIORI ERROR ...Element Method for Convection- Diffusion Problems. Part II: A Posteriori Error Estimates and Adaptivity W. G. Szvmczak and I. Babu~ka# Laboratory for

A simplified counter diffusion method combined with a 1D simulation program for optimizing crystallization conditions.

PubMed

Tanaka, Hiroaki; Inaka, Koji; Sugiyama, Shigeru; Takahashi, Sachiko; Sano, Satoshi; Sato, Masaru; Yoshitomi, Susumu

2004-01-01

We developed a new protein crystallization method has been developed using a simplified counter-diffusion method for optimizing crystallization condition. It is composed of only a single capillary, the gel in the silicon tube and the screw-top test tube, which are readily available in the laboratory. The one capillary can continuously scan a wide range of crystallization conditions (combination of the concentrations of the precipitant and the protein) unless crystallization occurs, which means that it corresponds to many drops in the vapor-diffusion method. The amount of the precipitant and the protein solutions can be much less than in conventional methods. In this study, lysozyme and alpha-amylase were used as model proteins for demonstrating the efficiency of this method. In addition, one-dimensional (1-D) simulations of the crystal growth were performed based on the 1-D diffusion model. The optimized conditions can be applied to the initial crystallization conditions for both other counter-diffusion methods with the Granada Crystallization Box (GCB) and for the vapor-diffusion method after some modification.

Study of moisture absorption by an organoplastic

NASA Astrophysics Data System (ADS)

Aniskevich, A. N.; Yanson, Yu. O.

1991-07-01

A complex experimental study of the state of sorbed moisture in a unidirectionally reinforced organoplastic was conducted. The methods of TG, DSC, DTA, and NMR showed that moisture absorption in OP is reversible up to 8%, the sorbed moisture does not crystallize in the temperature range from -70 to 0 °C, it is finely dispersely distributed and is in the strongly and weakly bound state, and there is almost no free moisture. The results of the sorption experiments conducted on OP and its structural components: microplastic and EDT-10 binder, in a wide range of temperature-humidity conditions and the data from physical studies showed that moisture absorption in the materials basically takes place by diffusion and is satisfactorily described by a phenomenological model based on the Fick equation. A method of accelerated determination of the sorption characteristics of anisotropic composite materials was developed, using the introduced concept of the fictitious diffusion coefficient and the extrapolation method of determining the limiting moisture content. The features of migration of moisture on the interface in a multiphase system were investigated, and the possibility of successive calculation estimation of the sorption characteristics of an organoplastic at different structural levels was demonstrated: components—unidirectionally reinforced composite—model laminated article. The tested phenomenological model of the sorption process and the experimentally obtained values of the characteristics of the material were the basis for a method of calculation determination of the resource of moisture-proofing properties of a model multilayer article of CM in nonstationary external conditions.

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

NASA Astrophysics Data System (ADS)

Qin, Jianwei; Lu, Renfu

2005-11-01

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

Solid-State Diffusional Behaviors of Functional Metal Oxides at Atomic Scale.

PubMed

Chen, Jui-Yuan; Huang, Chun-Wei; Wu, Wen-Wei

2018-02-01

Metal/metal oxides have attracted extensive research interest because of their combination of functional properties and compatibility with industry. Diffusion and thermal reliability have become essential issues that require detailed study to develop atomic-scaled functional devices. In this work, the diffusional reaction behavior that transforms piezoelectric ZnO into magnetic Fe 3 O 4 is investigated at the atomic scale. The growth kinetics of metal oxides are systematically studied through macro- and microanalyses. The growth rates are evaluated by morphology changes, which determine whether the growth behavior was a diffusion- or reaction-controlled process. Furthermore, atom attachment on the kink step is observed at the atomic scale, which has important implications for the thermodynamics of functional metal oxides. Faster growth planes simultaneously decrease, which result in the predominance of low surface energy planes. These results directly reveal the atomic formation process of metal oxide via solid-state diffusion. In addition, the nanofabricated method provides a novel approach to investigate metal oxide evolution and sheds light on diffusional reaction behavior. More importantly, the results and phenomena of this study provide considerable inspiration to enhance the material stability and reliability of metal/oxide-based devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Edge-based nonlinear diffusion for finite element approximations of convection-diffusion equations and its relation to algebraic flux-correction schemes.

PubMed

Barrenechea, Gabriel R; Burman, Erik; Karakatsani, Fotini

2017-01-01

For the case of approximation of convection-diffusion equations using piecewise affine continuous finite elements a new edge-based nonlinear diffusion operator is proposed that makes the scheme satisfy a discrete maximum principle. The diffusion operator is shown to be Lipschitz continuous and linearity preserving. Using these properties we provide a full stability and error analysis, which, in the diffusion dominated regime, shows existence, uniqueness and optimal convergence. Then the algebraic flux correction method is recalled and we show that the present method can be interpreted as an algebraic flux correction method for a particular definition of the flux limiters. The performance of the method is illustrated on some numerical test cases in two space dimensions.

Evaluation of the direct and diffusion methods for the determination of fluoride content in table salt

PubMed Central

Martínez-Mier, E. Angeles; Soto-Rojas, Armando E.; Buckley, Christine M.; Margineda, Jorge; Zero, Domenick T.

2010-01-01

Objective The aim of this study was to assess methods currently used for analyzing fluoridated salt in order to identify the most useful method for this type of analysis. Basic research design Seventy-five fluoridated salt samples were obtained. Samples were analyzed for fluoride content, with and without pretreatment, using direct and diffusion methods. Element analysis was also conducted in selected samples. Fluoride was added to ultra pure NaCl and non-fluoridated commercial salt samples and Ca and Mg were added to fluoride samples in order to assess fluoride recoveries using modifications to the methods. Results Larger amounts of fluoride were found and recovered using diffusion than direct methods (96%–100% for diffusion vs. 67%–90% for direct). Statistically significant differences were obtained between direct and diffusion methods using different ion strength adjusters. Pretreatment methods reduced the amount of recovered fluoride. Determination of fluoride content was influenced both by the presence of NaCl and other ions in the salt. Conclusion Direct and diffusion techniques for analysis of fluoridated salt are suitable methods for fluoride analysis. The choice of method should depend on the purpose of the analysis. PMID:20088217

Solution Phase Exciton Diffusion Dynamics of a Charge-Transfer Copolymer PTB7 and a Homopolymer P3HT

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

Cho, Sung; Rolczynski, Brian S.; Xu, Tao

2015-06-18

Using ultrafast polarization-controlled transient absorption (TA) measurements, dynamics of the initial exciton states were investigated on the time scale of tens of femtoseconds to about 80 ps in two different types of conjugated polymers extensively used in active layers of organic photovoltaic devices. These polymers are poly(3-fluorothienothiophenebenzodithiophene) (PTB7) and poly-3-hexylthiophene (P3HT), which are charge-transfer polymers and homopolymers, respectively. In PTB7, the initial excitons with excess vibrational energy display two observable ultrafast time constants, corresponding to coherent exciton diffusion before the vibrational relaxation, and followed by incoherent exciton diffusion processes to a neighboring local state after the vibrational relaxation. In contrast,more » P3HT shows only one exciton diffusion or conformational motion time constant of 34 ps, even though its exciton decay kinetics are multiexponential. Based on the experimental results, an exciton dynamics mechanism is conceived taking into account the excitation energy and structural dependence in coherent and incoherent exciton diffusion processes, as well as other possible deactivation processes including the formation of the pseudo-charge-transfer and charge separate states, as well as interchain exciton hopping or coherent diffusion.« less

Solution Phase Exciton Diffusion Dynamics of a Charge-Transfer Copolymer PTB7 and a Homopolymer P3HT.

PubMed

Cho, Sung; Rolczynski, Brian S; Xu, Tao; Yu, Luping; Chen, Lin X

2015-06-18

Using ultrafast polarization-controlled transient absorption (TA) measurements, dynamics of the initial exciton states were investigated on the time scale of tens of femtoseconds to about 80 ps in two different types of conjugated polymers extensively used in active layers of organic photovoltaic devices. These polymers are poly(3-fluorothienothiophenebenzodithiophene) (PTB7) and poly-3-hexylthiophene (P3HT), which are charge-transfer polymers and homopolymers, respectively. In PTB7, the initial excitons with excess vibrational energy display two observable ultrafast time constants, corresponding to coherent exciton diffusion before the vibrational relaxation, and followed by incoherent exciton diffusion processes to a neighboring local state after the vibrational relaxation. In contrast, P3HT shows only one exciton diffusion or conformational motion time constant of 34 ps, even though its exciton decay kinetics are multiexponential. Based on the experimental results, an exciton dynamics mechanism is conceived taking into account the excitation energy and structural dependence in coherent and incoherent exciton diffusion processes, as well as other possible deactivation processes including the formation of the pseudo-charge-transfer and charge separate states, as well as interchain exciton hopping or coherent diffusion.

Non-oscillatory and non-diffusive solution of convection problems by the iteratively reweighted least-squares finite element method

NASA Technical Reports Server (NTRS)

Jiang, Bo-Nan

1993-01-01

A comparative description is presented for the least-squares FEM (LSFEM) for 2D steady-state pure convection problems. In addition to exhibiting better control of the streamline derivative than the streamline upwinding Petrov-Galerkin method, numerical convergence rates are obtained which show the LSFEM to be virtually optimal. The LSFEM is used as a framework for an iteratively reweighted LSFEM yielding nonoscillatory and nondiffusive solutions for problems with contact discontinuities; this method is shown to convect contact discontinuities without error when using triangular and bilinear elements.

Image Halftoning Using Optimized Dot Diffusion

DTIC Science & Technology

1998-01-01

ppvnath@sys.caltech.edu ABSTRACT The dot diffusion method for digital halftoning has the advantage of parallelism unlike the error diffusion ...digital halftoning : ordered dither [1], error diffusion [2], neural-net based methods [8], and more recently direct binary search (DBS) [7]. Ordered...from periodic patterns. On the other hand error diffused halftones do not suffer from periodicity and offer blue noise characteristic [3] which is

Self-learning kinetic Monte Carlo simulations of diffusion in ferromagnetic α-Fe-Si alloys

NASA Astrophysics Data System (ADS)

Nandipati, Giridhar; Jiang, Xiujuan; Vemuri, Rama S.; Mathaudhu, Suveen; Rohatgi, Aashish

2018-01-01

Diffusion of Si atom and vacancy in the A2-phase of α-Fe-Si alloys in the ferromagnetic state, with and without magnetic order and in various temperature ranges, are studied using AKSOME, an on-lattice self-learning KMC code. Diffusion of the Si atom and the vacancy are studied in the dilute limit and up to 12 at.% Si, respectively, in the temperature range 350-700 K. Local Si neighborhood dependent activation energies for vacancy hops were calculated on-the-fly using a broken-bond model based on pairwise interaction. The migration barrier and prefactor for the Si diffusion in the dilute limit were obtained and found to agree with published data within the limits of uncertainty. Simulations results show that the prefactor and the migration barrier for the Si diffusion are approximately an order of magnitude higher, and a tenth of an electron-volt higher, respectively, in the magnetic disordered state than in the fully ordered state. However, the net result is that magnetic disorder does not have a significant effect on Si diffusivity within the range of parameters studied in this work. Nevertheless, with increasing temperature, the magnetic disorder increases and its effect on the Si diffusivity also increases. In the case of vacancy diffusion, with increasing Si concentration, its diffusion prefactor decreases while the migration barrier more or less remained constant and the effect of magnetic disorder increases with Si concentration. Important vacancy-Si/Fe atom exchange processes and their activation barriers were identified, and the effect of energetics on ordered phase formation in Fe-Si alloys are discussed.

Benchmarks and Reliable DFT Results for Spin Gaps of Small Ligand Fe(II) Complexes

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

Song, Suhwan; Kim, Min-Cheol; Sim, Eunji

2017-05-01

All-electron fixed-node diffusion Monte Carlo provides benchmark spin gaps for four Fe(II) octahedral complexes. Standard quantum chemical methods (semilocal DFT and CCSD(T)) fail badly for the energy difference between their high- and low-spin states. Density-corrected DFT is both significantly more accurate and reliable and yields a consistent prediction for the Fe-Porphyrin complex

Problems with heterogeneous and non-isotropic media or distorted grids

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

Hyman, J.; Shashkov, M.; Steinberg, S.

1996-08-01

This paper defines discretizations of the divergence and flux operators that produce symmetric, positive-definite, and accurate approximations to steady-state diffusion problems. Because discontinuous material properties and highly distorted grids are allowed, the flux operator, rather than the gradient, is used as a fundamental operator to be discretized. Resulting finite-difference scheme is similar to those obtained from the mixed finite-element method.

Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin—Molecular Dynamics Simulations of the Ground State and the M-Intermediate

PubMed Central

Grudinin, Sergei; Büldt, Georg; Gordeliy, Valentin; Baumgaertner, Artur

2005-01-01

Protein crystallography provides the structure of a protein, averaged over all elementary cells during data collection time. Thus, it has only a limited access to diffusive processes. This article demonstrates how molecular dynamics simulations can elucidate structure-function relationships in bacteriorhodopsin (bR) involving water molecules. The spatial distribution of water molecules and their corresponding hydrogen-bonded networks inside bR in its ground state (G) and late M intermediate conformations were investigated by molecular dynamics simulations. The simulations reveal a much higher average number of internal water molecules per monomer (28 in the G and 36 in the M) than observed in crystal structures (18 and 22, respectively). We found nine water molecules trapped and 19 diffusive inside the G-monomer, and 13 trapped and 23 diffusive inside the M-monomer. The exchange of a set of diffusive internal water molecules follows an exponential decay with a 1/e time in the order of 340 ps for the G state and 460 ps for the M state. The average residence time of a diffusive water molecule inside the protein is ∼95 ps for the G state and 110 ps for the M state. We have used the Grotthuss model to describe the possible proton transport through the hydrogen-bonded networks inside the protein, which is built up in the picosecond-to-nanosecond time domains. Comparing the water distribution and hydrogen-bonded networks of the two different states, we suggest possible pathways for proton hopping and water movement inside bR. PMID:15731388

Pseudo-time algorithms for the Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Swanson, R. C.; Turkel, E.

1986-01-01

A pseudo-time method is introduced to integrate the compressible Navier-Stokes equations to a steady state. This method is a generalization of a method used by Crocco and also by Allen and Cheng. We show that for a simple heat equation that this is just a renormalization of the time. For a convection-diffusion equation the renormalization is dependent only on the viscous terms. We implement the method for the Navier-Stokes equations using a Runge-Kutta type algorithm. This permits the time step to be chosen based on the inviscid model only. We also discuss the use of residual smoothing when viscous terms are present.

Simultaneous specimen current and time-dependent cathodoluminescence measurements on gallium nitride

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

Campo, E. M., E-mail: e.campo@bangor.ac.uk; Hopkins, L.; Pophristic, M.

2016-06-28

Time-dependent cathodoluminescence (CL) and specimen current (SC) are monitored to evaluate trapping behavior and evolution of charge storage. Examination of CL and SC suggests that the near band edge emission in GaN is reduced primarily by the activation of traps upon irradiation, and Gallium vacancies are prime candidates. At the steady state, measurement of the stored charge by empiric-analytical methods suggests that all available traps within the interaction volume have been filled, and that additional charge is being stored interstitially, necessarily beyond the interaction volume. Once established, the space charge region is responsible for the steady state CL emission and,more » prior to build up, it is responsible for the generation of diffusion currents. Since the non-recombination effects resulting from diffusion currents that develop early on are analogous to those leading to device failure upon aging, this study is fundamental toward a holistic insight into optical properties in GaN.« less

Measurement of thermal conductivity and thermal diffusivity using a thermoelectric module

NASA Astrophysics Data System (ADS)

Beltrán-Pitarch, Braulio; Márquez-García, Lourdes; Min, Gao; García-Cañadas, Jorge

2017-04-01

A proof of concept of using a thermoelectric module to measure both thermal conductivity and thermal diffusivity of bulk disc samples at room temperature is demonstrated. The method involves the calculation of the integral area from an impedance spectrum, which empirically correlates with the thermal properties of the sample through an exponential relationship. This relationship was obtained employing different reference materials. The impedance spectroscopy measurements are performed in a very simple setup, comprising a thermoelectric module, which is soldered at its bottom side to a Cu block (heat sink) and thermally connected with the sample at its top side employing thermal grease. Random and systematic errors of the method were calculated for the thermal conductivity (18.6% and 10.9%, respectively) and thermal diffusivity (14.2% and 14.7%, respectively) employing a BCR724 standard reference material. Although errors are somewhat high, the technique could be useful for screening purposes or high-throughput measurements at its current state. This new method establishes a new application for thermoelectric modules as thermal properties sensors. It involves the use of a very simple setup in conjunction with a frequency response analyzer, which provides a low cost alternative to most of currently available apparatus in the market. In addition, impedance analyzers are reliable and widely spread equipment, which facilities the sometimes difficult access to thermal conductivity facilities.

Diffusion bonding aeroengine components

NASA Astrophysics Data System (ADS)

Fitzpatrick, G. A.; Broughton, T.

1988-10-01

The use of diffusion bonding processes at Rolls-Royce for the manufacture of titanium-alloy aircraft engine components and structures is described. A liquid-phase diffusion bonding process called activated diffusion bonding has been developed for the manufacture of the hollow titanium wide chord fan blade. In addition, solid-state diffusion bonding is being used in the manufacture of hollow vane/blade airfoil constructions mainly in conjunction with superplastic forming and hot forming techniques.

A hybrid continuous-discrete method for stochastic reaction-diffusion processes.

PubMed

Lo, Wing-Cheong; Zheng, Likun; Nie, Qing

2016-09-01

Stochastic fluctuations in reaction-diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method.

Solid state oxygen sensor

DOEpatents

Garzon, Fernando H.; Chung, Brandon W.; Raistrick, Ian D.; Brosha, Eric L.

1996-01-01

Solid state oxygen sensors are provided with a yttria-doped zirconia as an electrolyte and use the electrochemical oxygen pumping of the zirconia electrolyte. A linear relationship between oxygen concentration and the voltage arising at a current plateau occurs when oxygen accessing the electrolyte is limited by a diffusion barrier. A diffusion barrier is formed herein with a mixed electronic and oxygen ion-conducting membrane of lanthanum-containing perovskite or zirconia-containing fluorite. A heater may be used to maintain an adequate oxygen diffusion coefficient in the mixed conducting layer.

An improved method to estimate reflectance parameters for high dynamic range imaging

NASA Astrophysics Data System (ADS)

Li, Shiying; Deguchi, Koichiro; Li, Renfa; Manabe, Yoshitsugu; Chihara, Kunihiro

2008-01-01

Two methods are described to accurately estimate diffuse and specular reflectance parameters for colors, gloss intensity and surface roughness, over the dynamic range of the camera used to capture input images. Neither method needs to segment color areas on an image, or to reconstruct a high dynamic range (HDR) image. The second method improves on the first, bypassing the requirement for specific separation of diffuse and specular reflection components. For the latter method, diffuse and specular reflectance parameters are estimated separately, using the least squares method. Reflection values are initially assumed to be diffuse-only reflection components, and are subjected to the least squares method to estimate diffuse reflectance parameters. Specular reflection components, obtained by subtracting the computed diffuse reflection components from reflection values, are then subjected to a logarithmically transformed equation of the Torrance-Sparrow reflection model, and specular reflectance parameters for gloss intensity and surface roughness are finally estimated using the least squares method. Experiments were carried out using both methods, with simulation data at different saturation levels, generated according to the Lambert and Torrance-Sparrow reflection models, and the second method, with spectral images captured by an imaging spectrograph and a moving light source. Our results show that the second method can estimate the diffuse and specular reflectance parameters for colors, gloss intensity and surface roughness more accurately and faster than the first one, so that colors and gloss can be reproduced more efficiently for HDR imaging.

Gravitational instability of filamentary molecular clouds, including ambipolar diffusion; non-isothermal filament

NASA Astrophysics Data System (ADS)

Hosseinirad, Mohammad; Abbassi, Shahram; Roshan, Mahmood; Naficy, Kazem

2018-04-01

Recent observations of the filamentary molecular clouds show that their properties deviate from the isothermal equation of state. Theoretical investigations proposed that the logatropic and the polytropic equations of state with negative indexes can provide a better description for these filamentary structures. Here, we aim to compare the effects of these softer non-isothermal equations of state with their isothermal counterpart on the global gravitational instability of a filamentary molecular cloud. By incorporating the ambipolar diffusion, we use the non-ideal magnetohydrodynamics framework for a filament that is threaded by a uniform axial magnetic field. We perturb the fluid and obtain the dispersion relation both for the logatropic and polytropic equations of state by taking the effects of magnetic field and ambipolar diffusion into account. Our results suggest that, in absence of the magnetic field, a softer equation of state makes the system more prone to gravitational instability. We also observed that a moderate magnetic field is able to enhance the stability of the filament in a way that is sensitive to the equation of state in general. However, when the magnetic field is strong, this effect is suppressed and all the equations of state have almost the same stability properties. Moreover, we find that for all the considered equations of state, the ambipolar diffusion has destabilizing effects on the filament.

Time-dependent simulation of oblique MHD cosmic-ray shocks using the two-fluid model

NASA Technical Reports Server (NTRS)

Frank, Adam; Jones, T. W.; Ryu, Dongsu

1995-01-01

Using a new, second-order accurate numerical method we present dynamical simulations of oblique MHD cosmic-ray (CR)-modified plane shock evolution. Most of the calculations are done with a two-fluid model for diffusive shock acceleration, but we provide also comparisons between a typical shock computed that way against calculations carried out using the more complete, momentum-dependent, diffusion-advection equation. We also illustrate a test showing that these simulations evolve to dynamical equilibria consistent with previously published steady state analytic calculations for such shocks. In order to improve understanding of the dynamical role of magnetic fields in shocks modified by CR pressure we have explored for time asymptotic states the parameter space of upstream fast mode Mach number, M(sub f), and plasma beta. We compile the results into maps of dynamical steady state CR acceleration efficiency, epsilon(sub c). We have run simulations using constant, and nonisotropic, obliquity (and hence spatially) dependent forms of the diffusion coefficient kappa. Comparison of the results shows that while the final steady states achieved are the same in each case, the history of CR-MHD shocks can be strongly modified by variations in kappa and, therefore, in the acceleration timescale. Also, the coupling of CR and MHD in low beta, oblique shocks substantially influences the transient density spike that forms in strongly CR-modified shocks. We find that inside the density spike a MHD slow mode wave can be generated that eventually steepens into a shock. A strong layer develops within the density spike, driven by MHD stresses. We conjecture that currents in the shear layer could, in nonplanar flows, results in enhanced particle accretion through drift acceleration.

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

DOE PAGES

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

2015-02-17

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

Effects of wingtip modifications on handling qualities of agricultural aircraft

NASA Technical Reports Server (NTRS)

Van Dam, C. P.

1981-01-01

The effect of wingtip modifications on the stability and control characteristics of an agricultural airplane has been studied by means of a nonplanar quasi-vortex-lattice method. The method is used to compute the changes in steady state and perturbed state lateral-directional stability and control derivatives produced by wingtip mounted winglets, vortex diffuser vanes, and tip extensions. The study shows that the combination of the excessive positive dihedral effect produced by the winglets and adverse yaw due to aileron deflection can have a detrimental effect on the roll control characteristics of the airplane. Introduction of an aileron-rudder-interconnect, and reduction of the effective dihedral by canting-in of the winglets, or addition of a lower winglet can eliminate the roll control problems.

Liquid-State NMR Analysis of Nanocelluloses.

PubMed

King, Alistair W T; Mäkelä, Valtteri; Kedzior, Stephanie A; Laaksonen, Tiina; Partl, Gabriel J; Heikkinen, Sami; Koskela, Harri; Heikkinen, Harri A; Holding, Ashley J; Cranston, Emily D; Kilpeläinen, Ilkka

2018-04-11

Recent developments in ionic liquid electrolytes for cellulose or biomass dissolution has also allowed for high-resolution 1 H and 13 C NMR on very high molecular weight cellulose. This permits the development of advanced liquid-state quantitative NMR methods for characterization of unsubstituted and low degree of substitution celluloses, for example, surface-modified nanocelluloses, which are insoluble in all molecular solvents. As such, we present the use of the tetrabutylphosphonium acetate ([P 4444 ][OAc]):DMSO- d 6 electrolyte in the 1D and 2D NMR characterization of poly(methyl methacrylate) (PMMA)-grafted cellulose nanocrystals (CNCs). PMMA- g-CNCs was chosen as a difficult model to study, to illustrate the potential of the technique. The chemical shift range of [P 4444 ][OAc] is completely upfield of the cellulose backbone signals, avoiding signal overlap. In addition, application of diffusion-editing for 1 H and HSQC was shown to be effective in the discrimination between PMMA polymer graft resonances and those from low molecular weight components arising from the solvent system. The bulk ratio of methyl methacrylate monomer to anhydroglucose unit was determined using a combination of HSQC and quantitative 13 C NMR. After detachment and recovery of the PMMA grafts, through methanolysis, DOSY NMR was used to determine the average self-diffusion coefficient and, hence, molecular weight of the grafts compared to self-diffusion coefficients for PMMA GPC standards. This finally led to a calculation of both graft length and graft density using liquid-state NMR techniques. In addition, it was possible to discriminate between triads and tetrads, associated with PMMA tacticity, of the PMMA still attached to the CNCs (before methanolysis). CNC reducing end and sulfate half ester resonances, from sulfuric acid hydrolysis, were also assignable. Furthermore, other biopolymers, such as hemicelluloses and proteins (silk and wool), were found to be soluble in the electrolyte media, allowing for wider application of this method beyond just cellulose analytics.

Instrumentation in Diffuse Optical Imaging

PubMed Central

Zhang, Xiaofeng

2014-01-01

Diffuse optical imaging is highly versatile and has a very broad range of applications in biology and medicine. It covers diffuse optical tomography, fluorescence diffuse optical tomography, bioluminescence, and a number of other new imaging methods. These methods of diffuse optical imaging have diversified instrument configurations but share the same core physical principle – light propagation in highly diffusive media, i.e., the biological tissue. In this review, the author summarizes the latest development in instrumentation and methodology available to diffuse optical imaging in terms of system architecture, light source, photo-detection, spectral separation, signal modulation, and lastly imaging contrast. PMID:24860804

Method for applying a diffusion barrier interlayer for high temperature components

DOEpatents

Wei, Ronghua; Cheruvu, Narayana S.

2016-03-08

A coated substrate and a method of forming a diffusion barrier coating system between a substrate and a MCrAl coating, including a diffusion barrier coating deposited onto at least a portion of a substrate surface, wherein the diffusion barrier coating comprises a nitride, oxide or carbide of one or more transition metals and/or metalloids and a MCrAl coating, wherein M includes a transition metal or a metalloid, deposited on at least a portion of the diffusion barrier coating, wherein the diffusion barrier coating restricts the inward diffusion of aluminum of the MCrAl coating into the substrate.

Twirling and Whirling: Viscous Dynamics of Rotating Elastica

NASA Astrophysics Data System (ADS)

Wolgemuth, Charles; Powers, Thomas; Goldstein, Raymond

1999-10-01

The stability of forced elastic filaments arise in several important biological settings involving bend and twist elasticity at low Reynolds number. Examples include DNA transcription and replication and bacterial flagellar motion. In order to elucidate fundamental processes common to these systems, we consider the model problem of a rotationally forced filament with twist and bend elasticity. Competition between twist injection, twist diffusion, and writhing instabilities is described by a novel pair of PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist/bend coupling and reveal two dynamical regimes seperated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. Experiments are proposed to examine these phenomena and the consequences for swimming investigated.

A fast semi-discrete Kansa method to solve the two-dimensional spatiotemporal fractional diffusion equation

NASA Astrophysics Data System (ADS)

Sun, HongGuang; Liu, Xiaoting; Zhang, Yong; Pang, Guofei; Garrard, Rhiannon

2017-09-01

Fractional-order diffusion equations (FDEs) extend classical diffusion equations by quantifying anomalous diffusion frequently observed in heterogeneous media. Real-world diffusion can be multi-dimensional, requiring efficient numerical solvers that can handle long-term memory embedded in mass transport. To address this challenge, a semi-discrete Kansa method is developed to approximate the two-dimensional spatiotemporal FDE, where the Kansa approach first discretizes the FDE, then the Gauss-Jacobi quadrature rule solves the corresponding matrix, and finally the Mittag-Leffler function provides an analytical solution for the resultant time-fractional ordinary differential equation. Numerical experiments are then conducted to check how the accuracy and convergence rate of the numerical solution are affected by the distribution mode and number of spatial discretization nodes. Applications further show that the numerical method can efficiently solve two-dimensional spatiotemporal FDE models with either a continuous or discrete mixing measure. Hence this study provides an efficient and fast computational method for modeling super-diffusive, sub-diffusive, and mixed diffusive processes in large, two-dimensional domains with irregular shapes.

Solutions of the two-dimensional Hubbard model: Benchmarks and results from a wide range of numerical algorithms

DOE PAGES

LeBlanc, J. P. F.; Antipov, Andrey E.; Becca, Federico; ...

2015-12-14

Numerical results for ground-state and excited-state properties (energies, double occupancies, and Matsubara-axis self-energies) of the single-orbital Hubbard model on a two-dimensional square lattice are presented, in order to provide an assessment of our ability to compute accurate results in the thermodynamic limit. Many methods are employed, including auxiliary-field quantum Monte Carlo, bare and bold-line diagrammatic Monte Carlo, method of dual fermions, density matrix embedding theory, density matrix renormalization group, dynamical cluster approximation, diffusion Monte Carlo within a fixed-node approximation, unrestricted coupled cluster theory, and multireference projected Hartree-Fock methods. Comparison of results obtained by different methods allows for the identification ofmore » uncertainties and systematic errors. The importance of extrapolation to converged thermodynamic-limit values is emphasized. Furthermore, cases where agreement between different methods is obtained establish benchmark results that may be useful in the validation of new approaches and the improvement of existing methods.« less

Measuring the 511 keV emission in the direction of 1E1740.7-2942 with BATSE

NASA Technical Reports Server (NTRS)

Wallyn, P.; Ling, J. C.; Mahoney, W. A.; Wheaton, W. A.; Durouchoux, P.; Corbel, S.; Astier-Perret, L.; Poirot, L.

1997-01-01

Observations of the 511 keV emission in the direction of 1E 1740.7-2942 (1E) using the earth burst and transient source experiment (BATSE) onboard the Compton Gamma Ray Observatory (CGRO), are presented. The CGRO phase 1 average spectrum of 1E is calculated using a method which assumes that a given source spectrum is the sum of the flux coming directly from the object and the contribution from the surrounding diffuse emission. The 1E light curve is calculated in the 40 to 150 keV range. It presents a constant flux excess of 70 mCrab in comparison with observations from the SIGMA gamma ray telescope onboard the GRANAT observatory. By removing this contribution, the 1E spectral transition from the low state to the high standard state observed by SIGMA is confirmed, and it is shown that the 511 keV flux is independent of the 1E long term evolution from low state to high standard state. It is concluded that the 511 keV emission of (4.2 +/- 1.3) x 140(exp -4) photons/sq cm s observed in the direction of 1E is mainly diffuse and spatially extended.

Active and passive transport of cargo in a corrugated channel: A lattice model study

NASA Astrophysics Data System (ADS)

Dey, Supravat; Ching, Kevin; Das, Moumita

2018-04-01

Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCCs) navigate the confining and crowded environment of the cytoskeletal network and other macromolecules. Motivated by this, we study a minimal two-state model of motor-driven cargo transport in confinement and predict transport properties that can be tested in experiments. We assume that the motion of the MCC is directly affected by the entropic barrier due to confinement if it is in the passive, unbound state but not in the active, bound state where it moves with a constant bound velocity. We construct a lattice model based on a Fokker Planck description of the two-state system, study it using a kinetic Monte Carlo method and compare our numerical results with analytical expressions for a mean field limit. We find that the effect of confinement strongly depends on the bound velocity and the binding kinetics of the MCC. Confinement effectively reduces the effective diffusivity and average velocity, except when it results in an enhanced average binding rate and thereby leads to a larger average velocity than when unconfined.

A Framework for Linear and Non-Linear Registration of Diffusion-Weighted MRIs Using Angular Interpolation

PubMed Central

Duarte-Carvajalino, Julio M.; Sapiro, Guillermo; Harel, Noam; Lenglet, Christophe

2013-01-01

Registration of diffusion-weighted magnetic resonance images (DW-MRIs) is a key step for population studies, or construction of brain atlases, among other important tasks. Given the high dimensionality of the data, registration is usually performed by relying on scalar representative images, such as the fractional anisotropy (FA) and non-diffusion-weighted (b0) images, thereby ignoring much of the directional information conveyed by DW-MR datasets itself. Alternatively, model-based registration algorithms have been proposed to exploit information on the preferred fiber orientation(s) at each voxel. Models such as the diffusion tensor or orientation distribution function (ODF) have been used for this purpose. Tensor-based registration methods rely on a model that does not completely capture the information contained in DW-MRIs, and largely depends on the accurate estimation of tensors. ODF-based approaches are more recent and computationally challenging, but also better describe complex fiber configurations thereby potentially improving the accuracy of DW-MRI registration. A new algorithm based on angular interpolation of the diffusion-weighted volumes was proposed for affine registration, and does not rely on any specific local diffusion model. In this work, we first extensively compare the performance of registration algorithms based on (i) angular interpolation, (ii) non-diffusion-weighted scalar volume (b0), and (iii) diffusion tensor image (DTI). Moreover, we generalize the concept of angular interpolation (AI) to non-linear image registration, and implement it in the FMRIB Software Library (FSL). We demonstrate that AI registration of DW-MRIs is a powerful alternative to volume and tensor-based approaches. In particular, we show that AI improves the registration accuracy in many cases over existing state-of-the-art algorithms, while providing registered raw DW-MRI data, which can be used for any subsequent analysis. PMID:23596381

A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

PubMed Central

Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Cheng, Xi; Chapman, Teresa; Wilm, Jakob; Rousseau, François

2014-01-01

This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3-D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and a experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to a state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function. PMID:24108711

Design, Construction and Testing of Annular Diffusers for High Speed Civil Transportation Combustor Applications

NASA Technical Reports Server (NTRS)

Okhio, Cyril B.

1996-01-01

A theoretical and an experimental design study of subsonic flow through curved-wall annular diffusers has been initiated under this award in order to establish the most pertinent design parameters and hence performance characteristics for such devices, an the implications of their application in the design of engine components in the aerospace industries. The diffusers under this study are expected to contain appreciable regions of stall and the effects of swirl on their performance are being studied. The experimental work involves the application of Computer Aided Design software tool to the development of a suitable annular diffuse geometry and the subsequent downloading of such data to a CNC machine at Central State University (CSU). Two experimental run segments have been completed so far during FY-95 involving flow visualization and diffuser performance evaluation based on Kinetic Energy Dissipation. The method of calculation of the performance of diffusers based on pressure recovery coefficient has been shown to have some shortcomings and so the kinetic energy dissipation approach has been introduced in the run segment two with some success. The application of the discretized, full Navier Stokes and Continuity equations to the numerical study of the problem described above for the time-mean flow is expected to follow. Various models of turbulence are being evaluated for adoption throughout the study and comparisons would be made with experimental data where they exist. Assessment of diffuser performance based on the dissipated mechanical energy would also be made. The result of the investigations are expected to indicate that more cost effective component design of such devices as diffusers which normally contain complex flows can still be achieved.

A Framework for Linear and Non-Linear Registration of Diffusion-Weighted MRIs Using Angular Interpolation.

PubMed

Duarte-Carvajalino, Julio M; Sapiro, Guillermo; Harel, Noam; Lenglet, Christophe

2013-01-01

Registration of diffusion-weighted magnetic resonance images (DW-MRIs) is a key step for population studies, or construction of brain atlases, among other important tasks. Given the high dimensionality of the data, registration is usually performed by relying on scalar representative images, such as the fractional anisotropy (FA) and non-diffusion-weighted (b0) images, thereby ignoring much of the directional information conveyed by DW-MR datasets itself. Alternatively, model-based registration algorithms have been proposed to exploit information on the preferred fiber orientation(s) at each voxel. Models such as the diffusion tensor or orientation distribution function (ODF) have been used for this purpose. Tensor-based registration methods rely on a model that does not completely capture the information contained in DW-MRIs, and largely depends on the accurate estimation of tensors. ODF-based approaches are more recent and computationally challenging, but also better describe complex fiber configurations thereby potentially improving the accuracy of DW-MRI registration. A new algorithm based on angular interpolation of the diffusion-weighted volumes was proposed for affine registration, and does not rely on any specific local diffusion model. In this work, we first extensively compare the performance of registration algorithms based on (i) angular interpolation, (ii) non-diffusion-weighted scalar volume (b0), and (iii) diffusion tensor image (DTI). Moreover, we generalize the concept of angular interpolation (AI) to non-linear image registration, and implement it in the FMRIB Software Library (FSL). We demonstrate that AI registration of DW-MRIs is a powerful alternative to volume and tensor-based approaches. In particular, we show that AI improves the registration accuracy in many cases over existing state-of-the-art algorithms, while providing registered raw DW-MRI data, which can be used for any subsequent analysis.

The size effect to O2- -Ce4+ charge transfer emission and band gap structure of Sr2 CeO4.

PubMed

Wang, Wenjun; Pan, Yu; Zhang, Wenying; Liu, Xiaoguang; Li, Ling

2018-04-24

Sr 2 CeO 4 phosphors with different crystalline sizes were synthesized by the sol-gel method or the solid-state reaction. Their crystalline size, luminescence intensity of O 2- -Ce 4+ charge transfer and energy gaps were obtained through the characterization by X-ray diffraction, photoluminescence spectra, as well as UV-visible diffuse reflectance measurements. An inverse relationship between photoluminescence (PL) spectra and crystalline size was observed when the heating temperature was from 1000°C to 1300°C. In addition, band energy calculated for all samples showed that a reaction temperature of 1200°C for the solid-state method and 1100°C for sol-gel method gave the largest values, which corresponded with the smallest crystalline size. Correlation between PL intensity and crystalline size showed an inverse relationship. Band structure, density of states and partial density of states of the crystal were calculated to analyze the mechanism using the cambrige sequential total energy package (CASTEP) module integrated with Materials Studio software. Copyright © 2018 John Wiley & Sons, Ltd.

Ex vivo studies for the passive transdermal delivery of low-dose naltrexone from a cream; detection of naltrexone and its active metabolite, 6β-naltrexol, using a novel LC Q-ToF MS assay.

PubMed

Dodou, Kalliopi; Armstrong, Andrew; Kelly, Ivan; Wilkinson, Simon; Carr, Kevin; Shattock, Paul; Whiteley, Paul

2015-01-01

Naltrexone (NTX) is a long-acting opiate antagonist. Low-dose naltrexone (LDN) therapy has shown promising results in the treatment of several autoimmune disorders. Our aim was to formulate NTX into a cream for the delivery of LDN and develop an analytical technique for the quantification of NTX and its active metabolite 6-β-naltrexol (NTXol) during transdermal diffusion cell permeation studies. A 1% w/w NTX cream was formulated and drug permeation was examined over 24 h using static Franz diffusion cells mounted with pig skin. A Liquid Chromatography Quadrupole-Time of Flight Mass Spectrometry (LC-MS Q-ToF) method was developed for the detection of NTX and NTXol in the receptor solution, skin membrane and residual cream on the donor chamber after completion of the diffusion studies. The cream formulation exhibited steady state release of NTX over 24 h after an initial lag time of 2.74 h. The bioconversion of NTX to NTXol in the skin membrane was 1.1%. It was concluded that the cream may be an effective formulation for the sustained transdermal delivery of LDN. The novel LC Q-ToF MS method allowed the accurate measurement of NTX and NTXol levels across the diffusion cell assemblies and the quantification of NTX metabolism in the skin.

Slip and barodiffusion phenomena in slow flows of a gas mixture

NASA Astrophysics Data System (ADS)

Zhdanov, V. M.

2017-03-01

The slip and barodiffusion problems for the slow flows of a gas mixture are investigated on the basis of the linearized moment equations following from the Boltzmann equation. We restrict ourselves to the set of the third-order moment equations and state two general relations (resembling conservation equations) for the moments of the distribution function similar to the conditions used by Loyalka [S. K. Loyalka, Phys. Fluids 14, 2291 (1971), 10.1063/1.1693331] in his approximation method (the modified Maxwell method). The expressions for the macroscopic velocities of the gas mixture species, the partial viscous stress tensors, and the reduced heat fluxes for the stationary slow flow of a gas mixture in the semi-infinite space over a plane wall are obtained as a result of the exact solution of the linearized moment equations in the 10- and 13-moment approximations. The general expression for the slip velocity and the simple and accurate expressions for the viscous, thermal, diffusion slip, and baroslip coefficients, which are given in terms of the basic transport coefficients, are derived by using the modified Maxwell method. The solutions of moment equations are also used for investigation of the flow and diffusion of a gas mixture in a channel formed by two infinite parallel plates. A fundamental result is that the barodiffusion factor in the cross-section-averaged expression for the diffusion flux contains contributions associated with the viscous transfer of momentum in the gas mixture and the effect of the Knudsen layer. Our study revealed that the barodiffusion factor is equal to the diffusion slip coefficient (correct to the opposite sign). This result is consistent with the Onsager's reciprocity relations for kinetic coefficients following from nonequilibrium thermodynamics of the discontinuous systems.

Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

PubMed

Lee, Hung-Wen; Chang, Chun-Ming; Hsing, Cheng-Rong

2017-02-28

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Ni n (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni 8-9 , two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.

Massively Parallel Simulations of Diffusion in Dense Polymeric Structures

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

Faulon, Jean-Loup, Wilcox, R.T.

1997-11-01

An original computational technique to generate close-to-equilibrium dense polymeric structures is proposed. Diffusion of small gases are studied on the equilibrated structures using massively parallel molecular dynamics simulations running on the Intel Teraflops (9216 Pentium Pro processors) and Intel Paragon(1840 processors). Compared to the current state-of-the-art equilibration methods this new technique appears to be faster by some orders of magnitude.The main advantage of the technique is that one can circumvent the bottlenecks in configuration space that inhibit relaxation in molecular dynamics simulations. The technique is based on the fact that tetravalent atoms (such as carbon and silicon) fit in themore » center of a regular tetrahedron and that regular tetrahedrons can be used to mesh the three-dimensional space. Thus, the problem of polymer equilibration described by continuous equations in molecular dynamics is reduced to a discrete problem where solutions are approximated by simple algorithms. Practical modeling applications include the constructing of butyl rubber and ethylene-propylene-dimer-monomer (EPDM) models for oxygen and water diffusion calculations. Butyl and EPDM are used in O-ring systems and serve as sealing joints in many manufactured objects. Diffusion coefficients of small gases have been measured experimentally on both polymeric systems, and in general the diffusion coefficients in EPDM are an order of magnitude larger than in butyl. In order to better understand the diffusion phenomena, 10, 000 atoms models were generated and equilibrated for butyl and EPDM. The models were submitted to a massively parallel molecular dynamics simulation to monitor the trajectories of the diffusing species.« less

An Extended Lagrangian Method

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing

1995-01-01

A unique formulation of describing fluid motion is presented. The method, referred to as 'extended Lagrangian method,' is interesting from both theoretical and numerical points of view. The formulation offers accuracy in numerical solution by avoiding numerical diffusion resulting from mixing of fluxes in the Eulerian description. The present method and the Arbitrary Lagrangian-Eulerian (ALE) method have a similarity in spirit-eliminating the cross-streamline numerical diffusion. For this purpose, we suggest a simple grid constraint condition and utilize an accurate discretization procedure. This grid constraint is only applied to the transverse cell face parallel to the local stream velocity, and hence our method for the steady state problems naturally reduces to the streamline-curvature method, without explicitly solving the steady stream-coordinate equations formulated a priori. Unlike the Lagrangian method proposed by Loh and Hui which is valid only for steady supersonic flows, the present method is general and capable of treating subsonic flows and supersonic flows as well as unsteady flows, simply by invoking in the same code an appropriate grid constraint suggested in this paper. The approach is found to be robust and stable. It automatically adapts to flow features without resorting to clustering, thereby maintaining rather uniform grid spacing throughout and large time step. Moreover, the method is shown to resolve multi-dimensional discontinuities with a high level of accuracy, similar to that found in one-dimensional problems.

Characterization of supersonic radiation diffusion waves

DOE PAGES

Moore, Alastair S.; Guymer, Thomas M.; Morton, John; ...

2015-02-27

Supersonic and diffusive radiation flow is an important test problem for the radiative transfer models used in radiation-hydrodynamics computer codes owing to solutions being accessible via analytic and numeric methods. We present experimental results with which we compare these solutions by studying supersonic and diffusive flow in the laboratory. Here, we present results of higher-accuracy experiments than previously possible studying radiation flow through up to 7 high-temperature mean free paths of low-density, chlorine-doped polystyrene foam and silicon dioxide aerogel contained by an Au tube. Measurements of the heat front position and absolute measurements of the x-ray emission arrival at themore » end of the tube are used to test numerical and analytical models. We find excellent absolute agreement with simulations provided that the opacity and the equation of state are adjusted within expected uncertainties; analytical models provide a good phenomenological match to measurements but are not in quantitative agreement due to their limited scope.« less

The Environmental Protection Agency’s Brownfields Pilot Program

PubMed Central

Greenberg, Michael R.; Hollander, Justin

2006-01-01

Objective. We studied the diffusion of the US Environmental Protection Agency’s national brownfields pilot innovation to more than 300 local governments between 1993 through 2002 to determine why some local governments received grants very early in the process while other awardees received funding later. Methods. We did an ordinal regression analysis of the characteristics of all local government award recipients, and we conducted interviews with early-award recipients. Results. The first set of local government awardees had lost much of their manufacturing base, had large concentrations of economically disadvantaged minority residents, and had local capacity to compete for funding. Federal and state officials catalyzed the diffusion of the innovation by working with local governments. Conclusions. The widely praised program was diffused selectively at first and then more widely later on the basis of local need, local capacity to compete, and networks of contacts among entrepreneurs and local governments. The economic, social, political, and public health impacts must be monitored and reviewed. PMID:16380572

A chaotic model for advertising diffusion problem with competition

NASA Astrophysics Data System (ADS)

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

2012-08-01

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

Balancing surface adsorption and diffusion of lithium-polysulfides on nonconductive oxides for lithium–sulfur battery design

DOE PAGES

Tao, Xinyong; Wang, Jianguo; Liu, Chong; ...

2016-04-05

Lithium–sulfur batteries have attracted attention due to their six-fold specific energy compared with conventional lithium-ion batteries. Dissolution of lithium polysulfides, volume expansion of sulfur and uncontrollable deposition of lithium sulfide are three of the main challenges for this technology. State-of-the-art sulfur cathodes based on metal-oxide nanostructures can suppress the shuttle-effect and enable controlled lithium sulfide deposition. However, a clear mechanistic understanding and corresponding selection criteria for the oxides are still lacking. Herein, various nonconductive metal-oxide nanoparticle-decorated carbon flakes are synthesized via a facile biotemplating method. The cathodes based on magnesium oxide, cerium oxide and lanthanum oxide show enhanced cycling performance.more » Adsorption experiments and theoretical calculations reveal that polysulfide capture by the oxides is via monolayered chemisorption. Moreover, we show that better surface diffusion leads to higher deposition efficiency of sulfide species on electrodes. Lastly, oxide selection is proposed to balance optimization between sulfide-adsorption and diffusion on the oxides.« less

Balancing surface adsorption and diffusion of lithium-polysulfides on nonconductive oxides for lithium-sulfur battery design

NASA Astrophysics Data System (ADS)

Tao, Xinyong; Wang, Jianguo; Liu, Chong; Wang, Haotian; Yao, Hongbin; Zheng, Guangyuan; Seh, Zhi Wei; Cai, Qiuxia; Li, Weiyang; Zhou, Guangmin; Zu, Chenxi; Cui, Yi

2016-04-01

Lithium-sulfur batteries have attracted attention due to their six-fold specific energy compared with conventional lithium-ion batteries. Dissolution of lithium polysulfides, volume expansion of sulfur and uncontrollable deposition of lithium sulfide are three of the main challenges for this technology. State-of-the-art sulfur cathodes based on metal-oxide nanostructures can suppress the shuttle-effect and enable controlled lithium sulfide deposition. However, a clear mechanistic understanding and corresponding selection criteria for the oxides are still lacking. Herein, various nonconductive metal-oxide nanoparticle-decorated carbon flakes are synthesized via a facile biotemplating method. The cathodes based on magnesium oxide, cerium oxide and lanthanum oxide show enhanced cycling performance. Adsorption experiments and theoretical calculations reveal that polysulfide capture by the oxides is via monolayered chemisorption. Moreover, we show that better surface diffusion leads to higher deposition efficiency of sulfide species on electrodes. Hence, oxide selection is proposed to balance optimization between sulfide-adsorption and diffusion on the oxides.

Balancing surface adsorption and diffusion of lithium-polysulfides on nonconductive oxides for lithium-sulfur battery design.

PubMed

Tao, Xinyong; Wang, Jianguo; Liu, Chong; Wang, Haotian; Yao, Hongbin; Zheng, Guangyuan; Seh, Zhi Wei; Cai, Qiuxia; Li, Weiyang; Zhou, Guangmin; Zu, Chenxi; Cui, Yi

2016-04-05

Lithium-sulfur batteries have attracted attention due to their six-fold specific energy compared with conventional lithium-ion batteries. Dissolution of lithium polysulfides, volume expansion of sulfur and uncontrollable deposition of lithium sulfide are three of the main challenges for this technology. State-of-the-art sulfur cathodes based on metal-oxide nanostructures can suppress the shuttle-effect and enable controlled lithium sulfide deposition. However, a clear mechanistic understanding and corresponding selection criteria for the oxides are still lacking. Herein, various nonconductive metal-oxide nanoparticle-decorated carbon flakes are synthesized via a facile biotemplating method. The cathodes based on magnesium oxide, cerium oxide and lanthanum oxide show enhanced cycling performance. Adsorption experiments and theoretical calculations reveal that polysulfide capture by the oxides is via monolayered chemisorption. Moreover, we show that better surface diffusion leads to higher deposition efficiency of sulfide species on electrodes. Hence, oxide selection is proposed to balance optimization between sulfide-adsorption and diffusion on the oxides.

Characterization of supersonic radiation diffusion waves

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

Moore, Alastair S.; Guymer, Thomas M.; Morton, John

Supersonic and diffusive radiation flow is an important test problem for the radiative transfer models used in radiation-hydrodynamics computer codes owing to solutions being accessible via analytic and numeric methods. We present experimental results with which we compare these solutions by studying supersonic and diffusive flow in the laboratory. Here, we present results of higher-accuracy experiments than previously possible studying radiation flow through up to 7 high-temperature mean free paths of low-density, chlorine-doped polystyrene foam and silicon dioxide aerogel contained by an Au tube. Measurements of the heat front position and absolute measurements of the x-ray emission arrival at themore » end of the tube are used to test numerical and analytical models. We find excellent absolute agreement with simulations provided that the opacity and the equation of state are adjusted within expected uncertainties; analytical models provide a good phenomenological match to measurements but are not in quantitative agreement due to their limited scope.« less

Balancing surface adsorption and diffusion of lithium-polysulfides on nonconductive oxides for lithium–sulfur battery design

PubMed Central

Tao, Xinyong; Wang, Jianguo; Liu, Chong; Wang, Haotian; Yao, Hongbin; Zheng, Guangyuan; Seh, Zhi Wei; Cai, Qiuxia; Li, Weiyang; Zhou, Guangmin; Zu, Chenxi; Cui, Yi

2016-01-01

Lithium–sulfur batteries have attracted attention due to their six-fold specific energy compared with conventional lithium-ion batteries. Dissolution of lithium polysulfides, volume expansion of sulfur and uncontrollable deposition of lithium sulfide are three of the main challenges for this technology. State-of-the-art sulfur cathodes based on metal-oxide nanostructures can suppress the shuttle-effect and enable controlled lithium sulfide deposition. However, a clear mechanistic understanding and corresponding selection criteria for the oxides are still lacking. Herein, various nonconductive metal-oxide nanoparticle-decorated carbon flakes are synthesized via a facile biotemplating method. The cathodes based on magnesium oxide, cerium oxide and lanthanum oxide show enhanced cycling performance. Adsorption experiments and theoretical calculations reveal that polysulfide capture by the oxides is via monolayered chemisorption. Moreover, we show that better surface diffusion leads to higher deposition efficiency of sulfide species on electrodes. Hence, oxide selection is proposed to balance optimization between sulfide-adsorption and diffusion on the oxides. PMID:27046216

Diffusion Monte Carlo studies of MB-pol (H{sub 2}O){sub 2−6} and (D{sub 2}O){sub 2−6} clusters: Structures and binding energies

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

Mallory, Joel D.; Mandelshtam, Vladimir A.

2016-08-14

We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H{sub 2}O){sub 2−6} clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitivemore » to the isotope substitution. Most remarkably, the ground state of the (H{sub 2}O){sub 6} hexamer is represented by four distinct cage structures, while that of (D{sub 2}O){sub 6} is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H{sub 2}O){sub 6} and (D{sub 2}O){sub 6}, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F.« less

Equatorial ground ice on Mars: Steady-state stability

NASA Technical Reports Server (NTRS)

Mellon, Michael T.; Jakosky, Bruce M.; Postawko, Susan E.

1993-01-01

Current Martian equatorial surface temperatures are too warm for water ice to exist at the surface for any appreciable length of time before subliming into the atmosphere. Subsurface temperatures are generally warmer still and, despite the presence of a diffusive barrier of porous regolith material, it has been shown by Smoluchowski, Clifford and Hillel, and Fanale et al. that buried ground ice will also sublime and be lost to the atmosphere in a relatively short time. We investigate the behavior of this subliming subsurface ice and show that it is possible for ice to maintain at a steady-state depth, where sublimation and diffusive loss to the atmosphere is balanced by resupply from beneath by diffusion and recondensation of either a deeper buried ice deposits or ground water. We examine the behavior of equatorial ground ice with a numercial time-marching molecular diffusion model. In our model we allow for diffusion of water vapor through a porous regolith, variations in diffusivity and porosity with ice content, and recondensation of sublimed water vapor. A regolith containing considerable amounts of ice can still be very porous, allowing water vapor to diffuse up from deeper within the ice layer where temperatures are warmer due to the geothermal gradient. This vapor can then recondense nearer to the surface where ice had previously sublimed and been lost to the atmosphere. As a result we find that ice deposits migrate to find a steady-state depth, which represents a balance between diffusive loss to the atmosphere through the overlying porous regolith and diffusive resupply through a porous icy regolith below. This depth depends primarily on the long-term mean surface temperature and the nature of the geothermal gradient, and is independent of the ice-free porosity and the regolith diffusivity. Only the rate of loss of ground ice depends on diffusive properties.

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.

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.

Combining DFT, Cluster Expansions, and KMC to Model Point Defects in Alloys

NASA Astrophysics Data System (ADS)

Modine, N. A.; Wright, A. F.; Lee, S. R.; Foiles, S. M.; Battaile, C. C.; Thomas, J. C.; van der Ven, A.

In an alloy, defect energies are sensitive to the occupations of nearby atomic sites, which leads to a distribution of defect properties. When radiation-induced defects diffuse from their initially non-equilibrium locations, this distribution becomes time-dependent. The defects can become trapped in energetically favorable regions of the alloy leading to a diffusion rate that slows dramatically with time. Density Functional Theory (DFT) allows the accurate determination of ground state and transition state energies for a defect in a particular alloy environment but requires thousands of processing hours for each such calculation. Kinetic Monte-Carlo (KMC) can be used to model defect diffusion and the changing distribution of defect properties but requires energy evaluations for millions of local environments. We have used the Cluster Expansion (CE) formalism to ``glue'' together these seemingly incompatible methods. The occupation of each alloy site is represented by an Ising-like variable, and products of these variables are used to expand quantities of interest. Once a CE is fit to a training set of DFT energies, it allows very rapid evaluation of the energy for an arbitrary configuration, while maintaining the accuracy of the underlying DFT calculations. These energy evaluations are then used to drive our KMC simulations. We will demonstrate the application of our DFT/MC/KMC approach to model thermal and carrier-induced diffusion of intrinsic point defects in III-V alloys. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE.

Time dependence of 222Rn, 220Rn and their progenies' distributions in a diffusion chamber

NASA Astrophysics Data System (ADS)

Stevanovic, N.; Markovic, V. M.; Nikezic, D.

2017-11-01

Diffusion chamber with SSNTD (Solid State Nuclear Track Detector) placed inside is a passive detector for measuring the activity of 222Rn and 220Rn (radon and thoron) and their progenies. Calibration from detected alpha particle tracks to progeny activity is often acquired from theoretical models. One common assumption related to these models found in literature is that concentrations of 222Rn and 220Rn at the entrance of a chamber are constant during the exposure. In this paper, concentrations of 222Rn and 220Rn at the entrance of the chamber are taken to be variable with time, which is actually the case in reality. Therefore, spatial distributions of 222Rn and 220Rn and their progenies inside the diffusion chamber should be time dependent. Variation of 222Rn and 220Rn concentrations on the entrance of the chamber was modeled on the basis of true measurements. Diffusion equations in cylindrical coordinates were solved using FDM (Finite Difference Method) to obtain spatial distributions as functions of time. It was shown that concentrations of 222Rn, 220Rn and their progenies were not homogeneously distributed in the chamber. Due to variable 222Rn and 220Rn concentrations at the entrance of the chamber, steady state (the case when concentration of 222Rn, 220Rn and their progenies inside the chamber remains unchanged with time) could not be reached. Deposition of progenies on the chamber walls was considered and it was shown that distributions of deposited progenies were not uniform over walls' surface.

DIFFUSION MEASUREMENTS DURING PERVAPORATION THROUGH A ZEOLITE MEMBRANE

EPA Science Inventory

An isotopic-transient technique was used to directly measure diffusion times of H2O, methanol, ethanol, 2-propanol, and acetone in pure and binary mixture feeds transporting through a zeolite membrane under steady-state pervaporation conditions. Diffusivities can be determ...

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.

Faster quantum searching with almost any diffusion operator

NASA Astrophysics Data System (ADS)

Tulsi, Avatar

2015-05-01

Grover's search algorithm drives a quantum system from an initial state |s > to a desired final state |t > by using selective phase inversions of these two states. Earlier, we studied a generalization of Grover's algorithm that relaxes the assumption of the efficient implementation of Is, the selective phase inversion of the initial state, also known as a diffusion operator. This assumption is known to become a serious handicap in cases of physical interest. Our general search algorithm works with almost any diffusion operator Ds with the only restriction of having |s > as one of its eigenstates. The price that we pay for using any operator is an increase in the number of oracle queries by a factor of O (B ) , where B is a characteristic of the eigenspectrum of Ds and can be large in some situations. Here we show that by using a quantum Fourier transform, we can regain the optimal query complexity of Grover's algorithm without losing the freedom of using any diffusion operator for quantum searching. However, the total number of operators required by the algorithm is still O (B ) times more than that of Grover's algorithm. So our algorithm offers an advantage only if the oracle operator is computationally more expensive than the diffusion operator, which is true in most search problems.

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

NASA Astrophysics Data System (ADS)

Baricci, Andrea; Casalegno, Andrea

2016-09-01

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

Multiconfiguration Pair-Density Functional Theory Spectral Calculations Are Stable to Adding Diffuse Basis Functions.

PubMed

Hoyer, Chad E; Gagliardi, Laura; Truhlar, Donald G

2015-11-05

Time-dependent Kohn-Sham density functional theory (TD-KS-DFT) is useful for calculating electronic excitation spectra of large systems, but the low-energy spectra are often complicated by artificially lowered higher-energy states. This affects even the lowest energy excited states. Here, by calculating the lowest energy spin-conserving excited state for atoms from H to K and for formaldehyde, we show that this problem does not occur in multiconfiguration pair-density functional theory (MC-PDFT). We use the tPBE on-top density functional, which is a translation of the PBE exchange-correlation functional. We compare to a robust multireference method, namely, complete active space second-order perturbation theory (CASPT2), and to TD-KS-DFT with two popular exchange-correlation functionals, PBE and PBE0. We find for atoms that the mean unsigned error (MUE) of MC-PDFT with the tPBE functional improves from 0.42 to 0.40 eV with a double set of diffuse functions, whereas the MUEs for PBE and PBE0 drastically increase from 0.74 to 2.49 eV and from 0.45 to 1.47 eV, respectively.

Diffusion coefficients of water in biobased hydrogel polymer matrices by nuclear magnetic resonance imaging

USDA-ARS?s Scientific Manuscript database

The diffusion coefficient of water in biobased hydrogels were measured utilizing a simple NMR method. This method tracks the migration of deuterium oxide through imaging data that is fit to a diffusion equation. The results show that a 5 wt% soybean oil based hydrogel gives aqueous diffusion of 1.37...

Evaluating Students' Understanding of Kinetic Particle Theory Concepts Relating to the States of Matter, Changes of State and Diffusion: A Cross-National Study

ERIC Educational Resources Information Center

Treagust, David F.; Chandrasegaran, A. L.; Crowley, Julianne; Yung, Benny H. W.; Cheong, Irene P.-A.; Othman, Jazilah

2010-01-01

This paper reports on the understanding of three key conceptual categories relating to the kinetic particle theory: (1) intermolecular spacing in solids, liquids and gases, (2) changes of state and intermolecular forces and (3) diffusion in liquids and gases, amongst 148 high school students from Brunei, Australia, Hong Kong and Singapore using 11…

Numerical method for angle-of-incidence correction factors for diffuse radiation incident photovoltaic modules

DOE PAGES

Marion, Bill

2017-03-27

Here, a numerical method is provided for solving the integral equation for the angle-of-incidence (AOI) correction factor for diffuse radiation incident photovoltaic (PV) modules. The types of diffuse radiation considered include sky, circumsolar, horizon, and ground-reflected. The method permits PV module AOI characteristics to be addressed when calculating AOI losses associated with diffuse radiation. Pseudo code is provided to aid users in the implementation, and results are shown for PV modules with tilt angles from 0° to 90°. Diffuse AOI losses are greatest for small PV module tilt angles. Including AOI losses associated with the diffuse irradiance will improve predictionsmore » of PV system performance.« less

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

PubMed

Haghverdi, Laleh; Buettner, Florian; Theis, Fabian J

2015-09-15

Single-cell technologies have recently gained popularity in cellular differentiation studies regarding their ability to resolve potential heterogeneities in cell populations. Analyzing such high-dimensional single-cell data has its own statistical and computational challenges. Popular multivariate approaches are based on data normalization, followed by dimension reduction and clustering to identify subgroups. However, in the case of cellular differentiation, we would not expect clear clusters to be present but instead expect the cells to follow continuous branching lineages. Here, we propose the use of diffusion maps to deal with the problem of defining differentiation trajectories. We adapt this method to single-cell data by adequate choice of kernel width and inclusion of uncertainties or missing measurement values, which enables the establishment of a pseudotemporal ordering of single cells in a high-dimensional gene expression space. We expect this output to reflect cell differentiation trajectories, where the data originates from intrinsic diffusion-like dynamics. Starting from a pluripotent stage, cells move smoothly within the transcriptional landscape towards more differentiated states with some stochasticity along their path. We demonstrate the robustness of our method with respect to extrinsic noise (e.g. measurement noise) and sampling density heterogeneities on simulated toy data as well as two single-cell quantitative polymerase chain reaction datasets (i.e. mouse haematopoietic stem cells and mouse embryonic stem cells) and an RNA-Seq data of human pre-implantation embryos. We show that diffusion maps perform considerably better than Principal Component Analysis and are advantageous over other techniques for non-linear dimension reduction such as t-distributed Stochastic Neighbour Embedding for preserving the global structures and pseudotemporal ordering of cells. The Matlab implementation of diffusion maps for single-cell data is available at https://www.helmholtz-muenchen.de/icb/single-cell-diffusion-map. fbuettner.phys@gmail.com, fabian.theis@helmholtz-muenchen.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Connecting complexity with spectral entropy using the Laplace transformed solution to the fractional diffusion equation

NASA Astrophysics Data System (ADS)

Liang, Yingjie; Chen, Wen; Magin, Richard L.

2016-07-01

Analytical solutions to the fractional diffusion equation are often obtained by using Laplace and Fourier transforms, which conveniently encode the order of the time and the space derivatives (α and β) as non-integer powers of the conjugate transform variables (s, and k) for the spectral and the spatial frequencies, respectively. This study presents a new solution to the fractional diffusion equation obtained using the Laplace transform and expressed as a Fox's H-function. This result clearly illustrates the kinetics of the underlying stochastic process in terms of the Laplace spectral frequency and entropy. The spectral entropy is numerically calculated by using the direct integration method and the adaptive Gauss-Kronrod quadrature algorithm. Here, the properties of spectral entropy are investigated for the cases of sub-diffusion and super-diffusion. We find that the overall spectral entropy decreases with the increasing α and β, and that the normal or Gaussian case with α = 1 and β = 2, has the lowest spectral entropy (i.e., less information is needed to describe the state of a Gaussian process). In addition, as the neighborhood over which the entropy is calculated increases, the spectral entropy decreases, which implies a spatial averaging or coarse graining of the material properties. Consequently, the spectral entropy is shown to provide a new way to characterize the temporal correlation of anomalous diffusion. Future studies should be designed to examine changes of spectral entropy in physical, chemical and biological systems undergoing phase changes, chemical reactions and tissue regeneration.

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

NASA Astrophysics Data System (ADS)

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

2002-02-01

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

A hybrid continuous-discrete method for stochastic reaction–diffusion processes

PubMed Central

Zheng, Likun; Nie, Qing

2016-01-01

Stochastic fluctuations in reaction–diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method. PMID:27703710

Diffusion measurements in the ischemic human brain with a steady-state sequence.

PubMed

Brüning, R; Wu, R H; Deimling, M; Porn, U; Haberl, R L; Reiser, M

1996-11-01

The authors evaluate the clinical usefulness of a diffusion-weighted steady-state free-precession (SSFP) sequence to detect acute and subacute ischemic changes. Twenty-four patients were examined on a 1.5-tesla scanner, using a SSFP-sequence (repetition time [TR]/ echo time [TE] = 22/3-8 mseconds). The slice thickness was 5 mm, 10 averages, 57 seconds per slice. The diffusion gradient strength was 23 millitesla/m, with b-values from 165 to 598 seconds/mm2. Diffusion-weighted images (DWI) were compared with T2-weighted images. The diffusion-weighted SSFP sequence produced diagnostic quality images in 23 of 24 patients. Diffusion depicted (group 1: 0-12 hours) more acute lesions (3 of 6) than T2-weighted images (2 of 6); the mean lesion diameter depicted by diffusion was 10.9 mm (standard deviation [SD], 12.3) and in T2-weighted images was 4.7 mm (SD 6.8). A significant correlation (P < 0.017) in subacute lesions was found when diffusion was compared with turbo spin echo (mean size difference/T2 = 18.5/17.5 mm, SD 13.2/12.2). The diffusion-weighted SSFP-sequence is more sensitive in acute ischemia and delineates likewise in subacute ischemia, when compared with T2-weighted imaging.

Hybrid Monte Carlo-Diffusion Method For Light Propagation in Tissue With a Low-Scattering Region

NASA Astrophysics Data System (ADS)

Hayashi, Toshiyuki; Kashio, Yoshihiko; Okada, Eiji

2003-06-01

The heterogeneity of the tissues in a head, especially the low-scattering cerebrospinal fluid (CSF) layer surrounding the brain has previously been shown to strongly affect light propagation in the brain. The radiosity-diffusion method, in which the light propagation in the CSF layer is assumed to obey the radiosity theory, has been employed to predict the light propagation in head models. Although the CSF layer is assumed to be a nonscattering region in the radiosity-diffusion method, fine arachnoid trabeculae cause faint scattering in the CSF layer in real heads. A novel approach, the hybrid Monte Carlo-diffusion method, is proposed to calculate the head models, including the low-scattering region in which the light propagation does not obey neither the diffusion approximation nor the radiosity theory. The light propagation in the high-scattering region is calculated by means of the diffusion approximation solved by the finite-element method and that in the low-scattering region is predicted by the Monte Carlo method. The intensity and mean time of flight of the detected light for the head model with a low-scattering CSF layer calculated by the hybrid method agreed well with those by the Monte Carlo method, whereas the results calculated by means of the diffusion approximation included considerable error caused by the effect of the CSF layer. In the hybrid method, the time-consuming Monte Carlo calculation is employed only for the thin CSF layer, and hence, the computation time of the hybrid method is dramatically shorter than that of the Monte Carlo method.

Hybrid Monte Carlo-diffusion method for light propagation in tissue with a low-scattering region.

PubMed

Hayashi, Toshiyuki; Kashio, Yoshihiko; Okada, Eiji

2003-06-01

The heterogeneity of the tissues in a head, especially the low-scattering cerebrospinal fluid (CSF) layer surrounding the brain has previously been shown to strongly affect light propagation in the brain. The radiosity-diffusion method, in which the light propagation in the CSF layer is assumed to obey the radiosity theory, has been employed to predict the light propagation in head models. Although the CSF layer is assumed to be a nonscattering region in the radiosity-diffusion method, fine arachnoid trabeculae cause faint scattering in the CSF layer in real heads. A novel approach, the hybrid Monte Carlo-diffusion method, is proposed to calculate the head models, including the low-scattering region in which the light propagation does not obey neither the diffusion approximation nor the radiosity theory. The light propagation in the high-scattering region is calculated by means of the diffusion approximation solved by the finite-element method and that in the low-scattering region is predicted by the Monte Carlo method. The intensity and mean time of flight of the detected light for the head model with a low-scattering CSF layer calculated by the hybrid method agreed well with those by the Monte Carlo method, whereas the results calculated by means of the diffusion approximation included considerable error caused by the effect of the CSF layer. In the hybrid method, the time-consuming Monte Carlo calculation is employed only for the thin CSF layer, and hence, the computation time of the hybrid method is dramatically shorter than that of the Monte Carlo method.

Near-infrared spectroscopic observation of the ageing process in archaeological wood using a deuterium exchange method.

PubMed

Tsuchikawa, Satoru; Yonenobu, Hitoshi; Siesler, H W

2005-03-01

The ageing degradation of the fine wood structure of dry-exposed archaeological wood was investigated by Fourier transform near-infrared spectroscopy with the aid of a deuterium exchange method. The archaeological wood sample was taken from an old wooden temple in Japan (late 7th century), which has been designated as a UNESCO world heritage site. Comparing the analytical results with those of a modern wood sample of the same species, the ageing process of archaeological wood was clarified as a change in the state of order on a macromolecular structural level. It can be concluded from NIR spectra that the amorphous region, and partially semi-crystalline region, in cellulose, hemicellulose, and lignin decreased by the ageing degradation, whereas the crystalline region in cellulose was not affected by the ageing. The accessibility of the diffusant to effect H/D-exchange was monitored by an OH-related absorption band obtained from FT-NIR transmission spectroscopy and characteristically varied with the ageing process of the wood samples, the absorption bands characteristic of a specific state of order and the diffusion agent. Finally, we proposed a morphological model to describe the variation of the fine structure of the microfibrils in the cell wall with ageing degradation. The state of microfibrils changed loosely by ageing, so that elementary fibrils were arranged loosely under 5 A, whereas several elementary fibrils in the modern wood were arranged in very close proximity under 3 A to each other.

Development of advanced methods for analysis of experimental data in diffusion

NASA Astrophysics Data System (ADS)

Jaques, Alonso V.

There are numerous experimental configurations and data analysis techniques for the characterization of diffusion phenomena. However, the mathematical methods for estimating diffusivities traditionally do not take into account the effects of experimental errors in the data, and often require smooth, noiseless data sets to perform the necessary analysis steps. The current methods used for data smoothing require strong assumptions which can introduce numerical "artifacts" into the data, affecting confidence in the estimated parameters. The Boltzmann-Matano method is used extensively in the determination of concentration - dependent diffusivities, D(C), in alloys. In the course of analyzing experimental data, numerical integrations and differentiations of the concentration profile are performed. These methods require smoothing of the data prior to analysis. We present here an approach to the Boltzmann-Matano method that is based on a regularization method to estimate a differentiation operation on the data, i.e., estimate the concentration gradient term, which is important in the analysis process for determining the diffusivity. This approach, therefore, has the potential to be less subjective, and in numerical simulations shows an increased accuracy in the estimated diffusion coefficients. We present a regression approach to estimate linear multicomponent diffusion coefficients that eliminates the need pre-treat or pre-condition the concentration profile. This approach fits the data to a functional form of the mathematical expression for the concentration profile, and allows us to determine the diffusivity matrix directly from the fitted parameters. Reformulation of the equation for the analytical solution is done in order to reduce the size of the problem and accelerate the convergence. The objective function for the regression can incorporate point estimations for error in the concentration, improving the statistical confidence in the estimated diffusivity matrix. Case studies are presented to demonstrate the reliability and the stability of the method. To the best of our knowledge there is no published analysis of the effects of experimental errors on the reliability of the estimates for the diffusivities. For the case of linear multicomponent diffusion, we analyze the effects of the instrument analytical spot size, positioning uncertainty, and concentration uncertainty on the resulting values of the diffusivities. These effects are studied using Monte Carlo method on simulated experimental data. Several useful scaling relationships were identified which allow more rigorous and quantitative estimates of the errors in the measured data, and are valuable for experimental design. To further analyze anomalous diffusion processes, where traditional diffusional transport equations do not hold, we explore the use of fractional calculus in analytically representing these processes is proposed. We use the fractional calculus approach for anomalous diffusion processes occurring through a finite plane sheet with one face held at a fixed concentration, the other held at zero, and the initial concentration within the sheet equal to zero. This problem is related to cases in nature where diffusion is enhanced relative to the classical process, and the order of differentiation is not necessarily a second--order differential equation. That is, differentiation is of fractional order alpha, where 1 ≤ alpha < 2. For alpha = 2, the presented solutions reduce to the classical second-order diffusion solution for the conditions studied. The solution obtained allows the analysis of permeation experiments. Frequently, hydrogen diffusion is analyzed using electrochemical permeation methods using the traditional, Fickian-based theory. Experimental evidence shows the latter analytical approach is not always appropiate, because reported data shows qualitative (and quantitative) deviation from its theoretical scaling predictions. Preliminary analysis of data shows better agreement with fractional diffusion analysis when compared to traditional square-root scaling. Although there is a large amount of work in the estimation of the diffusivity from experimental data, reported studies typically present only the analytical description for the diffusivity, without scattering. However, because these studies do not consider effects produced by instrument analysis, their direct applicability is limited. We propose alternatives to address these, and to evaluate their influence on the final resulting diffusivity values.

Application of optical non-invasive methods to diagnose the state of the lower limb tissues in patients with diabetes mellitus

NASA Astrophysics Data System (ADS)

Zharkikh, E. V.; Dremin, V. V.; Filina, M. A.; Makovik, I. N.; Potapova, E. V.; Zherebtsov, E. A.; Zherebtsova, A. I.; Dunaev, A. V.

2017-11-01

The paper shows the possibility of assessing the functional state of microcirculatory-tissue systems of patients with diabetes mellitus by laser Doppler flowmetry (LDF), diffuse reflectance spectroscopy (DRS) and fluorescence spectroscopy (FS) methods. A review of the existing non-invasive optical technologies used to assess the state of microcirculation and oxygen metabolism in tissues of patients with diabetes is conducted. A series of experimental studies involving 76 patients with diabetes and 46 healthy volunteers was carried out. A wavelet analysis of LDF-grams was used to evaluate the adaptive changes of microcirculation during the temperature tests. The obtained data revealed that the proposed methodology in the form of combined use of several diagnostic technologies (LDF, FS and DRS) allows us to detect the presence or absence of trophic disorders and to evaluate adaptation processes during thermal tests.

Weather data for simplified energy calculation methods. Volume II. Middle United States: TRY data

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

Olsen, A.R.; Moreno, S.; Deringer, J.

1984-08-01

The objective of this report is to provide a source of weather data for direct use with a number of simplified energy calculation methods available today. Complete weather data for a number of cities in the United States are provided for use in the following methods: degree hour, modified degree hour, bin, modified bin, and variable degree day. This report contains sets of weather data for 22 cities in the continental United States using Test Reference Year (TRY) source weather data. The weather data at each city has been summarized in a number of ways to provide differing levels ofmore » detail necessary for alternative simplified energy calculation methods. Weather variables summarized include dry bulb and wet bulb temperature, percent relative humidity, humidity ratio, wind speed, percent possible sunshine, percent diffuse solar radiation, total solar radiation on horizontal and vertical surfaces, and solar heat gain through standard DSA glass. Monthly and annual summaries, in some cases by time of day, are available. These summaries are produced in a series of nine computer generated tables.« less

Regression relation for pure quantum states and its implications for efficient computing.

PubMed

Elsayed, Tarek A; Fine, Boris V

2013-02-15

We obtain a modified version of the Onsager regression relation for the expectation values of quantum-mechanical operators in pure quantum states of isolated many-body quantum systems. We use the insights gained from this relation to show that high-temperature time correlation functions in many-body quantum systems can be controllably computed without complete diagonalization of the Hamiltonians, using instead the direct integration of the Schrödinger equation for randomly sampled pure states. This method is also applicable to quantum quenches and other situations describable by time-dependent many-body Hamiltonians. The method implies exponential reduction of the computer memory requirement in comparison with the complete diagonalization. We illustrate the method by numerically computing infinite-temperature correlation functions for translationally invariant Heisenberg chains of up to 29 spins 1/2. Thereby, we also test the spin diffusion hypothesis and find it in a satisfactory agreement with the numerical results. Both the derivation of the modified regression relation and the justification of the computational method are based on the notion of quantum typicality.

Progress Report for the Joint Services Electronics Program

DTIC Science & Technology

1991-06-30

AIGaAs MODFET layers. Both wet etching and reactive ion etching have been used to fabricate the channels. The CAIBE method will also be investigated in...potential for fabricating nanometer scale device structures through surface modification of various types. Using this JSEP research as a foundation...Kerkhoven, "Calculation of velocity overshoot in submicron devices using an augmented drift-diffusion model," Solid-State Electron. (to appear). (JSEP/NSF

Optimal Control of Evolution Mixed Variational Inclusions

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

Alduncin, Gonzalo, E-mail: alduncin@geofisica.unam.mx

2013-12-15

Optimal control problems of primal and dual evolution mixed variational inclusions, in reflexive Banach spaces, are studied. The solvability analysis of the mixed state systems is established via duality principles. The optimality analysis is performed in terms of perturbation conjugate duality methods, and proximation penalty-duality algorithms to mixed optimality conditions are further presented. Applications to nonlinear diffusion constrained problems as well as quasistatic elastoviscoplastic bilateral contact problems exemplify the theory.

Generalized Fourier analyses of the advection-diffusion equation - Part I: one-dimensional domains

NASA Astrophysics Data System (ADS)

Christon, Mark A.; Martinez, Mario J.; Voth, Thomas E.

2004-07-01

This paper presents a detailed multi-methods comparison of the spatial errors associated with finite difference, finite element and finite volume semi-discretizations of the scalar advection-diffusion equation. The errors are reported in terms of non-dimensional phase and group speed, discrete diffusivity, artificial diffusivity, and grid-induced anisotropy. It is demonstrated that Fourier analysis provides an automatic process for separating the discrete advective operator into its symmetric and skew-symmetric components and characterizing the spectral behaviour of each operator. For each of the numerical methods considered, asymptotic truncation error and resolution estimates are presented for the limiting cases of pure advection and pure diffusion. It is demonstrated that streamline upwind Petrov-Galerkin and its control-volume finite element analogue, the streamline upwind control-volume method, produce both an artificial diffusivity and a concomitant phase speed adjustment in addition to the usual semi-discrete artifacts observed in the phase speed, group speed and diffusivity. The Galerkin finite element method and its streamline upwind derivatives are shown to exhibit super-convergent behaviour in terms of phase and group speed when a consistent mass matrix is used in the formulation. In contrast, the CVFEM method and its streamline upwind derivatives yield strictly second-order behaviour. In Part II of this paper, we consider two-dimensional semi-discretizations of the advection-diffusion equation and also assess the affects of grid-induced anisotropy observed in the non-dimensional phase speed, and the discrete and artificial diffusivities. Although this work can only be considered a first step in a comprehensive multi-methods analysis and comparison, it serves to identify some of the relative strengths and weaknesses of multiple numerical methods in a common analysis framework. Published in 2004 by John Wiley & Sons, Ltd.

Vacancies and Vacancy-Mediated Self Diffusion in Cr 2 O 3 : A First-Principles Study

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

Medasani, Bharat; Sushko, Maria L.; Rosso, Kevin M.

Charged and neutral vacancies and vacancy mediated self diffusion in alpha-Cr2O3 were investigated using first principles density functional theory (DFT) and periodic supercell formalism. The vacancy formation energies of charged defects were calculated using the electrostatic finite-size corrections to account for electrostatic interactions between supercells and the corrections for the bandgap underestimation in DFT. Calculations predict that neutral oxygen (O) vacancies are predominant in chromium (Cr)-rich conditions and Cr vacancies with -2 charge state are the dominant defects in O-rich conditions. The charge transition levels of both O and Cr vacancies are deep within the bandgap indicating the stability ofmore » these defects. Transport calculations indicate that vacancy mediated diffusion along the basal plane has lower energy barriers for both O and Cr ions. The most favorable vacancy mediated self diffusion processes correspond to the diffusion of Cr ion in 3+ charge state and O ion in 2- state, respectively. Our calculations reveal that Cr triple defects comprised of Cr in octahedral interstitial sites with two adjacent Cr vacancies along the c-axis have a lower formation energy compared to that of charged Cr vacancies. The formation of such triple defects facilitate Cr self diffusion along the c-axis.« less

Study of the low energy spectrum of titanium by using QMC methods

NASA Astrophysics Data System (ADS)

Buendía, E.; Caballero, M. A.; Gálvez, F. J.

2018-02-01

We study the ground state and the low energy excited states of Ti. Each variational wave function is a product of a Jastrow correlation factor by a model function obtained within the parameterized optimized effective potential (POEP) framework by using a configuration mixing. Near degeneracy effects between the orbitals 4s and 4p, as well as excitations to the 3d orbital due to the strong competition between 4s and 3d orbitals in transition metal atoms are taken into account. All electron calculations have been carried out by using quantum Monte Carlo techniques, variational and diffusion.

Ultrathin cerium orthovanadate nanobelts for high-performance flexible all-solid-state asymmetric supercapacitors.

PubMed

He, Junzhi; Zhao, Junhong; Run, Zhen; Sun, Mengjun; Pang, Huan

2015-02-01

Ultrathin CeVO4 nanobelts were successfully synthesized by a hydrothermal method. The thickness of a single nanobelt is about 2.4 nm, which can effectively shorten the ion diffusion and fasten the charge pathway. More importantly, ultrathin CeVO4 nanobelts and graphene are easily assembled as a flexible all-solid-state asymmetric device, which shows a highly flexible property and achieves a maximum energy density of 0.78 mW h cm(-3) and a high life cycle of >6000 cycles. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Correlation Structure of Fractional Pearson Diffusions.

PubMed

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

2013-09-01

The stochastic solution to a diffusion equations with polynomial coefficients is called a Pearson diffusion. If the first time derivative is replaced by a Caputo fractional derivative of order less than one, the stochastic solution is called a fractional Pearson diffusion. This paper develops an explicit formula for the covariance function of a fractional Pearson diffusion in steady state, in terms of Mittag-Leffler functions. That formula shows that fractional Pearson diffusions are long range dependent, with a correlation that falls off like a power law, whose exponent equals the order of the fractional derivative.

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.

A one-shot-projection method for measurement of specular surfaces.

PubMed

Wang, Zhenzhou

2015-02-09

In this paper, a method is proposed to measure the shapes of specular surfaces with one-shot-projection of structured laser patterns. By intercepting the reflection of the reflected laser pattern twice with two diffusive planes, the closed form solution is achieved for each reflected ray. The points on the specular surface are reconstructed by computing the intersections of the incident rays and the reflected rays. The proposed method can measure both static and dynamic specular shapes due to its one-shot-projection, which is beyond the capability of most of state of art methods that need multiple projections. To our knowledge, the proposed method is the only method so far that could yield the closed form solutions for the dynamic and specular surfaces.

Perturbation expansions of stochastic wavefunctions for open quantum systems

NASA Astrophysics Data System (ADS)

Ke, Yaling; Zhao, Yi

2017-11-01

Based on the stochastic unravelling of the reduced density operator in the Feynman path integral formalism for an open quantum system in touch with harmonic environments, a new non-Markovian stochastic Schrödinger equation (NMSSE) has been established that allows for the systematic perturbation expansion in the system-bath coupling to arbitrary order. This NMSSE can be transformed in a facile manner into the other two NMSSEs, i.e., non-Markovian quantum state diffusion and time-dependent wavepacket diffusion method. Benchmarked by numerically exact results, we have conducted a comparative study of the proposed method in its lowest order approximation, with perturbative quantum master equations in the symmetric spin-boson model and the realistic Fenna-Matthews-Olson complex. It is found that our method outperforms the second-order time-convolutionless quantum master equation in the whole parameter regime and even far better than the fourth-order in the slow bath and high temperature cases. Besides, the method is applicable on an equal footing for any kind of spectral density function and is expected to be a powerful tool to explore the quantum dynamics of large-scale systems, benefiting from the wavefunction framework and the time-local appearance within a single stochastic trajectory.

Quasi-equilibria in reduced Liouville spaces.

PubMed

Halse, Meghan E; Dumez, Jean-Nicolas; Emsley, Lyndon

2012-06-14

The quasi-equilibrium behaviour of isolated nuclear spin systems in full and reduced Liouville spaces is discussed. We focus in particular on the reduced Liouville spaces used in the low-order correlations in Liouville space (LCL) simulation method, a restricted-spin-space approach to efficiently modelling the dynamics of large networks of strongly coupled spins. General numerical methods for the calculation of quasi-equilibrium expectation values of observables in Liouville space are presented. In particular, we treat the cases of a time-independent Hamiltonian, a time-periodic Hamiltonian (with and without stroboscopic sampling) and powder averaging. These quasi-equilibrium calculation methods are applied to the example case of spin diffusion in solid-state nuclear magnetic resonance. We show that there are marked differences between the quasi-equilibrium behaviour of spin systems in the full and reduced spaces. These differences are particularly interesting in the time-periodic-Hamiltonian case, where simulations carried out in the reduced space demonstrate ergodic behaviour even for small spins systems (as few as five homonuclei). The implications of this ergodic property on the success of the LCL method in modelling the dynamics of spin diffusion in magic-angle spinning experiments of powders is discussed.

Design of Multishell Sampling Schemes with Uniform Coverage in Diffusion MRI

PubMed Central

Caruyer, Emmanuel; Lenglet, Christophe; Sapiro, Guillermo; Deriche, Rachid

2017-01-01

Purpose In diffusion MRI, a technique known as diffusion spectrum imaging reconstructs the propagator with a discrete Fourier transform, from a Cartesian sampling of the diffusion signal. Alternatively, it is possible to directly reconstruct the orientation distribution function in q-ball imaging, providing so-called high angular resolution diffusion imaging. In between these two techniques, acquisitions on several spheres in q-space offer an interesting trade-off between the angular resolution and the radial information gathered in diffusion MRI. A careful design is central in the success of multishell acquisition and reconstruction techniques. Methods The design of acquisition in multishell is still an open and active field of research, however. In this work, we provide a general method to design multishell acquisition with uniform angular coverage. This method is based on a generalization of electrostatic repulsion to multishell. Results We evaluate the impact of our method using simulations, on the angular resolution in one and two bundles of fiber configurations. Compared to more commonly used radial sampling, we show that our method improves the angular resolution, as well as fiber crossing discrimination. Discussion We propose a novel method to design sampling schemes with optimal angular coverage and show the positive impact on angular resolution in diffusion MRI. PMID:23625329

Phantom Preparation and Optical Property Determination

NASA Astrophysics Data System (ADS)

He, Di; He, Jie; Mao, Heng

2018-12-01

Tissue-like optical phantoms are important in testing new imaging algorithms. Homogeneous optical phantoms with determined optical properties are the first step of making a proper heterogeneous phantom for multi-modality imaging. Typical recipes for such phantoms consist of epoxy resin, hardener, India ink and titanium oxide. By altering the concentration of India ink and titanium oxide, we are able to get multiple homogeneous phantoms with different absorption and scattering coefficients by carefully mixing all the ingredients. After fabricating the phantoms, we need to find their individual optical properties including the absorption and scattering coefficients. This is achieved by solving diffusion equation of each phantom as a homogeneous slab under canonical illumination. We solve the diffusion equation of homogeneous slab in frequency domain and get the formula for theoretical measurements. Under our steady-state diffused optical tomography (DOT) imaging system, we are able to obtain the real distribution of the incident light produced by a laser. With this source distribution we got and the formula we derived, numerical experiments show how measurements change while varying the value of absorption and scattering coefficients. Then we notice that the measurements alone will not be enough for us to get unique optical properties for steady-state DOT problem. Thus in order to determine the optical properties of a homogeneous slab we want to fix one of the coefficients first and use optimization methods to find another one. Then by assemble multiple homogeneous slab phantoms with different optical properties, we are able to obtain a heterogeneous phantom suitable for testing multi-modality imaging algorithms. In this paper, we describe how to make phantoms, derive a formula to solve the diffusion equation, demonstrate the non-uniqueness of steady-state DOT problem by analysing some numerical results of our formula, and finally propose a possible way to determine optical properties for homogeneous slab for our future work.

Testing the accuracy of correlations for multicomponent mass transport of adsorbed gases in metal-organic frameworks: diffusion of H2/CH4 mixtures in CuBTC.

PubMed

Keskin, Seda; Liu, Jinchen; Johnson, J Karl; Sholl, David S

2008-08-05

Mass transport of chemical mixtures in nanoporous materials is important in applications such as membrane separations, but measuring diffusion of mixtures experimentally is challenging. Methods that can predict multicomponent diffusion coefficients from single-component data can be extremely useful if these methods are known to be accurate. We present the first test of a method of this kind for molecules adsorbed in a metal-organic framework (MOF). Specifically, we examine the method proposed by Skoulidas, Sholl, and Krishna (SSK) ( Langmuir, 2003, 19, 7977) by comparing predictions made with this method to molecular simulations of mixture transport of H 2/CH 4 mixtures in CuBTC. These calculations provide the first direct information on mixture transport of any species in a MOF. The predictions of the SSK approach are in good agreement with our direct simulations of binary diffusion, suggesting that this approach may be a powerful one for examining multicomponent diffusion in MOFs. We also use our molecular simulation data to test the ideal adsorbed solution theory method for predicting binary adsorption isotherms and a method for predicting mixture self-diffusion coefficients.

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

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.

Using hybrid implicit Monte Carlo diffusion to simulate gray radiation hydrodynamics

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

Cleveland, Mathew A., E-mail: cleveland7@llnl.gov; Gentile, Nick

This work describes how to couple a hybrid Implicit Monte Carlo Diffusion (HIMCD) method with a Lagrangian hydrodynamics code to evaluate the coupled radiation hydrodynamics equations. This HIMCD method dynamically applies Implicit Monte Carlo Diffusion (IMD) [1] to regions of a problem that are opaque and diffusive while applying standard Implicit Monte Carlo (IMC) [2] to regions where the diffusion approximation is invalid. We show that this method significantly improves the computational efficiency as compared to a standard IMC/Hydrodynamics solver, when optically thick diffusive material is present, while maintaining accuracy. Two test cases are used to demonstrate the accuracy andmore » performance of HIMCD as compared to IMC and IMD. The first is the Lowrie semi-analytic diffusive shock [3]. The second is a simple test case where the source radiation streams through optically thin material and heats a thick diffusive region of material causing it to rapidly expand. We found that HIMCD proves to be accurate, robust, and computationally efficient for these test problems.« less

Solid state oxygen sensor

DOEpatents

Garzon, F.H.; Chung, B.W.; Raistrick, I.D.; Brosha, E.L.

1996-08-06

Solid state oxygen sensors are provided with a yttria-doped zirconia as an electrolyte and use the electrochemical oxygen pumping of the zirconia electrolyte. A linear relationship between oxygen concentration and the voltage arising at a current plateau occurs when oxygen accessing the electrolyte is limited by a diffusion barrier. A diffusion barrier is formed herein with a mixed electronic and oxygen ion-conducting membrane of lanthanum-containing perovskite or zirconia-containing fluorite. A heater may be used to maintain an adequate oxygen diffusion coefficient in the mixed conducting layer. 4 figs.

Numerical investigations of hybrid rocket engines

NASA Astrophysics Data System (ADS)

Betelin, V. B.; Kushnirenko, A. G.; Smirnov, N. N.; Nikitin, V. F.; Tyurenkova, V. V.; Stamov, L. I.

2018-03-01

Paper presents the results of numerical studies of hybrid rocket engines operating cycle including unsteady-state transition stage. A mathematical model is developed accounting for the peculiarities of diffusion combustion of fuel in the flow of oxidant, which is composed of oxygen-nitrogen mixture. Three dimensional unsteady-state simulations of chemically reacting gas mixture above thermochemically destructing surface are performed. The results show that the diffusion combustion brings to strongly non-uniform fuel mass regression rate in the flow direction. Diffusive deceleration of chemical reaction brings to the decrease of fuel regression rate in the longitudinal direction.

A global reaction route mapping-based kinetic Monte Carlo algorithm

NASA Astrophysics Data System (ADS)

Mitchell, Izaac; Irle, Stephan; Page, Alister J.

2016-07-01

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

A global reaction route mapping-based kinetic Monte Carlo algorithm.

PubMed

Mitchell, Izaac; Irle, Stephan; Page, Alister J

2016-07-14

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

Estimates of electronic coupling for excess electron transfer in DNA

NASA Astrophysics Data System (ADS)

Voityuk, Alexander A.

2005-07-01

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31G* and extended 6-31++G** basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.

Innovative model-based flow rate optimization for vanadium redox flow batteries

NASA Astrophysics Data System (ADS)

König, S.; Suriyah, M. R.; Leibfried, T.

2016-11-01

In this paper, an innovative approach is presented to optimize the flow rate of a 6-kW vanadium redox flow battery with realistic stack dimensions. Efficiency is derived using a multi-physics battery model and a newly proposed instantaneous efficiency determination technique. An optimization algorithm is applied to identify optimal flow rates for operation points defined by state-of-charge (SoC) and current. The proposed method is evaluated against the conventional approach of applying Faraday's first law of electrolysis, scaled to the so-called flow factor. To make a fair comparison, the flow factor is also optimized by simulating cycles with different charging/discharging currents. It is shown through the obtained results that the efficiency is increased by up to 1.2% points; in addition, discharge capacity is also increased by up to 1.0 kWh or 5.4%. Detailed loss analysis is carried out for the cycles with maximum and minimum charging/discharging currents. It is shown that the proposed method minimizes the sum of losses caused by concentration over-potential, pumping and diffusion. Furthermore, for the deployed Nafion 115 membrane, it is observed that diffusion losses increase with stack SoC. Therefore, to decrease stack SoC and lower diffusion losses, a higher flow rate during charging than during discharging is reasonable.

A Data-Gathering Scheme with Joint Routing and Compressive Sensing Based on Modified Diffusion Wavelets in Wireless Sensor Networks.

PubMed

Gu, Xiangping; Zhou, Xiaofeng; Sun, Yanjing

2018-02-28

Compressive sensing (CS)-based data gathering is a promising method to reduce energy consumption in wireless sensor networks (WSNs). Traditional CS-based data-gathering approaches require a large number of sensor nodes to participate in each CS measurement task, resulting in high energy consumption, and do not guarantee load balance. In this paper, we propose a sparser analysis that depends on modified diffusion wavelets, which exploit sensor readings' spatial correlation in WSNs. In particular, a novel data-gathering scheme with joint routing and CS is presented. A modified ant colony algorithm is adopted, where next hop node selection takes a node's residual energy and path length into consideration simultaneously. Moreover, in order to speed up the coverage rate and avoid the local optimal of the algorithm, an improved pheromone impact factor is put forward. More importantly, theoretical proof is given that the equivalent sensing matrix generated can satisfy the restricted isometric property (RIP). The simulation results demonstrate that the modified diffusion wavelets' sparsity affects the sensor signal and has better reconstruction performance than DFT. Furthermore, our data gathering with joint routing and CS can dramatically reduce the energy consumption of WSNs, balance the load, and prolong the network lifetime in comparison to state-of-the-art CS-based methods.

The Thermal Diffusivity Measurement of the Two-layer Ceramics Using the Laser Flash Methodn

NASA Astrophysics Data System (ADS)

Akoshima, Megumi; Ogwa, Mitsue; Baba, Tetsuya; Mizuno, Mineo

Ceramics-based thermal barrier coatings are used as heat and wear shields of gas turbines. There are strong needs to evaluate thermophysical properties of coating, such as thermal conductivity, thermal diffusivity and heat capacity of them. Since the coatings are attached on substrates, it is no easy to measure these properties separately. The laser flash method is one of the most popular thermal diffusivity measurement methods above room temperature for solid materials. The surface of the plate shape specimen is heated by the pulsed laser-beam, then the time variation of the temperature of the rear surface is observed by the infrared radiometer. The laser flash method is non-contact and short time measurement. In general, the thermal diffusivity of solids that are dense, homogeneous and stable, are measured by this method. It is easy to measure thermal diffusivity of a specimen which shows heat diffusion time about 1 ms to 1 s consistent with the specimen thickness of about 1 mm to 5 mm. On the other hand, this method can be applied to measure the specific heat capacity of the solids. And it is also used to estimate the thermal diffusivity of an unknown layer in the layered materials. In order to evaluate the thermal diffusivity of the coating attached on substrate, we have developed a measurement procedure using the laser flash method. The multi-layer model based on the response function method was applied to calculate the thermal diffusivity of the coating attached on substrate from the temperature history curve observed for the two-layer sample. We have verified applicability of the laser flash measurement with the multi-layer model using the measured results and the simulation. It was found that the laser flash measurement for the layered sample using the multi-layer model was effective to estimate the thermal diffusivity of an unknown layer in the sample. We have also developed the two-layer ceramics samples as the reference materials for this procedure.

Development of qualitative and quantitative analysis methods in pharmaceutical application with new selective signal excitation methods for 13 C solid-state nuclear magnetic resonance using 1 H T1rho relaxation time.

PubMed

Nasu, Mamiko; Nemoto, Takayuki; Mimura, Hisashi; Sako, Kazuhiro

2013-01-01

Most pharmaceutical drug substances and excipients in formulations exist in a crystalline or amorphous form, and an understanding of their state during manufacture and storage is critically important, particularly in formulated products. Carbon 13 solid-state nuclear magnetic resonance (NMR) spectroscopy is useful for studying the chemical and physical state of pharmaceutical solids in a formulated product. We developed two new selective signal excitation methods in (13) C solid-state NMR to extract the spectrum of a target component from such a mixture. These methods were based on equalization of the proton relaxation time in a single domain via rapid intraproton spin diffusion and the difference in proton spin-lattice relaxation time in the rotating frame ((1) H T1rho) of individual components in the mixture. Introduction of simple pulse sequences to one-dimensional experiments reduced data acquisition time and increased flexibility. We then demonstrated these methods in a commercially available drug and in a mixture of two saccharides, in which the (13) C signals of the target components were selectively excited, and showed them to be applicable to the quantitative analysis of individual components in solid mixtures, such as formulated products, polymorphic mixtures, or mixtures of crystalline and amorphous phases. Copyright © 2012 Wiley Periodicals, Inc.

Diffusion Milieus as a Focus of Research on Innovation in the Public Sector

ERIC Educational Resources Information Center

Feller, Irwin; Menzel, Donald C.

1977-01-01

Presents an approach to the diffusion of technological innovations in state and local governments that is organized around the concept of "diffusion milieus." Available from: Elsevier Scientific Publishing Company, Box 211, Amsterdam, The Netherlands; single issues supplied upon request. (Author/JG)

On the Nature of the Variability Power Decay towards Soft Spectral States in X-Ray Binaries. Case Study in Cyg X-1

NASA Technical Reports Server (NTRS)

Titarchuk, Lev; Shaposhinikov, Nikolai

2007-01-01

A characteristic feature of the Fourier Power Density Spectrum (PDS) observed from black hole X-ray binaries in low/hard and intermediate spectral states is a broad band-limited noise, characterized by a constant below some frequency (a "break" frequency) and a power law above this frequency. It has been shown that the variability of this type can be produced by the inward diffusion of the local driving perturbations in a bounded configuration (accretion disk or corona). In the framework of this model, the perturbation diffusion time to is related to the phenomenological break frequency, while the PDS power-law slope above the "break" is determined by the viscosity distribution over the configuration. The perturbation diffusion scenario explains the decay of the power of X-ray variability observed in a number of compact sources (containing black hole and neutron star) during an evolution of theses sources from low/hard to high/soft states. We compare the model predictions with the subset of data from Cyg X-1 collected by the Rossi X-ray Time Explorer (RXTE). Our extensive analysis of the Cyg X-1 PDSs demonstrates that the observed integrated power P(sub x), decreases approximately as a square root of the characteristic frequency of the driving oscillations v(sub dr). The RXTE observations of Cyg X-1 allow us to infer P(sub dr), and t(sub o) as a function of v(sub dr). We also apply the basic parameters of observed PDSs, power-law index and low frequency quasiperiodic oscillations. to infer Reynolds (Re) number from the observations using the method developed in our previous paper. Our analysis shows that Re-number increases from values about 10 in low/hard state to that about 70 during the high/soft state. Subject headings: accretion, accretion disks-black hole physics-stars:individual (Cyg X-1) :radiation mechanisms: nonthermal-physical data and processes

Heat transfer to and from vegetated surfaces - An analytical method for the bulk exchange coefficients

NASA Technical Reports Server (NTRS)

Massman, William J.

1987-01-01

The semianalytical model outlined in a previous study (Massman, 1987) to describe momentum exchange between the atmosphere and vegetated surfaces is extended to include the exchange of heat. The methods employed are based on one-dimensional turbulent diffusivities, and use analytical solutions to the steady-state diffusion equation. The model is used to assess the influence that the canopy foliage structure and density, the wind profile structure within the canopy, and the shelter factor can have upon the inverse surface Stanton number (kB exp -1), as well as to explore the consequences of introducing a scalar displacement height which can be different from the momentum displacement height. In general, the triangular foliage area density function gives results which agree more closely with observations than that for constant foliage area density. The intended application of this work is for parameterizing the bulk aerodynamic resistances for heat and momentum exchange for use within large-scale models of plant-atmosphere exchanges.

Experimental investigation on light propagation through apple tissue structures

NASA Astrophysics Data System (ADS)

Askoura, Mohamed Lamine; Piron, Vianney; Vaudelle, Fabrice; L'Huillier, Jean-Pierre; Madieta, Emmanuel; Mehinagic, Emira

2015-07-01

The interaction of light with biological materials, such as fruits and vegetables, is a complex process which involves both absorption, and scattering events at different scales. Measuring the optical properties of a fruit allows understanding the physical and chemical characteristics. In this paper, an optical bench based on the use of a continuous laser source and a CCD camera was developed to study the light diffusion inside apple tissue structures. The method refers to the well-known steady-state spatially resolved method. First, the optoelectronics system was tested with a tissue phantom in order to show the optimal sensing range required to obtain the best estimated optical properties. Second, experimental results were obtained using peeled and unpeeled apples as interrogated tissues. The data were confronted with a diffusion model in order to extract the optical properties at two wavelengths of 633, and 852 nm. To better understand the effect of the apple tissue structures, investigations into the propagation of light through a half cut apple were also performed.

A theoretical study of concentration of profiles of primary cytochemical-enzyme reaction products in membrane-bound cell organelles and its application to lysosomal acid phosphatase.

PubMed

Cornelisse, C J; Hermens, W T; Joe, M T; Duijndam, W A; van Duijn, P

1976-11-01

A numerical method was developed for computing the steady-state concentration gradient of a diffusible enzyme reaction product in a membrane-limited compartment of a simplified theoretical cell model. In cytochemical enzyme reactions proceeding according to the metal-capture principle, the local concentration of the primary reaction product is an important factor in the onset of the precipitation process and in the distribution of the final reaction product. The following variables were incorporated into the model: enzyme activity, substrate concentration, Km, diffusion coefficient of substrate and product, particle radius and cell radius. The method was applied to lysosomal acid phosphatase. Numerical values for the variables were estimated from experimental data in the literature. The results show that the calculated phosphate concentrations inside lysosomes are several orders of magnitude lower than the critical concentrations for efficient phosphate capture found in a previous experimental model study. Reasons for this apparent discrepancy are discussed.

Intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence.

PubMed

Bär, Sébastien; Weigel, Matthias; von Elverfeldt, Dominik; Hennig, Jürgen; Leupold, Jochen

2015-11-01

The purpose of this work was to analyze the intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence, meaning the observation of diffusion-induced attenuation of the bSSFP steady-state signal due to the imaging gradients. Although these diffusion effects are usually neglected for most clinical gradient systems, such strong gradient systems are employed for high resolution imaging of small animals or MR Microscopy. The impact on the bSSFP signal of the imaging gradients characterized by their b-values was analyzed with simulations and experiments at a 7T animal scanner using a gradient system with maximum gradient amplitude of approx. 700 mT/m. It was found that the readout gradients have a stronger impact on the attenuation than the phase encoding gradients. Also, as the PE gradients are varying with each repetition interval, the diffusion effects induce strong modulations of the bSSFP signal over the sequence repetition cycles depending on the phase encoding gradient table. It is shown that a signal gain can be obtained through a change of flip angle as a new optimal flip angle maximizing the signal can be defined. The dependency of the diffusion effects on relaxation times and b-values were explored with simulations. The attenuation increases with T2. In conclusion, diffusion attenuation of the bSSFP signal becomes significant for high resolution imaging voxel size (roughly < 100 μm) of long T2 substances. Copyright © 2015 John Wiley & Sons, Ltd.

Spatial pattern dynamics due to the fitness gradient flux in evolutionary games.

PubMed

deForest, Russ; Belmonte, Andrew

2013-06-01

We introduce a nondiffusive spatial coupling term into the replicator equation of evolutionary game theory. The spatial flux is based on motion due to local gradients in the relative fitness of each strategy, providing a game-dependent alternative to diffusive coupling. We study numerically the development of patterns in one dimension (1D) for two-strategy games including the coordination game and the prisoner's dilemma, and in two dimensions (2D) for the rock-paper-scissors game. In 1D we observe modified traveling wave solutions in the presence of diffusion, and asymptotic attracting states under a frozen-strategy assumption without diffusion. In 2D we observe spiral formation and breakup in the frozen-strategy rock-paper-scissors game without diffusion. A change of variables appropriate to replicator dynamics is shown to correctly capture the 1D asymptotic steady state via a nonlinear diffusion equation.

Spatial pattern dynamics due to the fitness gradient flux in evolutionary games

NASA Astrophysics Data System (ADS)

deForest, Russ; Belmonte, Andrew

2013-06-01

We introduce a nondiffusive spatial coupling term into the replicator equation of evolutionary game theory. The spatial flux is based on motion due to local gradients in the relative fitness of each strategy, providing a game-dependent alternative to diffusive coupling. We study numerically the development of patterns in one dimension (1D) for two-strategy games including the coordination game and the prisoner's dilemma, and in two dimensions (2D) for the rock-paper-scissors game. In 1D we observe modified traveling wave solutions in the presence of diffusion, and asymptotic attracting states under a frozen-strategy assumption without diffusion. In 2D we observe spiral formation and breakup in the frozen-strategy rock-paper-scissors game without diffusion. A change of variables appropriate to replicator dynamics is shown to correctly capture the 1D asymptotic steady state via a nonlinear diffusion equation.

A scaled-ionic-charge simulation model that reproduces enhanced and suppressed water diffusion in aqueous salt solutions.

PubMed

Kann, Z R; Skinner, J L

2014-09-14

Non-polarizable models for ions and water quantitatively and qualitatively misrepresent the salt concentration dependence of water diffusion in electrolyte solutions. In particular, experiment shows that the water diffusion coefficient increases in the presence of salts of low charge density (e.g., CsI), whereas the results of simulations with non-polarizable models show a decrease of the water diffusion coefficient in all alkali halide solutions. We present a simple charge-scaling method based on the ratio of the solvent dielectric constants from simulation and experiment. Using an ion model that was developed independently of a solvent, i.e., in the crystalline solid, this method improves the water diffusion trends across a range of water models. When used with a good-quality water model, e.g., TIP4P/2005 or E3B, this method recovers the qualitative behaviour of the water diffusion trends. The model and method used were also shown to give good results for other structural and dynamic properties including solution density, radial distribution functions, and ion diffusion coefficients.

Parameters estimation using the first passage times method in a jump-diffusion model

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

Khaldi, K., E-mail: kkhaldi@umbb.dz; LIMOSE Laboratory, Boumerdes University, 35000; Meddahi, S., E-mail: samia.meddahi@gmail.com

2016-06-02

The main purposes of this paper are two contributions: (1) it presents a new method, which is the first passage time (FPT method) generalized for all passage times (GPT method), in order to estimate the parameters of stochastic Jump-Diffusion process. (2) it compares in a time series model, share price of gold, the empirical results of the estimation and forecasts obtained with the GPT method and those obtained by the moments method and the FPT method applied to the Merton Jump-Diffusion (MJD) model.

Cross-Diffusion Driven Instability for a Lotka-Volterra Competitive Reaction-Diffusion System

NASA Astrophysics Data System (ADS)

Gambino, G.; Lombardo, M. C.; Sammartino, M.

2008-04-01

In this work we investigate the possibility of the pattern formation for a reaction-diffusion system with nonlinear diffusion terms. Through a linear stability analysis we find the conditions which allow a homogeneous steady state (stable for the kinetics) to become unstable through a Turing mechanism. In particular, we show how cross-diffusion effects are responsible for the initiation of spatial patterns. Finally, we find a Fisher amplitude equation which describes the weakly nonlinear dynamics of the system near the marginal stability.

Diffuse cloud chemistry. [in interstellar matter

NASA Technical Reports Server (NTRS)

Van Dishoeck, Ewine F.; Black, John H.

1988-01-01

The current status of models of diffuse interstellar clouds is reviewed. A detailed comparison of recent gas-phase steady-state models shows that both the physical conditions and the molecular abundances in diffuse clouds are still not fully understood. Alternative mechanisms are discussed and observational tests which may discriminate between the various models are suggested. Recent developments regarding the velocity structure of diffuse clouds are mentioned. Similarities and differences between the chemistries in diffuse clouds and those in translucent and high latitude clouds are pointed out.

Reassembling the Information Technology Innovation Process: An Actor Network Theory Method for Managing the Initiation, Production, and Diffusion of Innovations

NASA Astrophysics Data System (ADS)

Zendejas, Gerardo; Chiasson, Mike

This paper will propose and explore a method to enhance focal actors' abilities to enroll and control the many social and technical components interacting during the initiation, production, and diffusion of innovations. The reassembling and stabilizing of such components is the challenging goal of the focal actors involved in these processes. To address this possibility, a healthcare project involving the initiation, production, and diffusion of an IT-based innovation will be influenced by the researcher, using concepts from actor network theory (ANT), within an action research methodology (ARM). The experiences using this method, and the nature of enrolment and translation during its use, will highlight if and how ANT can provide a problem-solving method to help assemble the social and technical actants involved in the diffusion of an innovation. Finally, the paper will discuss the challenges and benefits of implementing such methods to attain widespread diffusion.

Two-photon Microscopy and Polarimetry for Assessment of Myocardial Tissue Organization

NASA Astrophysics Data System (ADS)

Archambault-Wallenburg, Marika

Optical methods can provide useful tissue characterization tools. For this project, two-photon microscopy and polarized light examinations (polarimetry) were used to assess the organizational state of myocardium in healthy, infarcted, and stem-cell regenerated states. Two-photon microscopy visualizes collagen through second-harmonic generation and myocytes through two-photon excitation autofluorescence, providing information on the composition and structure/organization of the tissue. Polarimetry measurements yield a value of linear retardance that can serve as an indicator of tissue anisotropy, and with a dual-projection method, information about the anisotropy axis orientation can also be extracted. Two-photon microscopy results reveal that stem-cell treated tissue retains more myocytes and structure than infarcted myocardium, while polarimetry findings suggest that the injury caused by temporary ligation of a coronary artery is less severe and more diffuse that than caused by a permanent ligation. Both these methods show potential for tissue characterization.

78 FR 30342 - United States Enrichment Corporation, Paducah Gaseous Diffusion Plant

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-22

... Corporation, Paducah Gaseous Diffusion Plant AGENCY: Nuclear Regulatory Commission. ACTION: Notice of... Compliance (CoC) for the Paducah Gaseous Diffusion Plant (PGDP). The existing CoC (No. GDP-1) authorizes... compliance for PGDP on November 26, 1996, and assumed regulatory oversight for the plant on March 3, 1997...

Thermal transport at the nanoscale: A Fourier's law vs. phonon Boltzmann equation study

NASA Astrophysics Data System (ADS)

Kaiser, J.; Feng, T.; Maassen, J.; Wang, X.; Ruan, X.; Lundstrom, M.

2017-01-01

Steady-state thermal transport in nanostructures with dimensions comparable to the phonon mean-free-path is examined. Both the case of contacts at different temperatures with no internal heat generation and contacts at the same temperature with internal heat generation are considered. Fourier's law results are compared to finite volume method solutions of the phonon Boltzmann equation in the gray approximation. When the boundary conditions are properly specified, results obtained using Fourier's law without modifying the bulk thermal conductivity are in essentially exact quantitative agreement with the phonon Boltzmann equation in the ballistic and diffusive limits. The errors between these two limits are examined in this paper. For the four cases examined, the error in the apparent thermal conductivity as deduced from a correct application of Fourier's law is less than 6%. We also find that the Fourier's law results presented here are nearly identical to those obtained from a widely used ballistic-diffusive approach but analytically much simpler. Although limited to steady-state conditions with spatial variations in one dimension and to a gray model of phonon transport, the results show that Fourier's law can be used for linear transport from the diffusive to the ballistic limit. The results also contribute to an understanding of how heat transport at the nanoscale can be understood in terms of the conceptual framework that has been established for electron transport at the nanoscale.

Modeling steady-state experiments with a scanning electrochemical microscope involving several independent diffusing species using the boundary element method.

PubMed

Sklyar, Oleg; Träuble, Markus; Zhao, Chuan; Wittstock, Gunther

2006-08-17

The BEM algorithm developed earlier for steady-state experiments in the scanning electrochemical microscopy (SECM) feedback mode has been expanded to allow for the treatment of more than one independently diffusing species. This allows the treatment of substrate-generation/tip-collection SECM experiments. The simulations revealed the interrelation of sample layout, local kinetics, imaging conditions, and the quality of the obtained SECM images. Resolution in the SECM SG/TC images has been evaluated, and it depends on several factors. For most practical situations, the resolution is limited by the diffusion profiles of the sample. When a dissolved compound is converted at the sample (e.g., oxygen reduction or enzymatic reaction at the sample), the working distance should be significantly larger than in SECM feedback experiments (ca. 3 r(T) for RG = 5) in order to avoid diffusional shielding of the active regions on the sample by the UME body. The resolution ability also depends on the kinetics of the active regions. The best resolution can be expected if all the active regions cause the same flux. In one simulated example, which might mimic a possible scenario of a low-density protein array, considerable compromises in the resolving power, were noted when the flux from two neighboring spots differs by more than a factor of 2.

On the diffusion of ferrocenemethanol in room-temperature ionic liquids: an electrochemical study.

PubMed

Lovelock, Kevin R J; Ejigu, Andinet; Loh, Sook Fun; Men, Shuang; Licence, Peter; Walsh, Darren A

2011-06-07

The electrochemical behaviour of ferrocenemethanol (FcMeOH) has been studied in a range of room-temperature ionic liquids (RTILs) using cyclic voltammetry, chronoamperomery and scanning electrochemical microscopy (SECM). The diffusion coefficient of FcMeOH, measured using chronoamperometry, decreased with increasing RTIL viscosity. Analysis of the mass transport properties of the RTILs revealed that the Stokes-Einstein equation did not apply to our data. The "correlation length" was estimated from diffusion coefficient data and corresponded well to the average size of holes (voids) in the liquid, suggesting that a model in which the diffusing species jumps between holes in the liquid is appropriate in these liquids. Cyclic voltammetry at ultramicroelectrodes demonstrated that the ability to record steady-state voltammograms during ferrocenemethanol oxidation depended on the voltammetric scan rate, the electrode dimensions and the RTIL viscosity. Similarly, the ability to record steady-state SECM feedback approach curves depended on the RTIL viscosity, the SECM tip radius and the tip approach speed. Using 1.3 μm Pt SECM tips, steady-state SECM feedback approach curves were obtained in RTILs, provided that the tip approach speed was low enough to maintain steady-state diffusion at the SECM tip. In the case where tip-induced convection contributed significantly to the SECM tip current, this effect could be accounted for theoretically using mass transport equations that include diffusive and convective terms. Finally, the rate of heterogeneous electron transfer across the electrode/RTIL interface during ferrocenemethanol oxidation was estimated using SECM, and k(0) was at least 0.1 cm s(-1) in one of the least viscous RTILs studied.

Stationary properties of maximum-entropy random walks.

PubMed

Dixit, Purushottam D

2015-10-01

Maximum-entropy (ME) inference of state probabilities using state-dependent constraints is popular in the study of complex systems. In stochastic systems, how state space topology and path-dependent constraints affect ME-inferred state probabilities remains unknown. To that end, we derive the transition probabilities and the stationary distribution of a maximum path entropy Markov process subject to state- and path-dependent constraints. A main finding is that the stationary distribution over states differs significantly from the Boltzmann distribution and reflects a competition between path multiplicity and imposed constraints. We illustrate our results with particle diffusion on a two-dimensional landscape. Connections with the path integral approach to diffusion are discussed.

Towards Thermal Reading of Magnetic States in Hall Crosses

NASA Astrophysics Data System (ADS)

Xu, Y.; Petit-Watelot, S.; Polewczyk, V.; Parent, G.; Montaigne, F.; Wegrowe, J.-E.; Mangin, S.; Lacroix, D.; Hehn, M.; Lacour, D.

2018-03-01

The 3 ω method is a standard way to measure the thermal conductivity of thin films. In this study, we apply the method to read the magnetic state of a perpendicularly magnetized CoTb ferrimagnetic Hall cross using a thermal excitation. In order to generate the thermal excitation, an oscillating current at an ω frequency is applied to the Hall cross using different geometries. The magnetic signals oscillating at ω , 2 ω , and 3 ω are probed using a lock-in technique. From the analysis of the power dependence, we can attribute the 3 ω response to the temperature oscillation and the 2 ω to the temperature-gradient oscillation. Finally, the frequency dependence of the magnetic signals can be understood by considering the heat diffusion in a two-dimensional model.

Steady-State Electrodiffusion from the Nernst-Planck Equation Coupled to Local Equilibrium Monte Carlo Simulations.

PubMed

Boda, Dezső; Gillespie, Dirk

2012-03-13

We propose a procedure to compute the steady-state transport of charged particles based on the Nernst-Planck (NP) equation of electrodiffusion. To close the NP equation and to establish a relation between the concentration and electrochemical potential profiles, we introduce the Local Equilibrium Monte Carlo (LEMC) method. In this method, Grand Canonical Monte Carlo simulations are performed using the electrochemical potential specified for the distinct volume elements. An iteration procedure that self-consistently solves the NP and flux continuity equations with LEMC is shown to converge quickly. This NP+LEMC technique can be used in systems with diffusion of charged or uncharged particles in complex three-dimensional geometries, including systems with low concentrations and small applied voltages that are difficult for other particle simulation techniques.

Calculation of the vibrational excited states of malonaldehyde and their tunneling splittings with the multi-configuration time-dependent Hartree method

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

Schröder, Markus, E-mail: Markus.Schroeder@pci.uni-heidelberg.de; Meyer, Hans-Dieter, E-mail: Hans-Dieter.Meyer@pci.uni-heidelberg.de

2014-07-21

We report energies and tunneling splittings of vibrational excited states of malonaldehyde which have been obtained using full dimensional quantum mechanical calculations. To this end we employed the multi configuration time-dependent Hartree method. The results have been obtained using a recently published potential energy surface [Y. Wang, B. J. Braams, J. M. Bowman, S. Carter, and D. P. Tew, J. Chem. Phys. 128, 224314 (2008)] which has been brought into a suitable form by a modified version of the n-mode representation which was used with two different arrangements of coordinates. The relevant terms of the expansion have been identified withmore » a Metropolis algorithm and a diffusion Monte-Carlo technique, respectively.« less

Examining eXtension: Diffusion, Disruption, and Adoption among Iowa State University Extension and Outreach Professionals

ERIC Educational Resources Information Center

Taylor, Cayla; Miller, Greg

2016-01-01

As eXtension unveils its new membership model, Iowa State University Extension and Outreach must determine how best to support professionals and clientele using the technology. This article reports on a study that used the diffusion of innovations and disruptive innovation theories to assess Iowa Extension professionals' adoption and perceptions…

Markov chain Monte Carlo estimation of quantum states

NASA Astrophysics Data System (ADS)

Diguglielmo, James; Messenger, Chris; Fiurášek, Jaromír; Hage, Boris; Samblowski, Aiko; Schmidt, Tabea; Schnabel, Roman

2009-03-01

We apply a Bayesian data analysis scheme known as the Markov chain Monte Carlo to the tomographic reconstruction of quantum states. This method yields a vector, known as the Markov chain, which contains the full statistical information concerning all reconstruction parameters including their statistical correlations with no a priori assumptions as to the form of the distribution from which it has been obtained. From this vector we can derive, e.g., the marginal distributions and uncertainties of all model parameters, and also of other quantities such as the purity of the reconstructed state. We demonstrate the utility of this scheme by reconstructing the Wigner function of phase-diffused squeezed states. These states possess non-Gaussian statistics and therefore represent a nontrivial case of tomographic reconstruction. We compare our results to those obtained through pure maximum-likelihood and Fisher information approaches.

Framework for shape analysis of white matter fiber bundles.

PubMed

Glozman, Tanya; Bruckert, Lisa; Pestilli, Franco; Yecies, Derek W; Guibas, Leonidas J; Yeom, Kristen W

2018-02-15

Diffusion imaging coupled with tractography algorithms allows researchers to image human white matter fiber bundles in-vivo. These bundles are three-dimensional structures with shapes that change over time during the course of development as well as in pathologic states. While most studies on white matter variability focus on analysis of tissue properties estimated from the diffusion data, e.g. fractional anisotropy, the shape variability of white matter fiber bundle is much less explored. In this paper, we present a set of tools for shape analysis of white matter fiber bundles, namely: (1) a concise geometric model of bundle shapes; (2) a method for bundle registration between subjects; (3) a method for deformation estimation. Our framework is useful for analysis of shape variability in white matter fiber bundles. We demonstrate our framework by applying our methods on two datasets: one consisting of data for 6 normal adults and another consisting of data for 38 normal children of age 11 days to 8.5 years. We suggest a robust and reproducible method to measure changes in the shape of white matter fiber bundles. We demonstrate how this method can be used to create a model to assess age-dependent changes in the shape of specific fiber bundles. We derive such models for an ensemble of white matter fiber bundles on our pediatric dataset and show that our results agree with normative human head and brain growth data. Creating these models for a large pediatric longitudinal dataset may improve understanding of both normal development and pathologic states and propose novel parameters for the examination of the pediatric brain. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Quantification of tissue oxygenation levels using diffuse reflectance spectroscopy

NASA Astrophysics Data System (ADS)

B. S., Suresh Anand; N., Sujatha

2011-08-01

Tumor growth is characterized by increased metabolic activity. The light absorption profile of hemoglobin in dysplastic tissue is different from a normal tissue. Neovascularization is a hallmark of many diseases and can serve as a predictive biomarker for the detection of cancers. Spectroscopic techniques can provide information about the metabolic and morphological changes related to the progression of neoplasia. Diffuse reflectance spectroscopy (DRS) measures the absorption and scattering properties of a biological tissue and this method can provide clinically useful information for the early diagnosis of epithelial precancers. We used tissue simulating phantoms with absorbing and scattering molecules for the determination of total hemoglobin concentration, hemoglobin oxygen saturation and intensity difference between the deoxy and oxy hemoglobin bands. The results show promising approach for the differentiating normal and malignant states of a tissue.

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

McDaniel, Jesse G.; Yethiraj, Arun, E-mail: yethiraj@chem.wisc.edu

The diffusion of protons in self-assembled systems is potentially important for the design of efficient proton exchange membranes. In this work, we study proton dynamics in a low-water content, lamellar phase of a sodium-carboxylate gemini surfactant/water system using computer simulations. The hopping of protons via the Grotthuss mechanism is explicitly allowed through the multi-state empirical valence bond method. We find that the hydronium ion is trapped on the hydrophobic side of the surfactant-water interface, and proton diffusion then proceeds by hopping between surface sites. The importance of hydrophobic traps is surprising because one would expect the hydronium ions to bemore » trapped at the charged headgroups. The physics illustrated in this system should be relevant to the proton dynamics in other amphiphilic membrane systems, whenever there exist exposed hydrophobic surface regions.« less

Metal intercalation-induced selective adatom mass transport on graphene

DOE PAGES

Liu, Xiaojie; Wang, Cai -Zhuang; Hupalo, Myron; ...

2016-03-29

Recent experiments indicate that metal intercalation is a very effective method to manipulate the graphene-adatom interaction and control metal nanostructure formation on graphene. A key question is mass transport, i.e., how atoms deposited uniformly on graphene populate different areas depending on the local intercalation. Using first-principles calculations, we show that partially intercalated graphene, with a mixture of intercalated and pristine areas, can induce an alternating electric field because of the spatial variations in electron doping, and thus, an oscillatory electrostatic potential. As a result, this alternating field can change normal stochastic adatom diffusion to biased diffusion, leading to selective massmore » transport and consequent nucleation, on either the intercalated or pristine areas, depending on the charge state of the adatoms.« less

Stabilization of a spatially uniform steady state in two systems exhibiting Turing patterns

NASA Astrophysics Data System (ADS)

Konishi, Keiji; Hara, Naoyuki

2018-05-01

This paper deals with the stabilization of a spatially uniform steady state in two coupled one-dimensional reaction-diffusion systems with Turing instability. This stabilization corresponds to amplitude death that occurs in a coupled system with Turing instability. Stability analysis of the steady state shows that stabilization does not occur if the two reaction-diffusion systems are identical. We derive a sufficient condition for the steady state to be stable for any length of system and any boundary conditions. Our analytical results are supported with numerical examples.

A screening tool for delineating subregions of steady recharge within groundwater models

USGS Publications Warehouse

Dickinson, Jesse; Ferré, T.P.A.; Bakker, Mark; Crompton, Becky

2014-01-01

We have developed a screening method for simplifying groundwater models by delineating areas within the domain that can be represented using steady-state groundwater recharge. The screening method is based on an analytical solution for the damping of sinusoidal infiltration variations in homogeneous soils in the vadose zone. The damping depth is defined as the depth at which the flux variation damps to 5% of the variation at the land surface. Groundwater recharge may be considered steady where the damping depth is above the depth of the water table. The analytical solution approximates the vadose zone diffusivity as constant, and we evaluated when this approximation is reasonable. We evaluated the analytical solution through comparison of the damping depth computed by the analytic solution with the damping depth simulated by a numerical model that allows variable diffusivity. This comparison showed that the screening method conservatively identifies areas of steady recharge and is more accurate when water content and diffusivity are nearly constant. Nomograms of the damping factor (the ratio of the flux amplitude at any depth to the amplitude at the land surface) and the damping depth were constructed for clay and sand for periodic variations between 1 and 365 d and flux means and amplitudes from nearly 0 to 1 × 10−3 m d−1. We applied the screening tool to Central Valley, California, to identify areas of steady recharge. A MATLAB script was developed to compute the damping factor for any soil and any sinusoidal flux variation.

A method for the estimate of the wall diffusion for non-axisymmetric fields using rotating external fields

NASA Astrophysics Data System (ADS)

Frassinetti, L.; Olofsson, K. E. J.; Fridström, R.; Setiadi, A. C.; Brunsell, P. R.; Volpe, F. A.; Drake, J.

2013-08-01

A new method for the estimate of the wall diffusion time of non-axisymmetric fields is developed. The method based on rotating external fields and on the measurement of the wall frequency response is developed and tested in EXTRAP T2R. The method allows the experimental estimate of the wall diffusion time for each Fourier harmonic and the estimate of the wall diffusion toroidal asymmetries. The method intrinsically considers the effects of three-dimensional structures and of the shell gaps. Far from the gaps, experimental results are in good agreement with the diffusion time estimated with a simple cylindrical model that assumes a homogeneous wall. The method is also applied with non-standard configurations of the coil array, in order to mimic tokamak-relevant settings with a partial wall coverage and active coils of large toroidal extent. The comparison with the full coverage results shows good agreement if the effects of the relevant sidebands are considered.

Diffusion behavior of the fluorescent proteins eGFP and Dreiklang in solvents of different viscosity monitored by fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Junghans, Cornelia; Schmitt, Franz-Josef; Vukojević, Vladana; Friedrich, Thomas

2016-12-01

Fluorescence correlation spectroscopy relies on temporal autocorrelation analysis of fluorescence intensity fluctuations that spontaneously arise in systems at equilibrium due to molecular motion and changes of state that cause changes in fluorescence, such as triplet state transition, photoisomerization and other photophysical transformations, to determine the rates of these processes. The stability of a fluorescent molecule against dark state conversion is of particular concern for chromophores intended to be used as reference tags for comparing diffusion processes on multiple time scales. In this work, we analyzed properties of two fluorescent proteins, the photoswitchable Dreiklang and its parental eGFP, in solvents of different viscosity to vary the diffusion time through the observation volume element by several orders of magnitude. In contrast to eGFP, Dreiklang undergoes a dark-state conversion on the time scale of tens to hundreds of microseconds under conditions of intense fluorescence excitation, which results in artificially shortened diffusion times if the diffusional motion through the observation volume is sufficiently slowed down. Such photophysical quenching processes have also been observed in FCS studies on other photoswitchable fluorescent proteins including Citrine, from which Dreiklang was derived by genetic engineering. This property readily explains the discrepancies observed previously between the diffusion times of eGFP- and Dreiklang-labeled plasma membrane protein complexes.

[An Improved Spectral Quaternion Interpolation Method of Diffusion Tensor Imaging].

PubMed

Xu, Yonghong; Gao, Shangce; Hao, Xiaofei

2016-04-01

Diffusion tensor imaging(DTI)is a rapid development technology in recent years of magnetic resonance imaging.The diffusion tensor interpolation is a very important procedure in DTI image processing.The traditional spectral quaternion interpolation method revises the direction of the interpolation tensor and can preserve tensors anisotropy,but the method does not revise the size of tensors.The present study puts forward an improved spectral quaternion interpolation method on the basis of traditional spectral quaternion interpolation.Firstly,we decomposed diffusion tensors with the direction of tensors being represented by quaternion.Then we revised the size and direction of the tensor respectively according to different situations.Finally,we acquired the tensor of interpolation point by calculating the weighted average.We compared the improved method with the spectral quaternion method and the Log-Euclidean method by the simulation data and the real data.The results showed that the improved method could not only keep the monotonicity of the fractional anisotropy(FA)and the determinant of tensors,but also preserve the tensor anisotropy at the same time.In conclusion,the improved method provides a kind of important interpolation method for diffusion tensor image processing.

Interferometric measurements of a dendritic growth front solutal diffusion layer

NASA Technical Reports Server (NTRS)

Hopkins, John A.; Mccay, T. D.; Mccay, Mary H.

1991-01-01

An experimental study was undertaken to measure solutal distributions in the diffusion layer produced during the vertical directional solidification (VDS) of an ammonium chloride - water (NH4Cl-H2O) solution. Interferometry was used to obtain concentration measurements in the 1-2 millimeter region defining the diffusion layer. These measurements were fitted to an exponential form to extract the characteristic diffusion parameter for various times after the start of solidification. The diffusion parameters are within the limits predicted by steady state theory and suggest that the effective solutal diffusivity is increasing as solidification progresses.

Heavy-tailed fractional Pearson diffusions.

PubMed

Leonenko, N N; Papić, I; Sikorskii, A; Šuvak, N

2017-11-01

We define heavy-tailed fractional reciprocal gamma and Fisher-Snedecor diffusions by a non-Markovian time change in the corresponding Pearson diffusions. Pearson diffusions are governed by the backward Kolmogorov equations with space-varying polynomial coefficients and are widely used in applications. The corresponding fractional reciprocal gamma and Fisher-Snedecor diffusions are governed by the fractional backward Kolmogorov equations and have heavy-tailed marginal distributions in the steady state. We derive the explicit expressions for the transition densities of the fractional reciprocal gamma and Fisher-Snedecor diffusions and strong solutions of the associated Cauchy problems for the fractional backward Kolmogorov equation.