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

PubMed

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

2010-09-27

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

Space-resolved diffusing wave spectroscopy measurements of the macroscopic deformation and the microscopic dynamics in tensile strain tests

NASA Astrophysics Data System (ADS)

Nagazi, Med-Yassine; Brambilla, Giovanni; Meunier, Gérard; Marguerès, Philippe; Périé, Jean-Noël; Cipelletti, Luca

2017-01-01

We couple a laser-based, space-resolved dynamic light scattering apparatus to a universal traction machine for mechanical extensional tests. We perform simultaneous optical and mechanical measurements on polyether ether ketone, a semi-crystalline polymer widely used in the industry. Due to the high turbidity of the sample, light is multiply scattered by the sample and the diffusing wave spectroscopy (DWS) formalism is used to interpret the data. Space-resolved DWS yields spatial maps of the sample strain and of the microscopic dynamics. An excellent agreement is found between the strain maps thus obtained and those measured by a conventional stereo-digital image correlation technique. The microscopic dynamics reveals both affine motion and plastic rearrangements. Thanks to the extreme sensitivity of DWS to displacements as small as 1 nm, plastic activity and its spatial localization can be detected at an early stage of the sample strain, making the technique presented here a valuable complement to existing material characterization methods.

A diffusion-matched principal component analysis (DM-PCA) based two-channel denoising procedure for high-resolution diffusion-weighted MRI

PubMed Central

Chang, Hing-Chiu; Bilgin, Ali; Bernstein, Adam; Trouard, Theodore P.

2018-01-01

Over the past several years, significant efforts have been made to improve the spatial resolution of diffusion-weighted imaging (DWI), aiming at better detecting subtle lesions and more reliably resolving white-matter fiber tracts. A major concern with high-resolution DWI is the limited signal-to-noise ratio (SNR), which may significantly offset the advantages of high spatial resolution. Although the SNR of DWI data can be improved by denoising in post-processing, existing denoising procedures may potentially reduce the anatomic resolvability of high-resolution imaging data. Additionally, non-Gaussian noise induced signal bias in low-SNR DWI data may not always be corrected with existing denoising approaches. Here we report an improved denoising procedure, termed diffusion-matched principal component analysis (DM-PCA), which comprises 1) identifying a group of (not necessarily neighboring) voxels that demonstrate very similar magnitude signal variation patterns along the diffusion dimension, 2) correcting low-frequency phase variations in complex-valued DWI data, 3) performing PCA along the diffusion dimension for real- and imaginary-components (in two separate channels) of phase-corrected DWI voxels with matched diffusion properties, 4) suppressing the noisy PCA components in real- and imaginary-components, separately, of phase-corrected DWI data, and 5) combining real- and imaginary-components of denoised DWI data. Our data show that the new two-channel (i.e., for real- and imaginary-components) DM-PCA denoising procedure performs reliably without noticeably compromising anatomic resolvability. Non-Gaussian noise induced signal bias could also be reduced with the new denoising method. The DM-PCA based denoising procedure should prove highly valuable for high-resolution DWI studies in research and clinical uses. PMID:29694400

Characterization of a time-resolved non-contact scanning diffuse optical imaging system exploiting fast-gated single-photon avalanche diode detection

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

Di Sieno, Laura, E-mail: laura.disieno@polimi.it; Dalla Mora, Alberto; Contini, Davide

2016-03-15

We present a system for non-contact time-resolved diffuse reflectance imaging, based on small source-detector distance and high dynamic range measurements utilizing a fast-gated single-photon avalanche diode. The system is suitable for imaging of diffusive media without any contact with the sample and with a spatial resolution of about 1 cm at 1 cm depth. In order to objectively assess its performances, we adopted two standardized protocols developed for time-domain brain imagers. The related tests included the recording of the instrument response function of the setup and the responsivity of its detection system. Moreover, by using liquid turbid phantoms with absorbingmore » inclusions, depth-dependent contrast and contrast-to-noise ratio as well as lateral spatial resolution were measured. To illustrate the potentialities of the novel approach, the characteristics of the non-contact system are discussed and compared to those of a fiber-based brain imager.« less

RESOLVE: A new algorithm for aperture synthesis imaging of extended emission in radio astronomy

NASA Astrophysics Data System (ADS)

Junklewitz, H.; Bell, M. R.; Selig, M.; Enßlin, T. A.

2016-02-01

We present resolve, a new algorithm for radio aperture synthesis imaging of extended and diffuse emission in total intensity. The algorithm is derived using Bayesian statistical inference techniques, estimating the surface brightness in the sky assuming a priori log-normal statistics. resolve estimates the measured sky brightness in total intensity, and the spatial correlation structure in the sky, which is used to guide the algorithm to an optimal reconstruction of extended and diffuse sources. During this process, the algorithm succeeds in deconvolving the effects of the radio interferometric point spread function. Additionally, resolve provides a map with an uncertainty estimate of the reconstructed surface brightness. Furthermore, with resolve we introduce a new, optimal visibility weighting scheme that can be viewed as an extension to robust weighting. In tests using simulated observations, the algorithm shows improved performance against two standard imaging approaches for extended sources, Multiscale-CLEAN and the Maximum Entropy Method.

Spatially resolved and time-resolved imaging of transport of indirect excitons in high magnetic fields

NASA Astrophysics Data System (ADS)

Dorow, C. J.; Hasling, M. W.; Calman, E. V.; Butov, L. V.; Wilkes, J.; Campman, K. L.; Gossard, A. C.

2017-06-01

We present the direct measurements of magnetoexciton transport. Excitons give the opportunity to realize the high magnetic-field regime for composite bosons with magnetic fields of a few tesla. Long lifetimes of indirect excitons allow the study of kinetics of magnetoexciton transport with time-resolved optical imaging of exciton photoluminescence. We performed spatially, spectrally, and time-resolved optical imaging of transport of indirect excitons in high magnetic fields. We observed that an increasing magnetic field slows down magnetoexciton transport. The time-resolved measurements of the magnetoexciton transport distance allowed for an experimental estimation of the magnetoexciton diffusion coefficient. An enhancement of the exciton photoluminescence energy at the laser excitation spot was found to anticorrelate with the exciton transport distance. A theoretical model of indirect magnetoexciton transport is presented and is in agreement with the experimental data.

Development of a high angular resolution diffusion imaging human brain template.

PubMed

Varentsova, Anna; Zhang, Shengwei; Arfanakis, Konstantinos

2014-05-01

Brain diffusion templates contain rich information about the microstructure of the brain, and are used as references in spatial normalization or in the development of brain atlases. The accuracy of diffusion templates constructed based on the diffusion tensor (DT) model is limited in regions with complex neuronal micro-architecture. High angular resolution diffusion imaging (HARDI) overcomes limitations of the DT model and is capable of resolving intravoxel heterogeneity. However, when HARDI is combined with multiple-shot sequences to minimize image artifacts, the scan time becomes inappropriate for human brain imaging. In this work, an artifact-free HARDI template of the human brain was developed from low angular resolution multiple-shot diffusion data. The resulting HARDI template was produced in ICBM-152 space based on Turboprop diffusion data, was shown to resolve complex neuronal micro-architecture in regions with intravoxel heterogeneity, and contained fiber orientation information consistent with known human brain anatomy. Copyright © 2014 Elsevier Inc. All rights reserved.

Diffusion lengths of silicon solar cells from luminescence images

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

Wuerfel, P.; Trupke, T.; Puzzer, T.

A method for spatially resolved measurement of the minority carrier diffusion length in silicon wafers and in silicon solar cells is introduced. The method, which is based on measuring the ratio of two luminescence images taken with two different spectral filters, is applicable, in principle, to both photoluminescence and electroluminescence measurements and is demonstrated experimentally by electroluminescence measurements on a multicrystalline silicon solar cell. Good agreement is observed with the diffusion length distribution obtained from a spectrally resolved light beam induced current map. In contrast to the determination of diffusion lengths from one single luminescence image, the method proposed heremore » gives absolute values of the diffusion length and, in comparison, it is much less sensitive to lateral voltage variations across the cell area as caused by local variations of the series resistance. It is also shown that measuring the ratio of two luminescence images allows distinguishing shunts or surface defects from bulk defects.« less

Comparison of spatially and temporally resolved diffuse transillumination measurement systems for extraction of optical properties of scattering media.

PubMed

Ortiz-Rascón, E; Bruce, N C; Garduño-Mejía, J; Carrillo-Torres, R; Hernández-Paredes, J; Álvarez-Ramos, M E

2017-11-20

This paper discusses the main differences between two different methods for determining the optical properties of tissue optical phantoms by fitting the spatial and temporal intensity distribution functions to the diffusion approximation theory. The consistency in the values of the optical properties is verified by changing the width of the recipient containing the turbid medium; as the optical properties are an intrinsic value of the scattering medium, independently of the recipient width, the stability in these values for different widths implies a better measurement system for the acquisition of the optical properties. It is shown that the temporal fitting method presents higher stability than the spatial fitting method; this is probably due to the addition of the time of flight parameter into the diffusion theory.

Quantitative fluorescence imaging of protein diffusion and interaction in living cells.

PubMed

Capoulade, Jérémie; Wachsmuth, Malte; Hufnagel, Lars; Knop, Michael

2011-08-07

Diffusion processes and local dynamic equilibria inside cells lead to nonuniform spatial distributions of molecules, which are essential for processes such as nuclear organization and signaling in cell division, differentiation and migration. To understand these mechanisms, spatially resolved quantitative measurements of protein abundance, mobilities and interactions are needed, but current methods have limited capabilities to study dynamic parameters. Here we describe a microscope based on light-sheet illumination that allows massively parallel fluorescence correlation spectroscopy (FCS) measurements and use it to visualize the diffusion and interactions of proteins in mammalian cells and in isolated fly tissue. Imaging the mobility of heterochromatin protein HP1α (ref. 4) in cell nuclei we could provide high-resolution diffusion maps that reveal euchromatin areas with heterochromatin-like HP1α-chromatin interactions. We expect that FCS imaging will become a useful method for the precise characterization of cellular reaction-diffusion processes.

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

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

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

2016-05-28

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

Optimal arrangements of fiber optic probes to enhance the spatial resolution in depth for 3D reflectance diffuse optical tomography with time-resolved measurements performed with fast-gated single-photon avalanche diodes

NASA Astrophysics Data System (ADS)

Puszka, Agathe; Di Sieno, Laura; Dalla Mora, Alberto; Pifferi, Antonio; Contini, Davide; Boso, Gianluca; Tosi, Alberto; Hervé, Lionel; Planat-Chrétien, Anne; Koenig, Anne; Dinten, Jean-Marc

2014-02-01

Fiber optic probes with a width limited to a few centimeters can enable diffuse optical tomography (DOT) in intern organs like the prostate or facilitate the measurements on extern organs like the breast or the brain. We have recently shown on 2D tomographic images that time-resolved measurements with a large dynamic range obtained with fast-gated single-photon avalanche diodes (SPADs) could push forward the imaged depth range in a diffusive medium at short source-detector separation compared with conventional non-gated approaches. In this work, we confirm these performances with the first 3D tomographic images reconstructed with such a setup and processed with the Mellin- Laplace transform. More precisely, we investigate the performance of hand-held probes with short interfiber distances in terms of spatial resolution and specifically demonstrate the interest of having a compact probe design featuring small source-detector separations. We compare the spatial resolution obtained with two probes having the same design but different scale factors, the first one featuring only interfiber distances of 15 mm and the second one, 10 mm. We evaluate experimentally the spatial resolution obtained with each probe on the setup with fast-gated SPADs for optical phantoms featuring two absorbing inclusions positioned at different depths and conclude on the potential of short source-detector separations for DOT.

Lateral eddy diffusivity estimates from simulated and observed drifter trajectories: a case study for the Agulhas Current system

NASA Astrophysics Data System (ADS)

Rühs, Siren; Zhurbas, Victor; Durgadoo, Jonathan V.; Biastoch, Arne

2017-04-01

The Lagrangian description of fluid motion by sets of individual particle trajectories is extensively used to characterize connectivity between distinct oceanic locations. One important factor influencing the connectivity is the average rate of particle dispersal, generally quantified as Lagrangian diffusivity. In addition to Lagrangian observing programs, Lagrangian analyses are performed by advecting particles with the simulated flow field of ocean general circulation models (OGCMs). However, depending on the spatio-temporal model resolution, not all scale-dependent processes are explicitly resolved in the simulated velocity fields. Consequently, the dispersal of advective Lagrangian trajectories has been assumed not to be sufficiently diffusive compared to observed particle spreading. In this study we present a detailed analysis of the spatially variable lateral eddy diffusivity characteristics of advective drifter trajectories simulated with realistically forced OGCMs and compare them with estimates based on observed drifter trajectories. The extended Agulhas Current system around South Africa, known for its intricate mesoscale dynamics, serves as a test case. We show that a state-of-the-art eddy-resolving OGCM indeed features theoretically derived dispersion characteristics for diffusive regimes and realistically represents Lagrangian eddy diffusivity characteristics obtained from observed surface drifter trajectories. The estimates for the maximum and asymptotic lateral single-particle eddy diffusivities obtained from the observed and simulated drifter trajectories show a good agreement in their spatial pattern and magnitude. We further assess the sensitivity of the simulated lateral eddy diffusivity estimates to the temporal and lateral OGCM output resolution and examine the impact of the different eddy diffusivity characteristics on the Lagrangian connectivity between the Indian Ocean and the South Atlantic.

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

PubMed Central

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

1985-01-01

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

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

PubMed

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

1985-06-01

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

Inverse Algorithm Optimization for Determining Optical Properties of Biological Materials from Spatially-Resolved Diffuse Reflectance

USDA-ARS?s Scientific Manuscript database

Optical characterization of biological materials is useful in many scientific and industrial applications like biomedical diagnosis and nondestructive quality evaluation of food and agricultural products. However, accurate determination of the optical properties from intact biological materials base...

Local diffusion and diffusion-T2 distribution measurements in porous media

NASA Astrophysics Data System (ADS)

Vashaee, S.; Newling, B.; MacMillan, B.; Marica, F.; Li, M.; Balcom, B. J.

2017-05-01

Slice-selective pulsed field gradient (PFG) and PFG-T2 measurements are developed to measure spatially-resolved molecular diffusion and diffusion-T2 distributions. A spatially selective adiabatic inversion pulse was employed for slice-selection. The slice-selective pulse is able to select a coarse slice, on the order of 1 cm, at an arbitrary position in the sample. The new method can be employed to characterize oil-water mixtures in porous media. The new technique has an inherent sensitivity advantage over phase encoding imaging based methods due to signal being localized from a thick slice. The method will be advantageous for magnetic resonance of porous media at low field where sensitivity is problematic. Experimental CPMG data, following PFG diffusion measurement, were compromised by a transient ΔB0(t) field offset. The off resonance effects of ΔB0(t) were examined by simulation. The ΔB0 offset artifact in D-T2 distribution measurements may be avoided by employing real data, instead of magnitude data.

Quantifying the correlation between spatially defined oxygen gradients and cell fate in an engineered three-dimensional culture model.

PubMed

Ardakani, Amir G; Cheema, Umber; Brown, Robert A; Shipley, Rebecca J

2014-09-06

A challenge in three-dimensional tissue culture remains the lack of quantitative information linking nutrient delivery and cellular distribution. Both in vivo and in vitro, oxygen is delivered by diffusion from its source (blood vessel or the construct margins). The oxygen level at a defined distance from its source depends critically on the balance of diffusion and cellular metabolism. Cells may respond to this oxygen environment through proliferation, death and chemotaxis, resulting in spatially resolved gradients in cellular density. This study extracts novel spatially resolved and simultaneous data on tissue oxygenation, cellular proliferation, viability and chemotaxis in three-dimensional spiralled, cellular collagen constructs. Oxygen concentration gradients drove preferential cellular proliferation rates and viability in the higher oxygen zones and induced chemotaxis along the spiral of the collagen construct; an oxygen gradient of 1.03 mmHg mm(-1) in the spiral direction induced a mean migratory speed of 1015 μm day(-1). Although this movement was modest, it was effective in balancing the system to a stable cell density distribution, and provided insights into the natural cell mechanism for adapting cell number and activity to a prevailing oxygen regime.

Resolvent positive linear operators exhibit the reduction phenomenon

PubMed Central

Altenberg, Lee

2012-01-01

The spectral bound, s(αA + βV), of a combination of a resolvent positive linear operator A and an operator of multiplication V, was shown by Kato to be convex in . Kato's result is shown here to imply, through an elementary “dual convexity” lemma, that s(αA + βV) is also convex in α > 0, and notably, ∂s(αA + βV)/∂α ≤ s(A). Diffusions typically have s(A) ≤ 0, so that for diffusions with spatially heterogeneous growth or decay rates, greater mixing reduces growth. Models of the evolution of dispersal in particular have found this result when A is a Laplacian or second-order elliptic operator, or a nonlocal diffusion operator, implying selection for reduced dispersal. These cases are shown here to be part of a single, broadly general, “reduction” phenomenon. PMID:22357763

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

PubMed

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

2015-06-23

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

Carrier Decay and Diffusion Dynamics in Single-Crystalline CdTe as seen via Microphotoluminescence

NASA Astrophysics Data System (ADS)

Mascarenhas, Angelo; Fluegel, Brian; Alberi, Kirstin; Zhang, Yong-Hang

2015-03-01

The ability to spatially resolve the degree to which extended defects impact carrier diffusion lengths and lifetimes is important for determining upper limits for defect densities in semiconductor devices. We show that a new spatially and temporally resolved photoluminescence (PL) imaging technique can be used to accurately extract carrier lifetimes in the immediate vicinity of dark-line defects in CdTe/MgCdTe double heterostructures. A series of PL images captured during the decay process show that extended defects with a density of 1.4x10-5 cm-2 deplete photogenerated charge carriers from the surrounding semiconductor material on a nanosecond time scale. The technique makes it possible to elucidate the interplay between nonradiative carrier recombination and carrier diffusion and reveals that they both combine to degrade the PL intensity over a fractional area that is much larger than the physical size of the defects. Carrier lifetimes are correctly determined from numerical simulations of the decay behavior by taking these two effects into account. Our study demonstrates that it is crucial to measure and account for the influence of local defects in the measurement of carrier lifetime and diffusion, which are key transport parameters for the design and modeling of advanced solar-cell and light-emitting devices. We acknowledge the financial support of the Department of Energy Office of Science under Grant No. DE-AC36-08GO28308.

Finite element modeling of light propagation in fruit under illumination of continuous-wave beam

USDA-ARS?s Scientific Manuscript database

Spatially-resolved spectroscopy provides a means for measuring the optical properties of biological tissues, based on analytical solutions to diffusion approximation for semi-infinite media under the normal illumination of infinitely small size light beam. The method is, however, prone to error in m...

Slaved diffusion in phospholipid bilayers

PubMed Central

Zhang, Liangfang; Granick, Steve

2005-01-01

The translational diffusion of phospholipids in supported fluid bilayers splits into two populations when polyelectrolytes adsorb at incomplete surface coverage. Spatially resolved measurements using fluorescence correlation spectroscopy show that a slow mode, whose magnitude scales inversely with the degree of polymerization of the adsorbate, coexists with a fast mode characteristic of naked lipid diffusion. Inner and outer leaflets of the bilayer are affected nearly equally. Mobility may vary from spot to spot on the membrane surface, despite the lipid composition being the same. This work offers a mechanism to explain how nanosized domains with reduced mobility arise in lipid membranes. PMID:15967988

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

PubMed

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

2005-07-10

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

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

PubMed

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

2013-01-01

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

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

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

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

2015-09-28

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

Noncontact blood species identification method based on spatially resolved near-infrared transmission spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Linna; Sun, Meixiu; Wang, Zhennan; Li, Hongxiao; Li, Yingxin; Li, Gang; Lin, Ling

2017-09-01

The inspection and identification of whole blood are crucially significant for import-export ports and inspection and quarantine departments. In our previous research, we proved Near-Infrared diffuse transmitted spectroscopy method was potential for noninvasively identifying three blood species, including macaque, human and mouse, with samples measured in the cuvettes. However, in open sampling cases, inspectors may be endangered by virulence factors in blood samples. In this paper, we explored the noncontact measurement for classification, with blood samples measured in the vacuum blood vessels. Spatially resolved near-infrared spectroscopy was used to improve the prediction accuracy. Results showed that the prediction accuracy of the model built with nine detection points was more than 90% in identification between all five species, including chicken, goat, macaque, pig and rat, far better than the performance of the model built with single-point spectra. The results fully supported the idea that spatially resolved near-infrared spectroscopy method can improve the prediction ability, and demonstrated the feasibility of this method for noncontact blood species identification in practical applications.

Finite element modeling of light propagation in turbid media under illumination of a continuous-wave beam

USDA-ARS?s Scientific Manuscript database

Spatially-resolved spectroscopy provides a means for measuring the optical properties of biological tissues, based on analytical solutions to diffusion approximation for semi-infinite media under the normal illumination of infinitely small size light beam. The method is, however, prone to error in m...

Measurement of fluorophore concentrations and fluorescence quantum yield in tissue-simulating phantoms using three diffusion models of steady-state spatially resolved fluorescence.

PubMed

Diamond, Kevin R; Farrell, Thomas J; Patterson, Michael S

2003-12-21

Steady-state diffusion theory models of fluorescence in tissue have been investigated for recovering fluorophore concentrations and fluorescence quantum yield. Spatially resolved fluorescence, excitation and emission reflectance Carlo simulations, and measured using a multi-fibre probe on tissue-simulating phantoms containing either aluminium phthalocyanine tetrasulfonate (AlPcS4), Photofrin meso-tetra-(4-sulfonatophenyl)-porphine dihydrochloride The accuracy of the fluorophore concentration and fluorescence quantum yield recovered by three different models of spatially resolved fluorescence were compared. The models were based on: (a) weighted difference of the excitation and emission reflectance, (b) fluorescence due to a point excitation source or (c) fluorescence due to a pencil beam excitation source. When literature values for the fluorescence quantum yield were used for each of the fluorophores, the fluorophore absorption coefficient (and hence concentration) at the excitation wavelength (mu(a,x,f)) was recovered with a root-mean-square accuracy of 11.4% using the point source model of fluorescence and 8.0% using the more complicated pencil beam excitation model. The accuracy was calculated over a broad range of optical properties and fluorophore concentrations. The weighted difference of reflectance model performed poorly, with a root-mean-square error in concentration of about 50%. Monte Carlo simulations suggest that there are some situations where the weighted difference of reflectance is as accurate as the other two models, although this was not confirmed experimentally. Estimates of the fluorescence quantum yield in multiple scattering media were also made by determining mu(a,x,f) independently from the fitted absorption spectrum and applying the various diffusion theory models. The fluorescence quantum yields for AlPcS4 and TPPS4 were calculated to be 0.59 +/- 0.03 and 0.121 +/- 0.001 respectively using the point source model, and 0.63 +/- 0.03 and 0.129 +/- 0.002 using the pencil beam excitation model. These results are consistent with published values.

Direct mapping of ion diffusion times on LiCoO2 surfaces with nanometer resolution

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

Guo, Senli; Jesse, Stephen; Kalnaus, Sergiy

2011-01-01

The strong coupling between the molar volume and mobile ion concentration in ionically-conductive solids is used for spatially-resolved studies of ionic transport on the polycrystalline LiCoO2 surface by time-resolved spectroscopy. Strong variability between ionic transport at the grain boundaries and within the grains is observed, and the relationship between relaxation and hysteresis loop formation is established. The use of the strain measurements allows ionic transport be probed on the nanoscale, and suggests enormous potential for probing ionic materials and devices.

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

NASA Astrophysics Data System (ADS)

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

2012-07-01

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

Particle image diffusometry: Resolving diffusion coefficient field from microscopy movie data without particle tracking

NASA Astrophysics Data System (ADS)

Hanasaki, Itsuo; Ooi, Yuto

2018-06-01

We propose a technique to evaluate the field of diffusion coefficient for particle dispersion where the Brownian motion is heterogeneous in space and single particle tracking (SPT) analysis is hindered by high concentration of the particles and/or their small size. We realize this "particle image diffusometry" by the principle of the differential dynamic microscopy (DDM). We extend the DDM by introducing the automated objective decision of the scaling regime itself. Label-free evaluation of spatially non-uniform diffusion coefficients without SPT is useful in the diverse applications including crystal nucleation and glass transition where non-invasive observation is desired.

Investigating the capability to resolve complex white matter structures with high b-value diffusion magnetic resonance imaging on the MGH-USC Connectom scanner.

PubMed

Fan, Qiuyun; Nummenmaa, Aapo; Witzel, Thomas; Zanzonico, Roberta; Keil, Boris; Cauley, Stephen; Polimeni, Jonathan R; Tisdall, Dylan; Van Dijk, Koene R A; Buckner, Randy L; Wedeen, Van J; Rosen, Bruce R; Wald, Lawrence L

2014-11-01

One of the major goals of the NIH Blueprint Human Connectome Project was to map and quantify the white matter connections in the brain using diffusion tractography. Given the prevalence of complex white matter structures, the capability of resolving local white matter geometries with multiple crossings in the diffusion magnetic resonance imaging (dMRI) data is critical. Increasing b-value has been suggested for delineation of the finer details of the orientation distribution function (ODF). Although increased gradient strength and duration increase sensitivity to highly restricted intra-axonal water, gradient strength limitations require longer echo times (TE) to accommodate the increased diffusion encoding times needed to achieve a higher b-value, exponentially lowering the signal-to-noise ratio of the acquisition. To mitigate this effect, the MGH-USC Connectom scanner was built with 300 mT/m gradients, which can significantly reduce the TE of high b-value diffusion imaging. Here we report comparisons performed across b-values based on q-ball ODF metrics to investigate whether high b-value diffusion imaging on the Connectom scanner can improve resolving complex white matter structures. The q-ball ODF features became sharper as the b-value increased, with increased power fraction in higher order spherical harmonic series of the ODF and increased peak heights relative to the overall size of the ODF. Crossing structures were detected in an increasingly larger fraction of white matter voxels and the spatial distribution of two-way and three-way crossing structures was largely consistent with known anatomy. Results indicate that dMRI with high diffusion encoding on the Connectom system is a promising tool to better characterize, and ultimately understand, the underlying structural organization and motifs in the human brain.

Experimental investigation of the velocity field in buoyant diffusion flames using PIV and TPIV algorithm

Treesearch

L. Sun; X. Zhou; S.M. Mahalingam; D.R. Weise

2005-01-01

We investigated a simultaneous temporally and spatially resolved 2-D velocity field above a burning circular pan of alcohol using particle image velocimetry (PIV). The results obtained from PIV were used to assess a thermal particle image velocimetry (TPIV) algorithm previously developed to approximate the velocity field using the temperature field, simultaneously...

Toward reliable retrieval of functional information of papillary dermis using spatially resolved diffuse reflectance spectroscopy

PubMed Central

Chen, Yu-Wen; Guo, Jun-Yen; Tzeng, Shih-Yu; Chou, Ting-Chun; Lin, Ming-Jen; Huang, Lynn Ling-Huei; Yang, Chao-Chun; Hsu, Chao-Kai; Tseng, Sheng-Hao

2016-01-01

Spatially resolved diffuse reflectance spectroscopy (SRDRS) has been employed to quantify tissue optical properties and its interrogation volume is majorly controlled by the source-to-detector separations (SDSs). To noninvasively quantify properties of dermis, a SRDRS setup that includes SDS shorter than 1 mm is required. It will be demonstrated in this study that Monte Carlo simulations employing the Henyey-Greenstein phase function cannot always precisely predict experimentally measured diffuse reflectance at such short SDSs, and we speculated this could be caused by the non-negligible backward light scattering at short SDSs that cannot be properly modeled by the Henyey-Greenstein phase function. To accurately recover the optical properties and functional information of dermis using SRDRS, we proposed the use of the modified two-layer (MTL) geometry. Monte Carlo simulations and phantom experiment results revealed that the MTL probing geometry was capable of faithfully recovering the optical properties of upper dermis. The capability of the MTL geometry in probing the upper dermis properties was further verified through a swine study, and it was found that the measurement results were reasonably linked to histological findings. Finally, the MTL probe was utilized to study psoriatic lesions. Our results showed that the MTL probe was sensitive to the physiological condition of tissue volumes within the papillary dermis and could be used in studying the physiology of psoriasis. PMID:26977361

Toward reliable retrieval of functional information of papillary dermis using spatially resolved diffuse reflectance spectroscopy.

PubMed

Chen, Yu-Wen; Guo, Jun-Yen; Tzeng, Shih-Yu; Chou, Ting-Chun; Lin, Ming-Jen; Huang, Lynn Ling-Huei; Yang, Chao-Chun; Hsu, Chao-Kai; Tseng, Sheng-Hao

2016-02-01

Spatially resolved diffuse reflectance spectroscopy (SRDRS) has been employed to quantify tissue optical properties and its interrogation volume is majorly controlled by the source-to-detector separations (SDSs). To noninvasively quantify properties of dermis, a SRDRS setup that includes SDS shorter than 1 mm is required. It will be demonstrated in this study that Monte Carlo simulations employing the Henyey-Greenstein phase function cannot always precisely predict experimentally measured diffuse reflectance at such short SDSs, and we speculated this could be caused by the non-negligible backward light scattering at short SDSs that cannot be properly modeled by the Henyey-Greenstein phase function. To accurately recover the optical properties and functional information of dermis using SRDRS, we proposed the use of the modified two-layer (MTL) geometry. Monte Carlo simulations and phantom experiment results revealed that the MTL probing geometry was capable of faithfully recovering the optical properties of upper dermis. The capability of the MTL geometry in probing the upper dermis properties was further verified through a swine study, and it was found that the measurement results were reasonably linked to histological findings. Finally, the MTL probe was utilized to study psoriatic lesions. Our results showed that the MTL probe was sensitive to the physiological condition of tissue volumes within the papillary dermis and could be used in studying the physiology of psoriasis.

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

PubMed

Donatini, Fabrice; Pernot, Julien

2018-03-09

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

Electron Currents and Heating in the Ion Diffusion Region of Asymmetric Reconnection

NASA Technical Reports Server (NTRS)

Graham, D. B.; Khotyaintsev, Yu. V.; Norgren, C.; Vaivads, A.; Andre, M.; Lindqvist, P. A.; Marklund, G. T.; Ergun, R. E.; Paterson, W. R.; Gershman, D. J.;

Time of flight dependent linearity in diffuse imaging: how effective is it to evaluate the spatial resolution by measuring the edge response function?

PubMed

Ortiz-Rascón, E; Bruce, N C; Rodríguez-Rosales, A A; Garduño-Mejía, J

2016-03-01

We describe the behavior of linearity in diffuse imaging by evaluating the differences between time-resolved images produced by photons arriving at the detector at different times. Two approaches are considered: Monte Carlo simulations and experimental results. The images of two complete opaque bars embedded in a transparent or in a turbid medium with a slab geometry are analyzed; the optical properties of the turbid medium sample are close to those of breast tissue. A simple linearity test was designed involving a direct comparison between the intensity profile produced by two bars scanned at the same time and the intensity profile obtained by adding two profiles of each bar scanned one at a time. It is shown that the linearity improves substantially when short time of flight photons are used in the imaging process, but even then the nonlinear behavior prevails. As the edge response function (ERF) has been used widely for testing the spatial resolution in imaging systems, the main implication of a time dependent linearity is the weakness of the linearity assumption when evaluating the spatial resolution through the ERF in diffuse imaging systems, and the need to evaluate the spatial resolution by other methods.

Integrated circuit-based electrochemical sensor for spatially resolved detection of redox-active metabolites in biofilms.

PubMed

Bellin, Daniel L; Sakhtah, Hassan; Rosenstein, Jacob K; Levine, Peter M; Thimot, Jordan; Emmett, Kevin; Dietrich, Lars E P; Shepard, Kenneth L

2014-01-01

Despite advances in monitoring spatiotemporal expression patterns of genes and proteins with fluorescent probes, direct detection of metabolites and small molecules remains challenging. A technique for spatially resolved detection of small molecules would benefit the study of redox-active metabolites that are produced by microbial biofilms and can affect their development. Here we present an integrated circuit-based electrochemical sensing platform featuring an array of working electrodes and parallel potentiostat channels. 'Images' over a 3.25 × 0.9 mm(2) area can be captured with a diffusion-limited spatial resolution of 750 μm. We demonstrate that square wave voltammetry can be used to detect, identify and quantify (for concentrations as low as 2.6 μM) four distinct redox-active metabolites called phenazines. We characterize phenazine production in both wild-type and mutant Pseudomonas aeruginosa PA14 colony biofilms, and find correlations with fluorescent reporter imaging of phenazine biosynthetic gene expression.

Integrated circuit-based electrochemical sensor for spatially resolved detection of redox-active metabolites in biofilms

PubMed Central

Bellin, Daniel L.; Sakhtah, Hassan; Rosenstein, Jacob K.; Levine, Peter M.; Thimot, Jordan; Emmett, Kevin; Dietrich, Lars E. P.; Shepard, Kenneth L.

2014-01-01

Despite advances in monitoring spatiotemporal expression patterns of genes and proteins with fluorescent probes, direct detection of metabolites and small molecules remains challenging. A technique for spatially resolved detection of small molecules would benefit the study of redox-active metabolites produced by microbial biofilms, which can drastically affect colony development. Here we present an integrated circuit-based electrochemical sensing platform featuring an array of working electrodes and parallel potentiostat channels. “Images” over a 3.25 × 0.9 mm area can be captured with a diffusion-limited spatial resolution of 750 μm. We demonstrate that square wave voltammetry can be used to detect, identify, and quantify (for concentrations as low as 2.6 μM) four distinct redox-active metabolites called phenazines. We characterize phenazine production in both wild-type and mutant Pseudomonas aeruginosa PA14 colony biofilms, and find correlations with fluorescent reporter imaging of phenazine biosynthetic gene expression. PMID:24510163

Fast reconstruction of optical properties for complex segmentations in near infrared imaging

NASA Astrophysics Data System (ADS)

Jiang, Jingjing; Wolf, Martin; Sánchez Majos, Salvador

2017-04-01

The intrinsic ill-posed nature of the inverse problem in near infrared imaging makes the reconstruction of fine details of objects deeply embedded in turbid media challenging even for the large amounts of data provided by time-resolved cameras. In addition, most reconstruction algorithms for this type of measurements are only suitable for highly symmetric geometries and rely on a linear approximation to the diffusion equation since a numerical solution of the fully non-linear problem is computationally too expensive. In this paper, we will show that a problem of practical interest can be successfully addressed making efficient use of the totality of the information supplied by time-resolved cameras. We set aside the goal of achieving high spatial resolution for deep structures and focus on the reconstruction of complex arrangements of large regions. We show numerical results based on a combined approach of wavelength-normalized data and prior geometrical information, defining a fully parallelizable problem in arbitrary geometries for time-resolved measurements. Fast reconstructions are obtained using a diffusion approximation and Monte-Carlo simulations, parallelized in a multicore computer and a GPU respectively.

Chandra/ACIS Observations of Rosette: Diffuse X-rays Discovered in a Galactic H II Region

NASA Astrophysics Data System (ADS)

Townsley, L. K.; Feigelson, E. D.; Broos, P. S.; Chu, Y.-H.; Montmerle, T.

2001-12-01

We present the first high-spatial-resolution X-ray images of the Rosette Nebula and Rosette Molecular Cloud (RMC), obtained in a series of 4 20-ksec snapshots with the Advanced CCD Imaging Spectrometer aboard the Chandra X-ray Observatory in January 2001. These images form a striking 1-degree X-ray panorama of a rich high-mass star formation region. The OB association is resolved at the arcsecond level into >300 sources. The other 3 pointings step across the RMC, with >100 X-ray sources in each. Soft diffuse emission is seen at the center of the H II region and is resolved from the point source population. This extended emission is most likely from the fast O-star winds, which thermalize and shock the surrounding media. Support for this effort was provided by the Chandra X-ray Observatory GO2 grant G01-2008X.

Exciton dynamics at a single dislocation in GaN probed by picosecond time-resolved cathodoluminescence

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

Liu, W., E-mail: we.liu@epfl.ch, E-mail: gwenole.jacopin@epfl.ch; Carlin, J.-F.; Grandjean, N.

2016-07-25

We investigate the dynamics of donor bound excitons (D°X{sub A}) at T = 10 K around an isolated single edge dislocation in homoepitaxial GaN, using a picosecond time-resolved cathodoluminescence (TR-CL) setup with high temporal and spatial resolutions. An ∼ 1.3 meV dipole-like energy shift of D°X{sub A} is observed around the dislocation, induced by the local strain fields. By simultaneously recording the variations of both the exciton lifetime and the CL intensity across the dislocation, we directly assess the dynamics of excitons around the defect. Our observations are well reproduced by a diffusion model. It allows us to deduce an exciton diffusion length ofmore » ∼24 nm as well as an effective area of the dislocation with a radius of ∼95 nm, where the recombination can be regarded as entirely non-radiative.« less

Mapping the nanoscale energetic landscape in conductive polymer films with spatially super-resolved exciton dynamics

NASA Astrophysics Data System (ADS)

Ginsberg, Naomi

2015-03-01

The migration of Frenkel excitons, tightly-bound electron-hole pairs, in polymeric organic semiconducting films is critical to the efficiency of bulk heterojunction solar cells. While these materials exhibit a high degree of structural heterogeneity on the nanoscale, traditional measurements of exciton diffusion lengths are performed on bulk samples. Since both the characteristic length scales of structural heterogeneity and the reported bulk diffusion lengths are smaller than the optical diffraction limit, we adapt far-field super-resolution fluorescence imaging to uncover the correlations between the structural and energetic landscapes that the excitons explore.

Anisotropic Mesoscale Eddy Transport in Ocean General Circulation Models

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Spatially resolved D-T(2) correlation NMR of porous media.

PubMed

Zhang, Yan; Blümich, Bernhard

2014-05-01

Within the past decade, 2D Laplace nuclear magnetic resonance (NMR) has been developed to analyze pore geometry and diffusion of fluids in porous media on the micrometer scale. Many objects like rocks and concrete are heterogeneous on the macroscopic scale, and an integral analysis of microscopic properties provides volume-averaged information. Magnetic resonance imaging (MRI) resolves this spatial average on the contrast scale set by the particular MRI technique. Desirable contrast parameters for studies of fluid transport in porous media derive from the pore-size distribution and the pore connectivity. These microscopic parameters are accessed by 1D and 2D Laplace NMR techniques. It is therefore desirable to combine MRI and 2D Laplace NMR to image functional information on fluid transport in porous media. Because 2D Laplace resolved MRI demands excessive measuring time, this study investigates the possibility to restrict the 2D Laplace analysis to the sum signals from low-resolution pixels, which correspond to pixels of similar amplitude in high-resolution images. In this exploratory study spatially resolved D-T2 correlation maps from glass beads and mortar are analyzed. Regions of similar contrast are first identified in high-resolution images to locate corresponding pixels in low-resolution images generated with D-T2 resolved MRI for subsequent pixel summation to improve the signal-to-noise ratio of contrast-specific D-T2 maps. This method is expected to contribute valuable information on correlated sample heterogeneity from the macroscopic and the microscopic scales in various types of porous materials including building materials and rock. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Spatially-resolved magnetic resonance study of the dissolution interface between soaps and water

NASA Astrophysics Data System (ADS)

Ciampi, E.; Goerke, U.; McDonald, P. J.; Chambers, J. G.; Newling, B.

2002-06-01

The developing interfacial region between a soap bar and water has been studied using a suite of spatially resolved NMR techniques. Stray field imaging (STRAFI) allowed the dynamics of water ingress into a shop-bought, commercial soap to be followed. A simplistic analysis of the data shows the ingress to be a Fickian process (∝t1/2) in the first 4 h. The T2 contrast employed in the STRAFI method is not sufficient to resolve detail of the mesophase formation at the interface. However, double quantum filtered 2H spectroscopy at different positions in the interfacial region allowed water concentration (and mesophase distribution) to be mapped over the first 120 h of dissolution. A simple model shows good agreement with the water concentration data. In the isotropic soap solution above the interfacial region, J-cyclic cross polarization was used to selectively interrogate the CH2 1H of the soap alkyl chains and, in combination with a pulsed field gradient measurement of self-diffusion, suggests a micellar solution in which the hydrodynamic radius of the micelles is ~5nm.

Frequency-resolved Raman for transient thermal probing and thermal diffusivity measurement

DOE PAGES

Wang, Tianyu; Xu, Shen; Hurley, David H.; ...

2015-12-18

Steady state Raman has been widely used for temperature probing and thermal conductivity/conductance measurement in combination with temperature coefficient calibration. In this work, a new transient Raman thermal probing technique: frequency-resolved Raman (FR-Raman) is developed for probing the transient thermal response of materials and measuring their thermal diffusivity. The FR-Raman uses an amplitude modulated square-wave laser for simultaneous material heating and Raman excitation. The evolution profile of Raman properties: intensity, Raman wavenumber, and emission, against frequency are measured experimentally and reconstructed theoretically. They are used for fitting to determine the thermal diffusivity of the material under test. A Si cantilevermore » is used to investigate the capacity of this new technique. The cantilever’s thermal diffusivity is determined as 9.57 × 10 -5 m 2/s, 11.00 × 10 -5 m 2/s and 9.02 × 10 -5 m 2/s by fitting the Raman intensity, wavenumber and emission. The deviation from the reference value is largely attributed to thermal stress-induced material deflection and Raman drift, which could be significantly suppressed by using a higher sensitivity Raman spectrometer with lower laser energy. As a result, the FR-Raman provides a novel way for transient thermal characterization of materials with a ?m spatial resolution.« less

NMR investigation of gaseous SF6 confinement into EPDM rubber.

PubMed

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

2005-02-01

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

Workshop on MQW Mixing and its Application to Optoelectronic Devices

DTIC Science & Technology

1990-09-01

21st SEPTEMBER 1990 L Approvsd to; Puiic~ zeleaaeg serc .., 90 ! ;>:.01. . 𔃻 i OR 3ANISING COMMITTEE: . . . . B L Weiss (Chairman) University of...temperature photoluminescence ( PL ) and PL excitation (PLE) spectroscopies were used to monitor exciton energies before and after processing. After RTA...generated near the surface. Spatially resolved PL spectroscopy verified that the lateral diffusion of surface vacancies was less than that of the

Bayesian Scalar-on-Image Regression with Application to Association Between Intracranial DTI and Cognitive Outcomes

PubMed Central

Huang, Lei; Goldsmith, Jeff; Reiss, Philip T.; Reich, Daniel S.; Crainiceanu, Ciprian M.

2013-01-01

Diffusion tensor imaging (DTI) measures water diffusion within white matter, allowing for in vivo quantification of brain pathways. These pathways often subserve specific functions, and impairment of those functions is often associated with imaging abnormalities. As a method for predicting clinical disability from DTI images, we propose a hierarchical Bayesian “scalar-on-image” regression procedure. Our procedure introduces a latent binary map that estimates the locations of predictive voxels and penalizes the magnitude of effect sizes in these voxels, thereby resolving the ill-posed nature of the problem. By inducing a spatial prior structure, the procedure yields a sparse association map that also maintains spatial continuity of predictive regions. The method is demonstrated on a simulation study and on a study of association between fractional anisotropy and cognitive disability in a cross-sectional sample of 135 multiple sclerosis patients. PMID:23792220

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.

PubMed

Schaff, James C; Gao, Fei; Li, Ye; Novak, Igor L; Slepchenko, Boris M

2016-12-01

Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations of reaction-diffusion systems are not widely available. Here we describe fundamentals of a general-purpose spatial hybrid method. The method generates realizations of a spatially inhomogeneous hybrid system by appropriately integrating capabilities of a deterministic partial differential equation solver with a popular particle-based stochastic simulator, Smoldyn. Rigorous validation of the algorithm is detailed, using a simple model of calcium 'sparks' as a testbed. The solver is then applied to a deterministic-stochastic model of spontaneous emergence of cell polarity. The approach is general enough to be implemented within biologist-friendly software frameworks such as Virtual Cell.

Probing for Exoplanets Hiding in Dusty Debris Disks: Disk Imaging, Characterization, and Exploration with HST-STIS Multi-roll Coronagraphy

NASA Technical Reports Server (NTRS)

Schneider, Glenn; Grady, Carol A.; Hines, Dean C.; Stark, Christopher C.; Debes, John; Carson, Joe; Kuchner, Marc J.; Perrin, Marshall; Weinberger, Alycia; Wisniewski, John P.;

Probing for exoplanets hiding in dusty debris disks: Disk imaging, characterization, and exploration with HST/STIS multi-roll coronagraphy

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

Schneider, Glenn; Hinz, Phillip M.; Grady, Carol A.

Spatially resolved scattered-light images of circumstellar debris in exoplanetary systems constrain the physical properties and orbits of the dust particles in these systems. They also inform on co-orbiting (but unseen) planets, the systemic architectures, and forces perturbing the starlight-scattering circumstellar material. Using Hubble Space Telescope (HST)/Space Telescope Imaging Spectrograph (STIS) broadband optical coronagraphy, we have completed the observational phase of a program to study the spatial distribution of dust in a sample of 10 circumstellar debris systems and 1 'mature' protoplanetrary disk, all with HST pedigree, using point-spread-function-subtracted multi-roll coronagraphy. These observations probe stellocentric distances ≥5 AU for the nearestmore » systems, and simultaneously resolve disk substructures well beyond corresponding to the giant planet and Kuiper Belt regions within our own solar system. They also disclose diffuse very low-surface-brightness dust at larger stellocentric distances. Herein we present new results inclusive of fainter disks such as HD 92945 (F {sub disk}/F {sub star} = 5 × 10{sup –5}), confirming, and better revealing, the existence of a narrow inner debris ring within a larger diffuse dust disk. Other disks with ring-like substructures and significant asymmetries and complex morphologies include HD 181327, for which we posit a spray of ejecta from a recent massive collision in an exo-Kuiper Belt; HD 61005, suggested to be interacting with the local interstellar medium; and HD 15115 and HD 32297, also discussed in the context of putative environmental interactions. These disks and HD 15745 suggest that debris system evolution cannot be treated in isolation. For AU Mic's edge-on disk, we find out-of-plane surface brightness asymmetries at ≥5 AU that may implicate the existence of one or more planetary perturbers. Time-resolved images of the MP Mus protoplanetary disk provide spatially resolved temporal variability in the disk illumination. These and other new images from our HST/STIS GO/12228 program enable direct inter-comparison of the architectures of these exoplanetary debris systems in the context of our own solar system.« less

Spatially Resolved Hard X-ray Emission in the Central 5 kpc of the Galaxy Merger NGC 6240

NASA Astrophysics Data System (ADS)

Wang, Junfeng; Nardini, E.; Fabbiano, G.; Karovska, M.; Elvis, M.; Pellegrini, S.; Max, C. E.; Risaliti, G.; U, V.; Zezas, A.

2013-04-01

We have obtained a deep, sub-arcsecond resolution X-ray image of the nuclear region of the luminous galaxy merger NGC 6240 with Chandra, which resolves the X-ray emission from the pair of active nuclei and the diffuse hot gas in great detail. We detect extended hard X-ray emission from 70 million K hot gas over a spatial scale of 5 kpc, indicating the presence of fast shocks with velocity of 2200 km/s. For the first time we obtain spatial distribution of this highly ionized gas emitting FeXXV and find that it shows a remarkable correspondence to the large scale morphology of H_2(1-0) S(1) line emission and Hα filaments. Propagation of fast shocks originated in the starburst driven wind into the ambient dense gas can account for this morphological correspondence. Both the energetics and the iron mass in the hot gas are consistent with the expected injection from the supernovae explosion during the starburst that is commensurate with its high star formation rate.

Resolvent-based modeling of passive scalar dynamics in wall-bounded turbulence

NASA Astrophysics Data System (ADS)

Dawson, Scott; Saxton-Fox, Theresa; McKeon, Beverley

2017-11-01

The resolvent formulation of the Navier-Stokes equations expresses the system state as the output of a linear (resolvent) operator acting upon a nonlinear forcing. Previous studies have demonstrated that a low-rank approximation of this linear operator predicts many known features of incompressible wall-bounded turbulence. In this work, this resolvent model for wall-bounded turbulence is extended to include a passive scalar field. This formulation allows for a number of additional simplifications that reduce model complexity. Firstly, it is shown that the effect of changing scalar diffusivity can be approximated through a transformation of spatial wavenumbers and temporal frequencies. Secondly, passive scalar dynamics may be studied through the low-rank approximation of a passive scalar resolvent operator, which is decoupled from velocity response modes. Thirdly, this passive scalar resolvent operator is amenable to approximation by semi-analytic methods. We investigate the extent to which this resulting hierarchy of models can describe and predict passive scalar dynamics and statistics in wall-bounded turbulence. The support of AFOSR under Grant Numbers FA9550-16-1-0232 and FA9550-16-1-0361 is gratefully acknowledged.

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

PubMed Central

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

2010-01-01

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

Influence of cost functions and optimization methods on solving the inverse problem in spatially resolved diffuse reflectance spectroscopy

NASA Astrophysics Data System (ADS)

Rakotomanga, Prisca; Soussen, Charles; Blondel, Walter C. P. M.

2017-03-01

Diffuse reflectance spectroscopy (DRS) has been acknowledged as a valuable optical biopsy tool for in vivo characterizing pathological modifications in epithelial tissues such as cancer. In spatially resolved DRS, accurate and robust estimation of the optical parameters (OP) of biological tissues is a major challenge due to the complexity of the physical models. Solving this inverse problem requires to consider 3 components: the forward model, the cost function, and the optimization algorithm. This paper presents a comparative numerical study of the performances in estimating OP depending on the choice made for each of the latter components. Mono- and bi-layer tissue models are considered. Monowavelength (scalar) absorption and scattering coefficients are estimated. As a forward model, diffusion approximation analytical solutions with and without noise are implemented. Several cost functions are evaluated possibly including normalized data terms. Two local optimization methods, Levenberg-Marquardt and TrustRegion-Reflective, are considered. Because they may be sensitive to the initial setting, a global optimization approach is proposed to improve the estimation accuracy. This algorithm is based on repeated calls to the above-mentioned local methods, with initial parameters randomly sampled. Two global optimization methods, Genetic Algorithm (GA) and Particle Swarm Optimization (PSO), are also implemented. Estimation performances are evaluated in terms of relative errors between the ground truth and the estimated values for each set of unknown OP. The combination between the number of variables to be estimated, the nature of the forward model, the cost function to be minimized and the optimization method are discussed.

Quantifying the Precipitation Loss of Radiation Belt Electrons During a Rapid Dropout Event

NASA Astrophysics Data System (ADS)

Pham, K. H.; Tu, W.; Xiang, Z.

2017-10-01

Relativistic electron flux in the radiation belt can drop by orders of magnitude within the timespan of hours. In this study, we used the drift-diffusion model that includes azimuthal drift and pitch angle diffusion of electrons to simulate low-altitude electron distribution observed by POES/MetOp satellites for rapid radiation belt electron dropout event occurring on 1 May 2013. The event shows fast dropout of MeV energy electrons at L > 4 over a few hours, observed by the Van Allen Probes mission. By simulating the electron distributions observed by multiple POES satellites, we resolve the precipitation loss with both high spatial and temporal resolutions and a range of energies. We estimate the pitch angle diffusion coefficients as a function of energy, pitch angle, and L-shell and calculate corresponding electron lifetimes during the event. The simulation results show fast electron precipitation loss at L > 4 during the electron dropout, with estimated electron lifetimes on the order of half an hour for MeV energies. The electron loss rate shows strong energy dependence with faster loss at higher energies, which suggest that this dropout event is dominated by quick and localized scattering process that prefers higher energy electrons. The improved temporal and spatial resolutions of electron precipitation rates provided by multiple low-altitude observations can resolve fast-varying electron loss during rapid electron dropouts (over a few hours), which occur too fast for a single low-altitude satellite. The capability of estimating the fast-varying electron lifetimes during rapid dropout events is an important step in improving radiation belt model accuracy.

Spatially inhomogeneous acceleration of electrons in solar flares

NASA Astrophysics Data System (ADS)

Stackhouse, Duncan J.; Kontar, Eduard P.

2018-04-01

The imaging spectroscopy capabilities of the Reuven Ramaty high energy solar spectroscopic imager (RHESSI) enable the examination of the accelerated electron distribution throughout a solar flare region. In particular, it has been revealed that the energisation of these particles takes place over a region of finite size, sometimes resolved by RHESSI observations. In this paper, we present, for the first time, a spatially distributed acceleration model and investigate the role of inhomogeneous acceleration on the observed X-ray emission properties. We have modelled transport explicitly examining scatter-free and diffusive transport within the acceleration region and compare with the analytic leaky-box solution. The results show the importance of including this spatial variation when modelling electron acceleration in solar flares. The presence of an inhomogeneous, extended acceleration region produces a spectral index that is, in most cases, different from the simple leaky-box prediction. In particular, it results in a generally softer spectral index than predicted by the leaky-box solution, for both scatter-free and diffusive transport, and thus should be taken into account when modelling stochastic acceleration in solar flares.

A novel method for computing effective diffusivity: Application to helium implanted α-Fe thin films

NASA Astrophysics Data System (ADS)

Dunn, Aaron; Agudo-Merida, Laura; Martin-Bragado, Ignacio; McPhie, Mathieu; Cherkaoui, Mohammed; Capolungo, Laurent

2014-05-01

The effective diffusivity of helium in thin iron films is quantified using spatially resolved stochastic cluster dynamics and object kinetic Monte Carlo simulations. The roles of total displacement dose (in DPA), damage rate, helium to DPA ratio, layer thickness, and damage type (cascade damage vs Frenkel pair implantation) on effective He diffusivity are investigated. Helium diffusivity is found to decrease with increasing total damage and decreasing damage rate. Arrhenius plots show strongly increased helium diffusivity at high temperatures, high total implantation, and low implantation rates due to decreased vacancy and vacancy cluster concentrations. At low temperatures, effective diffusivity is weakly dependent on foil thickness while at high temperatures, narrower foils prevent defect accumulation by releasing all defects at the free surfaces. Helium to DPA ratio is not shown to strongly change helium diffusivity in the range of irradiation conditions simulated. Frenkel pair implantation is shown to cause higher effective diffusivity and more complex diffusion mechanisms than cascade implantation. The results of these simulations indicate that the differences in damage rates between implantation experiments and fission or fusion environments may result in differences in the final microstructure.

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology

PubMed Central

Gao, Fei; Li, Ye; Novak, Igor L.; Slepchenko, Boris M.

2016-01-01

Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations of reaction-diffusion systems are not widely available. Here we describe fundamentals of a general-purpose spatial hybrid method. The method generates realizations of a spatially inhomogeneous hybrid system by appropriately integrating capabilities of a deterministic partial differential equation solver with a popular particle-based stochastic simulator, Smoldyn. Rigorous validation of the algorithm is detailed, using a simple model of calcium ‘sparks’ as a testbed. The solver is then applied to a deterministic-stochastic model of spontaneous emergence of cell polarity. The approach is general enough to be implemented within biologist-friendly software frameworks such as Virtual Cell. PMID:27959915

SDSS-IV MaNGA: identification of active galactic nuclei in optical integral field unit surveys

NASA Astrophysics Data System (ADS)

Wylezalek, Dominika; Zakamska, Nadia L.; Greene, Jenny E.; Riffel, Rogemar A.; Drory, Niv; Andrews, Brett H.; Merloni, Andrea; Thomas, Daniel

2018-02-01

In this paper, we investigate 2727 galaxies observed by MaNGA as of 2016 June to develop spatially resolved techniques for identifying signatures of active galactic nuclei (AGNs). We identify 303 AGN candidates. The additional spatial dimension imposes challenges in identifying AGNs due to contamination from diffuse ionized gas, extraplanar gas and photoionization by hot stars. We show that the combination of spatially resolved line diagnostic diagrams and additional cuts on H α surface brightness and H α equivalent width can distinguish between AGN-like signatures and high-metallicity galaxies with low-ionization nuclear emission-line regions-like spectra. Low-mass galaxies with high specific star formation rates are particularly difficult to diagnose and routinely show diagnostic line ratios outside of the standard star formation locus. We develop a new diagnostic - the distance from the standard diagnostic line in the line-ratio space - to evaluate the significance of the deviation from the star formation locus. We find 173 galaxies that would not have been selected as AGN candidates based on single-fibre spectral measurements but exhibit photoionization signatures suggestive of AGN activity in the Mapping Nearby Galaxies at APO resolved observations, underscoring the power of large integral field unit surveys. A complete census of these new AGN candidates is necessary to understand their nature and probe the complex co-evolution of supermassive black holes and their hosts.

Explicit Global Simulation of Gravity Waves up to the Lower Thermosphere

NASA Astrophysics Data System (ADS)

Becker, E.

2016-12-01

At least for short-term simulations, middle atmosphere general circulation models (GCMs) can be run with sufficiently high resolution in order to describe a good part of the gravity wave spectrum explicitly. Nevertheless, the parameterization of unresolved dynamical scales remains an issue, especially when the scales of parameterized gravity waves (GWs) and resolved GWs become comparable. In addition, turbulent diffusion must always be parameterized along with other subgrid-scale dynamics. A practical solution to the combined closure problem for GWs and turbulent diffusion is to dispense with a parameterization of GWs, apply a high spatial resolution, and to represent the unresolved scales by a macro-turbulent diffusion scheme that gives rise to wave damping in a self-consistent fashion. This is the approach of a few GCMs that extend from the surface to the lower thermosphere and simulate a realistic GW drag and summer-to-winter-pole residual circulation in the upper mesosphere. In this study we describe a new version of the Kuehlungsborn Mechanistic general Circulation Model (KMCM), which includes explicit (though idealized) computations of radiative transfer and the tropospheric moisture cycle. Particular emphasis is spent on 1) the turbulent diffusion scheme, 2) the attenuation of resolved GWs at critical levels, 3) the generation of GWs in the middle atmosphere from body forces, and 4) GW-tidal interactions (including the energy deposition of GWs and tides).

Observation and modeling of interspecies ion separation in inertial confinement fusion implosions via imaging x-ray spectroscopy

DOE PAGES

Joshi, Tirtha Raj; Hakel, Peter; Hsu, Scott C.; ...

2017-03-22

In this article, we report the first direct experimental evidence of interspecies ion separation in direct-drive inertial confinement fusion experiments performed at the OMEGA laser facility via spectrally, temporally, and spatially resolved imaging x-ray-spectroscopy data [S. C. Hsu et al., Europhys. Lett. 115, 65001 (2016)]. These experiments were designed based on the expectation that interspecies ion thermo-diffusion would be the strongest for species with a large mass and charge difference. The targets were spherical plastic shells filled with D2 and a trace amount of Ar (0.1% or 1% by atom). Ar K-shell spectral features were observed primarily between the timemore » of first-shock convergence and slightly before the neutron bang time, using a time- and space-integrated spectrometer, a streaked crystal spectrometer, and two gated multi-monochromatic x-ray imagers fielded along quasi-orthogonal lines of sight. Detailed spectroscopic analyses of spatially resolved Ar K-shell lines reveal the deviation from the initial 1% Ar gas fill and show both Ar-concentration enhancement and depletion at different times and radial positions of the implosion. The experimental results are interpreted using radiation-hydrodynamic simulations that include recently implemented, first-principles models of interspecies ion diffusion. Lastly, the experimentally inferred Ar-atom fraction profiles agree reasonably with calculated profiles associated with the incoming and rebounding first shock.« less

Synchronous parallel spatially resolved stochastic cluster dynamics

DOE PAGES

Dunn, Aaron; Dingreville, Rémi; Martínez, Enrique; ...

2016-04-23

In this work, a spatially resolved stochastic cluster dynamics (SRSCD) model for radiation damage accumulation in metals is implemented using a synchronous parallel kinetic Monte Carlo algorithm. The parallel algorithm is shown to significantly increase the size of representative volumes achievable in SRSCD simulations of radiation damage accumulation. Additionally, weak scaling performance of the method is tested in two cases: (1) an idealized case of Frenkel pair diffusion and annihilation, and (2) a characteristic example problem including defect cluster formation and growth in α-Fe. For the latter case, weak scaling is tested using both Frenkel pair and displacement cascade damage.more » To improve scaling of simulations with cascade damage, an explicit cascade implantation scheme is developed for cases in which fast-moving defects are created in displacement cascades. For the first time, simulation of radiation damage accumulation in nanopolycrystals can be achieved with a three dimensional rendition of the microstructure, allowing demonstration of the effect of grain size on defect accumulation in Frenkel pair-irradiated α-Fe.« less

Opening the closed box: lattice diffusion in zircon?

NASA Astrophysics Data System (ADS)

Wheeler, J.; MacDonald, J.; Goodenough, K. M.; Crowley, Q.; Harley, S.; Mariani, E.

2015-12-01

In principle, any radiogenic parent or daughter element can diffuse through any crystalline lattice. Given improved analytic techniques and mathematical models, geochronology is beginning to take such diffusion into account in a quantitative fashion. Whilst lattice diffusion compromises simple interpretation of radiometric data, it can, when combined with spatially resolved data, provide more detailed insight into thermal histories. In regions that have experienced particularly high temperatures diffusion may become significant in minerals normally thought to be reliably closed. We have modelled Pb diffusion in zircon, building on earlier work on Ar diffusion in micas - the mathematics being basically the same. We are motivated by some challenging isotope data from zircon in the Lewisian Complex of NW Scotland (a TTG region with a long Archaean and Proterozoic history). For example we have grains with old rims and younger cores. Whilst other explanations are possible, we show how lattice diffusion of Pb is plausible, using experimental diffusion data together with estimates of ultra-high temperatures from the region. We have modified a previous model for Ar diffusion ("Diffarg") to include variations in parent isotope concentration, so we can understand the consequences of U zonation within zircon grains during prolonged thermal histories. This is also relevant to asking why Pb has apparently not diffused in zircon from other UHT regions - or has it?

Spatial distribution of defect luminescence in GaN nanowires.

PubMed

Li, Qiming; Wang, George T

2010-05-12

The spatial distribution of defect-related and band-edge luminescence from GaN nanowires grown by metal-organic chemical vapor deposition was studied by spatially resolved cathodoluminescence imaging and spectroscopy. A surface layer exhibiting strong yellow luminescence (YL) near 566 nm in the nanowires was revealed, compared to weak YL in the bulk. In contrast, other defect-related luminescence near 428 nm (blue luminescence) and 734 nm (red luminescence), in addition to band-edge luminescence (BEL) at 366 nm, were observed in the bulk of the nanowires but were largely absent at the surface. As the nanowire width approaches a critical dimension, the surface YL layer completely quenches the BEL. The surface YL is attributed to the diffusion and piling up of mobile point defects, likely isolated gallium vacancies, at the surface during growth.

Experimental and theoretical comparison of Sb, As, and P diffusion mechanisms and doping in CdTe

NASA Astrophysics Data System (ADS)

Colegrove, E.; Yang, J.-H.; Harvey, S. P.; Young, M. R.; Burst, J. M.; Duenow, J. N.; Albin, D. S.; Wei, S.-H.; Metzger, W. K.

2018-02-01

Fundamental material doping challenges have limited CdTe electro-optical applications. In this work, the As atomistic diffusion mechanisms in CdTe are examined by spatially resolving dopant incorporation in both single-crystalline and polycrystalline CdTe over a range of experimental conditions. Density-functional theory calculations predict experimental activation energies and indicate that As diffuses slowly through the Te sublattice and quickly along GBs similar to Sb. Because of its atomic size and associated defect chemistry, As does not have a fast interstitial diffusion component similar to P. Experiments to incorporate and activate P, As, and Sb in polycrystalline CdTe are conducted to examine if ex situ Group V doping can overcome historic polycrystalline doping limits. The distinct P, As, and Sb diffusion characteristics create different strategies for increasing hole density. Because fast interstitial diffusion is prominent for P, less aggressive diffusion conditions followed by Cd overpressure to relocate the Group V element to the Te lattice site is effective. For larger atoms, slower diffusion through the Te sublattice requires more aggressive diffusion, however further activation is not always necessary. Based on the new physical understanding, we have obtained greater than 1016 cm-3 hole density in polycrystalline CdTe films by As and P diffusion.

Experimental and theoretical comparison of Sb, As, and P diffusion mechanisms and doping in CdTe

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

Colegrove, E.; Yang, J-H; Harvey, S. P.

Fundamental material doping challenges have limited CdTe electro-optical applications. In this work, the As atomistic diffusion mechanisms in CdTe are examined by spatially resolving dopant incorporation in both single-crystalline and polycrystalline CdTe over a range of experimental conditions. Density-functional theory calculations predict experimental activation energies and indicate As diffuses slowly through the Te sublattice and quickly along GBs similar to Sb. Because of its atomic size and associated defect chemistry, As does not have a fast interstitial diffusion component similar to P. Experiments to incorporate and activate P, As, and Sb in polycrystalline CdTe are conducted to examine if ex-situmore » Group V doping can overcome historic polycrystalline doping limits. The distinct P, As, and Sb diffusion characteristics create different strategies for increasing hole density. Because fast interstitial diffusion is prominent for P, less aggressive diffusion conditions followed by Cd overpressure to relocate the Group V element to the Te lattice site is effective. For larger atoms, slower diffusion through the Te sublattice requires more aggressive diffusion, however further activation is not always necessary. Based on the new physical understanding, we have obtained greater than 10^16 cm^-3 hole density in polycrystalline CdTe films by As and P diffusion.« less

Experimental and theoretical comparison of Sb, As, and P diffusion mechanisms and doping in CdTe

DOE PAGES

Colegrove, E.; Yang, J-H; Harvey, S. P.; ...

2018-01-29

Fundamental material doping challenges have limited CdTe electro-optical applications. In this work, the As atomistic diffusion mechanisms in CdTe are examined by spatially resolving dopant incorporation in both single-crystalline and polycrystalline CdTe over a range of experimental conditions. Density-functional theory calculations predict experimental activation energies and indicate As diffuses slowly through the Te sublattice and quickly along GBs similar to Sb. Because of its atomic size and associated defect chemistry, As does not have a fast interstitial diffusion component similar to P. Experiments to incorporate and activate P, As, and Sb in polycrystalline CdTe are conducted to examine if ex-situmore » Group V doping can overcome historic polycrystalline doping limits. The distinct P, As, and Sb diffusion characteristics create different strategies for increasing hole density. Because fast interstitial diffusion is prominent for P, less aggressive diffusion conditions followed by Cd overpressure to relocate the Group V element to the Te lattice site is effective. For larger atoms, slower diffusion through the Te sublattice requires more aggressive diffusion, however further activation is not always necessary. Based on the new physical understanding, we have obtained greater than 10^16 cm^-3 hole density in polycrystalline CdTe films by As and P diffusion.« less

Resolving the Shell of the Superbubble 30 Doradus C with Chandra

NASA Astrophysics Data System (ADS)

Lopez, Laura

2017-09-01

We propose to observe the superbubble (SB) 30 Doradus C (30 Dor C) with ACIS-S for 100 ks to resolve and characterize the non-thermal shell, point sources, and the young supernova remnant (SNR) J0536 6913 at sub-arcsecond scales. 30 Dor C has been imaged off axis repeatedly by Chandra due to its proximity to SN 1987A, but the majority of the shell has only been observed <20 ks at off-axis distances of >10 arcminutes. The on-axis spatial resolution, sensitivity, and low background of ACIS-S are necessary to disentangle point sources from diffuse emission, to localize synchrotron filaments associated with accelerated electrons, and to investigate the SNR J0536 6913.

Divertor electron temperature and impurity diffusion measurements with a spectrally resolved imaging radiometer.

PubMed

Clayton, D J; Jaworski, M A; Kumar, D; Stutman, D; Finkenthal, M; Tritz, K

2012-10-01

A divertor imaging radiometer (DIR) diagnostic is being studied to measure spatially and spectrally resolved radiated power P(rad)(λ) in the tokamak divertor. A dual transmission grating design, with extreme ultraviolet (~20-200 Å) and vacuum ultraviolet (~200-2000 Å) gratings placed side-by-side, can produce coarse spectral resolution over a broad wavelength range covering emission from impurities over a wide temperature range. The DIR can thus be used to evaluate the separate P(rad) contributions from different ion species and charge states. Additionally, synthetic spectra from divertor simulations can be fit to P(rad)(λ) measurements, providing a powerful code validation tool that can also be used to estimate electron divertor temperature and impurity transport.

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

Naughton, M.J.; Bourke, W.; Browning, G.L.

The convergence of spectral model numerical solutions of the global shallow-water equations is examined as a function of the time step and the spectral truncation. The contributions to the errors due to the spatial and temporal discretizations are separately identified and compared. Numerical convergence experiments are performed with the inviscid equations from smooth (Rossby-Haurwitz wave) and observed (R45 atmospheric analysis) initial conditions, and also with the diffusive shallow-water equations. Results are compared with the forced inviscid shallow-water equations case studied by Browning et al. Reduction of the time discretization error by the removal of fast waves from the solution usingmore » initialization is shown. The effects of forcing and diffusion on the convergence are discussed. Time truncation errors are found to dominate when a feature is large scale and well resolved; spatial truncation errors dominate for small-scale features and also for large scale after the small scales have affected them. Possible implications of these results for global atmospheric modeling are discussed. 31 refs., 14 figs., 4 tabs.« less

Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface.

PubMed

Knodel, Markus M; Nägel, Arne; Reiter, Sebastian; Vogel, Andreas; Targett-Adams, Paul; McLauchlan, John; Herrmann, Eva; Wittum, Gabriel

2018-01-08

Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.

Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface

PubMed Central

Nägel, Arne; Reiter, Sebastian; Vogel, Andreas; McLauchlan, John; Herrmann, Eva; Wittum, Gabriel

2018-01-01

Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles. PMID:29316722

Resolving power for the diffusion orientation distribution function.

PubMed

Jensen, Jens H; Helpern, Joseph A

2016-08-01

The diffusion orientation distribution function (dODF) is primarily used for white matter fiber tractography. Here the resolving power of the dODF is investigated for a simple diffusion model of two intersecting axonal fiber bundles. The resolving power for the dODF is evaluated using the Sparrow criterion. This is determined for the exact dODF and also for q-space imaging (QSI), q-ball, and kurtosis approximations. Based on theoretical and numerical calculations, the resolving power is found to depend on the eigenvalues of the diffusion model and on the degree of radial weighting for the dODF. The resolving powers of the QSI and q-ball dODFs improve with increased b-value. The kurtosis dODF has a resolving power similar to that of the exact dODF. The dODFs, whether exact or approximate, have finite resolving powers that limit their sensitivity to fiber crossings. The resolving powers for the different dODFs considered here provide convenient benchmarks for assessing and comparing their performance. Magn Reson Med 76:679-688, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Local probing of ionic diffusion by electrochemical strain microscopy: Spatial resolution and signal formation mechanisms

NASA Astrophysics Data System (ADS)

Morozovska, A. N.; Eliseev, E. A.; Balke, N.; Kalinin, S. V.

2010-09-01

Electrochemical insertion-deintercalation reactions are typically associated with significant change in molar volume of the host compound. This strong coupling between ionic currents and strains underpins image formation mechanisms in electrochemical strain microscopy (ESM), and allows exploring the tip-induced electrochemical processes locally. Here we analyze the signal formation mechanism in ESM, and develop the analytical description of operation in frequency and time domains. The ESM spectroscopic modes are compared to classical electrochemical methods including potentiostatic and galvanostatic intermittent titration, and electrochemical impedance spectroscopy. This analysis illustrates the feasibility of spatially resolved studies of Li-ion dynamics on the sub-10-nm level using electromechanical detection.

Resolving Molecular Clouds in the Nearby Galaxy NGC 300

NASA Astrophysics Data System (ADS)

Faesi, Christopher; Lada, Charles J.; Forbrich, Jan

2015-01-01

We present results from our ongoing Submillimeter Array (SMA) survey in which we resolve Giant Molecular Clouds (GMCs) for the first time in the nearby (D = 1.9 Mpc) spiral galaxy NGC 300. We have conducted CO(2-1) and 1.3 mm dust continuum observations of several massive star-forming regions in NGC 300, following up on the Atacama Pathfinder Experiment (APEX) survey of Faesi et al. (2014). We find that the unresolved CO sources detected with APEX at ~250 pc resolution typically resolve into one dominant GMC in our SMA observations, which have a resolution of ~3.5' (30 pc). The majority of sources are significantly detected in CO, but only one exhibits dust continuum emission. Comparing with archival H-alpha, GALEX far-ultraviolet, and Spitzer 24 micron images, we note physical offsets between the young star clusters, warm dust, and ionized and molecular gas components in these regions. We recover a widely varying fraction -- between 30% and almost 100% -- of the full APEX single dish flux with our interferometric observations. This implies that the fraction of CO-emitting molecular gas that is in a diffuse state (i.e. with characteristic spatial scales > 100 pc) differs greatly amongst star forming regions in NGC 300. We investigate potential trends in the implied diffuse molecular gas fraction with GMC properties and star formation activity. We compute virial masses and analyze the velocity structure of these resolved extragalactic GMCs and compare to results from surveys of the Milky Way and other nearby galaxies.

Investigating the Eddy Diffusivity Concept in the Coastal Ocean

NASA Astrophysics Data System (ADS)

Rypina, I.; Kirincich, A.; Lentz, S. J.; Sundermeyer, M. A.

2016-12-01

We test the validity, utility, and limitations of the lateral eddy diffusivity concept in a coastal environment through analyzing data from coupled drifter and dye releases within the footprint of a high-resolution (800 m) high-frequency radar south of Martha's Vineyard, Massachusetts. Specifically, we investigate how well a combination of radar-based velocities and drifter-derived diffusivities can reproduce observed dye spreading over an 8-h time interval. A drifter-based estimate of an anisotropic diffusivity tensor is used to parameterize small-scale motions that are unresolved and under-resolved by the radar system. This leads to a significant improvement in the ability of the radar to reproduce the observed dye spreading. Our drifter-derived diffusivity estimates are O(10 m2/s), are consistent with the diffusivity inferred from aerial images of the dye taken using the quadcopter-mounted digital camera during the dye release, and are roughly an order of magnitude larger than diffusivity estimates of Okubo (O(1 m2/s)) for similar spatial scales ( 1 km). Despite the fact that the drifter-based diffusivity approach was successful in improving the ability of the radar to reproduce the observed dye spreading, the dispersion of drifters was, for the most part, not consistent with the diffusive spreading regime.

Subdiffusive exciton transport in quantum dot solids.

PubMed

Akselrod, Gleb M; Prins, Ferry; Poulikakos, Lisa V; Lee, Elizabeth M Y; Weidman, Mark C; Mork, A Jolene; Willard, Adam P; Bulović, Vladimir; Tisdale, William A

2014-06-11

Colloidal quantum dots (QDs) are promising materials for use in solar cells, light-emitting diodes, lasers, and photodetectors, but the mechanism and length of exciton transport in QD materials is not well understood. We use time-resolved optical microscopy to spatially visualize exciton transport in CdSe/ZnCdS core/shell QD assemblies. We find that the exciton diffusion length, which exceeds 30 nm in some cases, can be tuned by adjusting the inorganic shell thickness and organic ligand length, offering a powerful strategy for controlling exciton movement. Moreover, we show experimentally and through kinetic Monte Carlo simulations that exciton diffusion in QD solids does not occur by a random-walk process; instead, energetic disorder within the inhomogeneously broadened ensemble causes the exciton diffusivity to decrease over time. These findings reveal new insights into exciton dynamics in disordered systems and demonstrate the flexibility of QD materials for photonic and optoelectronic applications.

Why do veins appear blue? A new look at an old question

NASA Astrophysics Data System (ADS)

Kienle, Alwin; Hibst, Raimund; Steiner, Rudolf; Lilge, Lothar; Vitkin, I. Alex; Wilson, Brian C.; Patterson, Michael S.

1996-03-01

We investigate why vessels that contain blood, which has a red or a dark red color, may look bluish in human tissue. A CCD camera was used to make images of diffusely reflected light at different wavelengths. Measurements of reflectance that are due to model blood vessels in scattering media and of human skin containing a prominent vein are presented. Monte Carlo simulations were used to calculate the spatially resolved diffuse reflectance for both situations. We show that the color of blood vessels is scattering and absorption characteristics of skin at different wavelengths, (ii) the oxygenation state of blood, which affects its absorption properties, (iii) the diameter and the depth of the vessels, and (iv) the visual perception process.

Fast and Furious: Shock Heated Gas as the Origin of Spatially Resolved Hard X-Ray Emission in the Central 5 kpc of the Galaxy Merger NGC 6240

NASA Astrophysics Data System (ADS)

Wang, Junfeng; Nardini, Emanuele; Fabbiano, Giuseppina; Karovska, Margarita; Elvis, Martin; Pellegrini, Silvia; Max, Claire; Risaliti, Guido; U, Vivian; Zezas, Andreas

2014-01-01

We have obtained a deep, subarcsecond resolution X-ray image of the nuclear region of the luminous galaxy merger NGC 6240 with Chandra, which resolves the X-ray emission from the pair of active nuclei and the diffuse hot gas in great detail. We detect extended hard X-ray emission from kT ~ 6 keV (~70 MK) hot gas over a spatial scale of 5 kpc, indicating the presence of fast shocks with a velocity of ~2200 km s-1. For the first time, we obtain the spatial distribution of this highly ionized gas emitting Fe XXV, which shows a remarkable correspondence to the large-scale morphology of H2(1-0) S(1) line emission and Hα filaments. Propagation of fast shocks originating in the starburst-driven wind into the ambient dense gas can account for this morphological correspondence. With an observed L 0.5-8 keV = 5.3 × 1041 erg s-1, the diffuse hard X-ray emission is ~100 times more luminous than that observed in the classic starburst galaxy M82. Assuming a filling factor of 1% for the 70 MK temperature gas, we estimate its total mass (M hot = 1.8 × 108 M ⊙) and thermal energy (E th = 6.5 × 1057 erg). The total iron mass in the highly ionized plasma is M Fe = 4.6 × 105 M ⊙. Both the energetics and the iron mass in the hot gas are consistent with the expected injection from the supernovae explosion during the starburst that is commensurate with its high star formation rate. No evidence for fluorescent Fe I emission is found in the CO filament connecting the two nuclei.

NuSTAR Study of Hard X-ray Morphology and Spectroscopy G21.5-0.9

NASA Technical Reports Server (NTRS)

Nynka, Melania; Hailey, Charles J.; Reynolds, Stephen P.; An, Hongjun; Baganoff, Frederick K.; Boggs, Steven E.; Christensen, Finn E.; Craig, William W.; Gotthelf, Eric V.; Grefenstette, Brian W.;

k-space and q-space: combining ultra-high spatial and angular resolution in diffusion imaging using ZOOPPA at 7 T.

PubMed

Heidemann, Robin M; Anwander, Alfred; Feiweier, Thorsten; Knösche, Thomas R; Turner, Robert

2012-04-02

There is ongoing debate whether using a higher spatial resolution (sampling k-space) or a higher angular resolution (sampling q-space angles) is the better way to improve diffusion MRI (dMRI) based tractography results in living humans. In both cases, the limiting factor is the signal-to-noise ratio (SNR), due to the restricted acquisition time. One possible way to increase the spatial resolution without sacrificing either SNR or angular resolution is to move to a higher magnetic field strength. Nevertheless, dMRI has not been the preferred application for ultra-high field strength (7 T). This is because single-shot echo-planar imaging (EPI) has been the method of choice for human in vivo dMRI. EPI faces several challenges related to the use of a high resolution at high field strength, for example, distortions and image blurring. These problems can easily compromise the expected SNR gain with field strength. In the current study, we introduce an adapted EPI sequence in conjunction with a combination of ZOOmed imaging and Partially Parallel Acquisition (ZOOPPA). We demonstrate that the method can produce high quality diffusion-weighted images with high spatial and angular resolution at 7 T. We provide examples of in vivo human dMRI with isotropic resolutions of 1 mm and 800 μm. These data sets are particularly suitable for resolving complex and subtle fiber architectures, including fiber crossings in the white matter, anisotropy in the cortex and fibers entering the cortex. Copyright © 2011 Elsevier Inc. All rights reserved.

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

PubMed

Jastrzebska, M; Kocot, A

2004-06-01

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

Interferometric Near-Infrared Spectroscopy (iNIRS) for determination of optical and dynamical properties of turbid media

PubMed Central

Borycki, Dawid; Kholiqov, Oybek; Chong, Shau Poh; Srinivasan, Vivek J.

2016-01-01

We introduce and implement interferometric near-infrared spectroscopy (iNIRS), which simultaneously extracts optical and dynamical properties of turbid media through analysis of a spectral interference fringe pattern. The spectral interference fringe pattern is measured using a Mach-Zehnder interferometer with a frequency-swept narrow linewidth laser. Fourier analysis of the detected signal is used to determine time-of-flight (TOF)-resolved intensity, which is then analyzed over time to yield TOF-resolved intensity autocorrelations. This approach enables quantification of optical properties, which is not possible in conventional, continuous-wave near-infrared spectroscopy (NIRS). Furthermore, iNIRS quantifies scatterer motion based on TOF-resolved autocorrelations, which is a feature inaccessible by well-established diffuse correlation spectroscopy (DCS) techniques. We prove this by determining TOF-resolved intensity and temporal autocorrelations for light transmitted through diffusive fluid phantoms with optical thicknesses of up to 55 reduced mean free paths (approximately 120 scattering events). The TOF-resolved intensity is used to determine optical properties with time-resolved diffusion theory, while the TOF-resolved intensity autocorrelations are used to determine dynamics with diffusing wave spectroscopy. iNIRS advances the capabilities of diffuse optical methods and is suitable for in vivo tissue characterization. Moreover, iNIRS combines NIRS and DCS capabilities into a single modality. PMID:26832264

Tempo-spatially resolved scattering correlation spectroscopy under dark-field illumination and its application to investigate dynamic behaviors of gold nanoparticles in live cells.

PubMed

Liu, Heng; Dong, Chaoqing; Ren, Jicun

2014-02-19

In this study, a new tempo-spatially resolved fluctuation spectroscopy under dark-field illumination is described, named dark-field illumination-based scattering correlation spectroscopy (DFSCS). DFSCS is a single-particle method, whose principle is similar to that of fluorescence correlation spectroscopy (FCS). DFSCS correlates the fluctuations of the scattered light from single nanoparticle under dark-field illumination. We developed a theoretical model for translational diffusion of nanoparticles in DFSCS system. The results of computer simulations documented that this model was able to well describe the diffusion behaviors of nanoparticles in uniformly illuminated field. The experimental setup of DFSCS was achieved by introducing a dark-field condenser to the frequently used bright-field microscope and an electron multiplying charge-coupled device (EMCCD) as the array detector. In the optimal condition, a stack of 500 000 frames were collected simultaneously on 64 detection channels for a single measurement with acquisition rate of 0.5 ms per frame. We systematically investigated the effect of certain factors such as particle concentration, viscosity of the solution, and heterogeneity of gold nanoparticles (GNPs) samples on DFSCS measurements. The experiment data confirmed theoretical model proposed. Furthermore, this new method was successfully used for investigating dynamic behaviors of GNPs in live cells. Our preliminary results demonstrate that DFSCS is a practical and affordable tool for ordinary laboratories to investigate the dynamic information of nanoparticles in vitro as well as in vivo.

Spatially resolved bimodal spectroscopy for classification/evaluation of mouse skin inflammatory and pre-cancerous stages

NASA Astrophysics Data System (ADS)

Díaz-Ayil, Gilberto; Amouroux, Marine; Clanché, Fabien; Granjon, Yves; Blondel, Walter C. P. M.

2009-07-01

Spatially-resolved bimodal spectroscopy (multiple AutoFluorescence AF excitation and Diffuse Reflectance DR), was used in vivo to discriminate various healthy and precancerous skin stages in a pre-clinical model (UV-irradiated mouse): Compensatory Hyperplasia CH, Atypical Hyperplasia AH and Dysplasia D. A specific data preprocessing scheme was applied to intensity spectra (filtering, spectral correction and intensity normalization), and several sets of spectral characteristics were automatically extracted and selected based on their discrimination power, statistically tested for every pair-wise comparison of histological classes. Data reduction with Principal Components Analysis (PCA) was performed and 3 classification methods were implemented (k-NN, LDA and SVM), in order to compare diagnostic performance of each method. Diagnostic performance was studied and assessed in terms of Sensibility (Se) and Specificity (Sp) as a function of the selected features, of the combinations of 3 different inter-fibres distances and of the numbers of principal components, such that: Se and Sp ~ 100% when discriminating CH vs. others; Sp ~ 100% and Se > 95% when discriminating Healthy vs. AH or D; Sp ~ 74% and Se ~ 63% for AH vs. D.

Dielectric-barrier-discharge plasma-assisted hydrogen diffusion flame. Part 1: Temperature, oxygen, and fuel measurements by one-dimensional fs/ps rotational CARS imaging

DOE PAGES

Retter, Jonathan E.; Elliott, Gregory S.; Kearney, Sean P.

2018-02-21

One-dimensional hybrid fs/ps CARS imaging provides single-laser-shot measurements of temperature, oxygen, and hydrogen in a plasma-assisted hydrogen diffusion flame. The coaxial dielectric-barrier-discharge burner collapses the Re ~50 hydrogen diffusion flame to within ~5 mm of the burner surface at an applied AC potential of 8.75 kV at 18 kHz, coinciding nicely with the full spatial extent of the 1D CARS measurements. Translating the burner through the measurement volume allowed for measurements at numerous radial locations in increments of 1 mm with a resolution of 140 µm × 30 µm × 600 µm, sufficient to resolve spatial gradients in this unsteadymore » flame. Longer probe delays, required for improved dynamic range in regions of high temperature fluctuations, proved difficult to model as a result of a nontrivial decay in the O 2 Raman coherence arising from complexities associated with the triplet ground electronic state of the O 2 molecule. Oxygen linewidths were treated empirically using the observed O 2 coherence decay in spectra acquired from the product gases of lean, near-adiabatic H 2/air flames stabilized on a Hencken flat-flame burner. While still leading to errors up to 10% at worst, the empirically determined Raman linewidth factors eliminated any systematic error in the O 2/N 2 measurements with probe delay. Temperature measurements in the Hencken Burner flames proved to be insensitive to probe pulse delay, providing robust thermometry. Here, demonstration of this technique in both the canonical Hencken burner flames and a new DBD burner validates its effectiveness in producing multiple spatially resolved measurements in combustion environments. Measurements in the DBD burner revealed an unsteady, counterflow flattened flame structure near the fuel orifice which became unsteady as the reaction zone curves towards the surface for larger radial positions. Lastly, fluctuations in the fuel concentration were largest at the source, as the large, plasma-generated, unsteady external toroidal vortex that dominates the transport in this flame provides enhanced ventilation of the flame surface in close proximity to the fuel tube.« less

Dielectric-barrier-discharge plasma-assisted hydrogen diffusion flame. Part 1: Temperature, oxygen, and fuel measurements by one-dimensional fs/ps rotational CARS imaging

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

Retter, Jonathan E.; Elliott, Gregory S.; Kearney, Sean P.

One-dimensional hybrid fs/ps CARS imaging provides single-laser-shot measurements of temperature, oxygen, and hydrogen in a plasma-assisted hydrogen diffusion flame. The coaxial dielectric-barrier-discharge burner collapses the Re ~50 hydrogen diffusion flame to within ~5 mm of the burner surface at an applied AC potential of 8.75 kV at 18 kHz, coinciding nicely with the full spatial extent of the 1D CARS measurements. Translating the burner through the measurement volume allowed for measurements at numerous radial locations in increments of 1 mm with a resolution of 140 µm × 30 µm × 600 µm, sufficient to resolve spatial gradients in this unsteadymore » flame. Longer probe delays, required for improved dynamic range in regions of high temperature fluctuations, proved difficult to model as a result of a nontrivial decay in the O 2 Raman coherence arising from complexities associated with the triplet ground electronic state of the O 2 molecule. Oxygen linewidths were treated empirically using the observed O 2 coherence decay in spectra acquired from the product gases of lean, near-adiabatic H 2/air flames stabilized on a Hencken flat-flame burner. While still leading to errors up to 10% at worst, the empirically determined Raman linewidth factors eliminated any systematic error in the O 2/N 2 measurements with probe delay. Temperature measurements in the Hencken Burner flames proved to be insensitive to probe pulse delay, providing robust thermometry. Here, demonstration of this technique in both the canonical Hencken burner flames and a new DBD burner validates its effectiveness in producing multiple spatially resolved measurements in combustion environments. Measurements in the DBD burner revealed an unsteady, counterflow flattened flame structure near the fuel orifice which became unsteady as the reaction zone curves towards the surface for larger radial positions. Lastly, fluctuations in the fuel concentration were largest at the source, as the large, plasma-generated, unsteady external toroidal vortex that dominates the transport in this flame provides enhanced ventilation of the flame surface in close proximity to the fuel tube.« less

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

PubMed

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

2008-10-01

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

Hyperspectral imaging-based spatially-resolved technique for accurate measurement of the optical properties of horticultural products

NASA Astrophysics Data System (ADS)

Cen, Haiyan

Hyperspectral imaging-based spatially-resolved technique is promising for determining the optical properties and quality attributes of horticultural and food products. However, considerable challenges still exist for accurate determination of spectral absorption and scattering properties from intact horticultural products. The objective of this research was, therefore, to develop and optimize hyperspectral imaging-based spatially-resolved technique for accurate measurement of the optical properties of horticultural products. Monte Carlo simulations and experiments for model samples of known optical properties were performed to optimize the inverse algorithm of a single-layer diffusion model and the optical designs, for extracting the absorption (micro a) and reduced scattering (micros') coefficients from spatially-resolved reflectance profiles. The logarithm and integral data transformation and the relative weighting methods were found to greatly improve the parameter estimation accuracy with the relative errors of 10.4%, 10.7%, and 11.4% for micro a, and 6.6%, 7.0%, and 7.1% for micros', respectively. More accurate measurements of optical properties were obtained when the light beam was of Gaussian type with the diameter of less than 1 mm, and the minimum and maximum source-detector distances were 1.5 mm and 10--20 transport mean free paths, respectively. An optical property measuring prototype was built, based on the optimization results, and evaluated for automatic measurement of absorption and reduced scattering coefficients for the wavelengths of 500--1,000 nm. The instrument was used to measure the optical properties, and assess quality/maturity, of 500 'Redstar' peaches and 1039 'Golden Delicious' (GD) and 1040 'Delicious' (RD) apples. A separate study was also conducted on confocal laser scanning and scanning electron microscopic image analysis and compression test of fruit tissue specimens to measure the structural and mechanical properties of 'Golden Delicious' and 'Granny Smith' (GS) apples under accelerated softening at high temperature (22 ºC)/high humidity (95%) for up to 30 days. The absorption spectra of peach and apple fruit were featured with the absorption peaks of major pigments (i.e., chlorophylls and anthocyanin) and water, while the reduced scattering coefficient generally decreased with the increase of wavelength. Partial least squares regression resulted in various levels of correlation of microa and micros' with the firmness, soluble solids content, and skin and flesh color parameters of peaches (r = 0.204--0.855) and apples (r = 0.460--0.885), and the combination of the two optical parameters generally gave higher correlations (up to 0.893). The mean value of microa and micros' for GD and GS apples for each storage date was positively correlated with acoustic/impact firmness, Young's modulus, and cell parameters (r = 0.585--0.948 for GD and r = 0.292--0.993 for GS). A two-layer diffusion model for determining the optical properties of fruit skin and flesh was further investigated through solid model samples. The average errors of determining two and four optical parameters were 6.8% and 15.3%, respectively, for the Monte Carlo reflectance data. The errors of determining the first or surface layer of the model samples were approximately 23.0% for microa and 18.4% for micros', indicating the difficulty and also potential in applying the two-layer diffusion model for fruit. This research has demonstrated the usefulness of hyperspectral imaging-based spatially-resolved technique for determining the optical properties and maturity/quality of fruits. However, further research is needed to reduce measurement variability or error caused by irregular or rough surface of fruit and the presence of fruit skin, and apply the technique to other foods and biological materials.

Quantifying the Precipitation Loss of Radiation Belt Electrons during a Rapid Dropout Event

NASA Astrophysics Data System (ADS)

Pham, K. H.; Tu, W.; Xiang, Z.

2017-12-01

Relativistic electron flux in the radiation belt can drop by orders of magnitude within the timespan of hours. In this study, we used the drift-diffusion model that includes azimuthal drift and pitch angle diffusion of electrons to simulate low-altitude electron distribution observed by POES/MetOp satellites for rapid radiation belt electron dropout event occurring on May 1, 2013. The event shows fast dropout of MeV energy electrons at L>4 over a few hours, observed by the Van Allen Probes mission. By simulating the electron distributions observed by multiple POES satellites, we resolve the precipitation loss with both high spatial and temporal resolution and a range of energies. We estimate the pitch angle diffusion coefficients as a function of energy, pitch angle, and L-shell, and calculate corresponding electron lifetimes during the event. The simulation results show fast electron precipitation loss at L>4 during the electron dropout, with estimated electron lifetimes on the order of half an hour for MeV energies. The electron loss rate show strong energy dependence with faster loss at higher energies, which suggest that this dropout event is dominated by quick and localized scattering process that prefers higher energy electrons. The estimated pitch angle diffusion rates from the model are then compared with in situ wave measurements from Van Allen Probes to uncover the underlying wave-particle-interaction mechanisms that are responsible for the fast electron precipitation. Comparing the resolved precipitation loss with the observed electron dropouts at high altitudes, our results will suggest the relative role of electron precipitation loss and outward radial diffusion to the radiation belt dropouts during storm and non-storm times, in addition to its energy and L dependence.

Eight-channel time-resolved tissue oximeter for functional muscle studies

NASA Astrophysics Data System (ADS)

Cubeddu, Rinaldo; Biscotti, Giovanni; Pifferi, Antonio; Taroni, Paola; Torricelli, Alessandro; Ferrari, Marco; Quaresima, Valentina

2003-07-01

A portable instrument for tissue oximetry based on time-resolved reflectance spectroscopy was developed. The output pulses of 2 laser diodes (683 and 785 nm, 80 MHz pulse repetition rate, 1 mW average power, 100 ps FWHM) are delayed and coupled into a multimode graded-index fiber (50/125 μm and injected into the tissue. The reflectance photons are collected by 8 independent 1 mm fibers and detected by a 16-anode photomultiplier. A time-correlated single photon counting PC board is used for the parallel acquisition of the curves. Simultaneous estimate of the transport scattering and absorption coefficients is achieved by best fitting of time-resolved reflectance curves with a standard model of Diffusion Theory. The performances of the system were tested on phantoms in terms of stability, reproducibility among channels, and accuracy in the determination of the optical properties. Preliminary in vivo measurements were performed on healthy volunteers to monitor spatial changes in calf (medical and lateral gastrocnemius) oxygen hemoglobin saturation and blood volume during dynamic plantar flexion exercise.

Near-field transport imaging applied to photovoltaic materials

DOE PAGES

Xiao, Chuanxiao; Jiang, Chun -Sheng; Moseley, John; ...

2017-05-26

We developed and applied a new analytical technique - near-field transport imaging (NF-TI or simply TI) - to photovoltaic materials. Charge-carrier transport is an important factor in solar cell performance, and TI is an innovative approach that integrates a scanning electron microscope with a near-field scanning optical microscope, providing the possibility to study luminescence associated with recombination and transport with high spatial resolution. In this paper, we describe in detail the technical barriers we had to overcome to develop the technique for routine application and the data-fitting procedure used to calculate minority-carrier diffusion length values. The diffusion length measured bymore » TI agrees well with the results calculated by time-resolved photoluminescence on well-controlled gallium arsenide (GaAs) thin-film samples. We report for the first time on measurements on thin-film cadmium telluride using this technique, including the determination of effective carrier diffusion length, as well as the first near-field imaging of the effect of a single localized defect on carrier transport and recombination in a GaAs heterostructure. Furthermore, by changing the scanning setup, we were able to demonstrate near-field cathodoluminescence (CL), and correlated the results with standard CL measurements. In conclusion, the TI technique shows great potential for mapping transport properties in solar cell materials with high spatial resolution.« less

Diffusion in biofilms respiring on electrodes

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

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

2012-11-15

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

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

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

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

2016-01-07

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

A priori analysis of differential diffusion for model development for scale-resolving simulations

NASA Astrophysics Data System (ADS)

Hunger, Franziska; Dietzsch, Felix; Gauding, Michael; Hasse, Christian

2018-01-01

The present study analyzes differential diffusion and the mechanisms responsible for it with regard to the turbulent/nonturbulent interface (TNTI) with special focus on model development for scale-resolving simulations. In order to analyze differences between resolved and subfilter phenomena, direct numerical simulation (DNS) data are compared with explicitly filtered data. The DNS database stems from a temporally evolving turbulent plane jet transporting two passive scalars with Schmidt numbers of unity and 0.25 presented by Hunger et al. [F. Hunger et al., J. Fluid Mech. 802, R5 (2016), 10.1017/jfm.2016.471]. The objective of this research is twofold: (i) to compare the position of the turbulent-nonturbulent interface between the original DNS data and the filtered data and (ii) to analyze differential diffusion and the impact of the TNTI with regard to scale resolution in the filtered DNS data. For the latter, differential diffusion quantities are studied, clearly showing the decrease of differential diffusion at the resolved scales with increasing filter width. A transport equation for the scalar differences is evaluated. Finally, the existence of large scalar gradients, gradient alignment, and the diffusive fluxes being the physical mechanisms responsible for the separation of the two scalars are compared between the resolved and subfilter scales.

Molecular binoculars: how to spatially resolve environmental fluctuations by following two or more single-molecule spectral trails at a time.

PubMed

Lubchenko, Vassiliy; Silbey, Robert J

2013-10-24

We propose a novel type of spectral diffusion experiment that enables one to decouple spatial characteristics of the environmental fluctuations, such as their concentration, from the interaction with the chromophore. Traditional hole broadening experiments do not allow for such decoupling in the common case when the chromophore-environment interaction is scale invariant. Here we propose to simultaneously follow the spectral trails of a small number of nearby chromophores--two or more--which thereby sense a highly overlapping set of the fluctuations. To this end, we estimate the combined probability distribution for the frequencies of a set of chromophores contained within the same sample. The present setup introduces a new length scale, i.e., the interchromophore distance, which breaks the aforementioned scale invariance and enables one to determine independently the concentration of the environmental fluctuations and their coupling to the chromophores, by monitoring the time after which spectral diffusion of distinct chromophores becomes uncorrelated. We illustrate these results with structural excitations in low temperature glasses.

Laser-Induced Incandescence Measurements in Low Gravity

NASA Technical Reports Server (NTRS)

VanderWal, R. L.

1997-01-01

A low-gravity environment offers advantages to investigations concerned with soot growth or flame radiation by eliminating of buoyancy-induced convection. Basic to each type of study is knowledge of spatially resolved soot volume fraction, (f(sub v). Laser-induced incandescence (LII) has emerged as a diagnostic for soot volume fraction determination because it possesses high temporal and spatial resolution, geometric versatility and high sensitivity. Implementation and system characterization of LII in a drop tower that provides 2.2 sec of low-gravity (micro)g) at the NASA Lewis Research Center are described here. Validation of LII for soot volume fraction determination in (micro)g is performed by comparison between soot volume fraction measurements obtained by light extinction [20] and LII in low-gravity for a 50/50 mixture (by volume) of 0 acetylene/nitrogen issuing into quiescent air. Quantitative soot volume fraction measurements within other laminar flames of ethane and propane and a turbulent diffusion flame in (micro)g via LII are also demonstrated. An analysis of LII images of a turbulent acetylene diffusion flame in 1-g and (micro)g is presented.

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

PubMed Central

2011-01-01

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

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

PubMed

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

2011-05-01

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

Monitoring and Manipulating Motions of Single Molecules/Nanoparticles

NASA Astrophysics Data System (ADS)

Chen, Fang

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

Dynamical response of the summer MLT to tropospheric global warming: Results from a mechanistic GCM with resolved gravity waves

NASA Astrophysics Data System (ADS)

Becker, E.

2009-04-01

The sensitivity of the mesosphere and lower thermosphere (MLT) to climate variability of the troposphere is largely controlled by the generation, propagation, and dissipation of gravity waves (GWs). Conventional climate models cannot fully describe this sensitivity since GWs must be parameterized by invoking strong assumptions. Since the Eliassen-Palm flux (EPF) of low-frequency inertia GWs is negligible, the main contribution to the EPF divergence at high latitudes of the MLT is due to mid- and high-frequency GWs with periods of a few hours or less. In order to resolve at least a good portion of these waves in a GCM, a high spatial resolution from the boundary layer to the lower thermosphere is required. Furthermore, both the generation and dissipation of resolved GWs is expected to depend strongly on the details of the parameterization of turbulence. The present study proposes a new formulation of the Kuehlungsborn mechanistic general circulation model (KMCM) with high spatial resolution and Smagorinsky-type horizontal and vertical diffusion coefficients that are both scaled by the Richardson criterion. This model version allows for an explicit and self-consistent simulation of the gravity-wave drag in the MLT. A sensitivity experiment is conducted in which the main changes associated with tropospheric global warming are imposed by the differential heating, i.e., reduced static stability in the lower troposphere along with a reduced equator-to-pole temperature difference and enhanced latent heating in the intertropical convergence zone. These changes result in both a stronger Lorenz energy cycle and enhanced gravity-wave activity in the upper troposphere at middle latitudes. The altered gravity-wave sources result in the following remote effects in the summer MLT: downward shift of the residual circulation, as well as lower temperatures and reduced easterlies below the mesopause. These changes are consistent with enhanced turbulent diffusion and dissipation below the mesopause due to larger gravity-wave amplitudes.

OT1_tvelusam_2: HIFI studies of the small-scale structures in the Galactic diffuse clouds with [CII] and [CI

NASA Astrophysics Data System (ADS)

Velusamy, T.

2010-07-01

The 1.9 THz [CII] observations provide a powerful probe of warm diffuse clouds, because they can observe them in emission and are useful as a tracer of their molecular H2 not directly traced by CO or other means. HIFI observations of [CII] provide a high resolution of 12 arcsec, better than that for single dish CO (> 30 arcsec) maps, and much better than HI (>30 arcsec). Thus with HIFI we have an opportunity probe the small scale structures in diffuse clouds in the inner Galaxy at distances > 3 kpc. To study the structure of diffuse ISM gas at small scales we propose HIFI maps of 1.9 THz (158 micron) [CII] line emission in a selection of 16 lines of sight (LOSs) towards the inner Galaxy, which are also being observed as part of the GOT C+ survey of [CII] in the Galactic plane. GOT C+ provides mainly single point spectra without any spatial data. Maps of [CII] will constrain better the cloud properties and models when combining [CII] and HI data. The proposed OTF X map will be along the longitude and latitude centered on 18 selected GOT C+ LOS over a length of 3 arcmin in each direction, which is adequate enough to provide sufficient spatial information on the small scale structures at larger distances (>3 kpc) and to characterize the CII filling factor in the larger beams of the ancillary (HI, CO, and CI data). The [CI] 609 & 370micron and the 12CO(7-6) (which lies within the CI band) are excellent diagnostics of the physical conditions of transition clouds and PDRs. We will use the ratio of the [CI] lines to constrain the kinetic temperature and volume density of the CII/CI/CO transition zones in molecular clouds using radiative transfer codes. We also propose OTF X maps in both the [CI] lines for all CII target LOSs. We anticipate fully resolved structural data in [CII] on at least 300 velocity resolved clouds along with their [CI] emissions. We request a total of 33.2 hrs of HIFI observing time.

Advanced nodal neutron diffusion method with space-dependent cross sections: ILLICO-VX

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

Rajic, H.L.; Ougouag, A.M.

1987-01-01

Advanced transverse integrated nodal methods for neutron diffusion developed since the 1970s require that node- or assembly-homogenized cross sections be known. The underlying structural heterogeneity can be accurately accounted for in homogenization procedures by the use of heterogeneity or discontinuity factors. Other (milder) types of heterogeneity, burnup-induced or due to thermal-hydraulic feedback, can be resolved by explicitly accounting for the spatial variations of material properties. This can be done during the nodal computations via nonlinear iterations. The new method has been implemented in the code ILLICO-VX (ILLICO variable cross-section method). Numerous numerical tests were performed. As expected, the convergence ratemore » of ILLICO-VX is lower than that of ILLICO, requiring approx. 30% more outer iterations per k/sub eff/ computation. The methodology has also been implemented as the NOMAD-VX option of the NOMAD, multicycle, multigroup, two- and three-dimensional nodal diffusion depletion code. The burnup-induced heterogeneities (space dependence of cross sections) are calculated during the burnup steps.« less

Imaging Spatial Variations in the Dissipation and Transport of Thermal Energy within Individual Silicon Nanowires Using Ultrafast Microscopy.

PubMed

Cating, Emma E M; Pinion, Christopher W; Van Goethem, Erika M; Gabriel, Michelle M; Cahoon, James F; Papanikolas, John M

2016-01-13

Thermal management is an important consideration for most nanoelectronic devices, and an understanding of the thermal conductivity of individual device components is critical for the design of thermally efficient systems. However, it can be difficult to directly probe local changes in thermal conductivity within a nanoscale system. Here, we utilize the time-resolved and diffraction-limited imaging capabilities of ultrafast pump-probe microscopy to determine, in a contact-free configuration, the local thermal conductivity in individual Si nanowires (NWs). By suspending single NWs across microfabricated trenches in a quartz substrate, the properties of the same NW both on and off the substrate are directly compared. We find the substrate has no effect on the recombination lifetime or diffusion length of photogenerated charge carriers; however, it significantly impacts the thermal relaxation properties of the NW. In substrate-supported regions, thermal energy deposited into the lattice by the ultrafast laser pulse dissipates within ∼10 ns through thermal diffusion and coupling to the substrate. In suspended regions, the thermal energy persists for over 100 ns, and we directly image the time-resolved spatial motion of the thermal signal. Quantitative analysis of the transient images permits direct determination of the NW's local thermal conductivity, which we find to be a factor of ∼4 smaller than in bulk Si. Our results point to the strong potential of pump-probe microscopy to be used as an all-optical method to quantify the effects of localized environment and morphology on the thermal transport characteristics of individual nanostructured components.

Applications of nonlinear science and kinetic equations to the spread of epidemics

NASA Astrophysics Data System (ADS)

Macinnis, David Robert

The study of the spread of epidemics is currently growing into a successful subfield of a combination of nonlinear science and statistical mechanics. Topics studied in this field include kinetic and mean field levels of epidemiological models. This thesis consists of the analysis of such topics and specifically directed at the Hantavirus, West Nile virus, and the Bubonic Plague. A successful reaction-diffusion equation approach developed recently by Abramson and Kenkre was able to describe spatiotemporal patterns of the Hantavirus model. From measurements of the parameters of their model it was found that the mice, the carriers of the infection, must be regarded as moving diffusively within attractive potentials representative of home ranges. Several attempts have been made to incorporate home ranges into their model. Two of these attempts are discussed within this thesis. A model to explain the transmission of the West Nile virus within bird and mosquito populations was recently developed by Kenkre, Parmenter, Peixoto, and Sadasiv who showed how spatially resolved issues could be discussed but restricted their analysis to mean field considerations. This thesis extends that study by investigating spatial resolution of the infected populations. Traveling waves of the bird and mosquito populations are found in the West Nile context. Infection control of various epidemics has become increasingly important to limit the potential force of infection into the human population. This thesis contains a quantitative attempt at a theory of such control (for the West Nile virus) via spraying of the mosquito population. Mean field and kinetic level models are proposed in this thesis to describe the transmission of the Bubonic Plague which involves flea and mammal populations. The various populations are found to undergo a variety of bifurcations as well as hysteresis in their steady state regime. Spatially resolved analysis of the populations is also presented.

Prediction of nonlinear evolution character of energetic-particle-driven instabilities

DOE PAGES

Duarte, Vinicius N.; Berk, H. L.; Gorelenkov, N. N.; ...

2017-03-17

A general criterion is proposed and found to successfully predict the emergence of chirping oscillations of unstable Alfvénic eigenmodes in tokamak plasma experiments. The model includes realistic eigenfunction structure, detailed phase-space dependences of the instability drive, stochastic scattering and the Coulomb drag. The stochastic scattering combines the effects of collisional pitch angle scattering and micro-turbulence spatial diffusion. Furthermore, the latter mechanism is essential to accurately identify the transition between the fixed-frequency mode behavior and rapid chirping in tokamaks and to resolve the disparity with respect to chirping observation in spherical and conventional tokamaks.

Prediction of nonlinear evolution character of energetic-particle-driven instabilities

NASA Astrophysics Data System (ADS)

Duarte, V. N.; Berk, H. L.; Gorelenkov, N. N.; Heidbrink, W. W.; Kramer, G. J.; Nazikian, R.; Pace, D. C.; Podestà, M.; Tobias, B. J.; Van Zeeland, M. A.

2017-05-01

A general criterion is proposed and found to successfully predict the emergence of chirping oscillations of unstable Alfvénic eigenmodes in tokamak plasma experiments. The model includes realistic eigenfunction structure, detailed phase-space dependences of the instability drive, stochastic scattering and the Coulomb drag. The stochastic scattering combines the effects of collisional pitch angle scattering and micro-turbulence spatial diffusion. The latter mechanism is essential to accurately identify the transition between the fixed-frequency mode behavior and rapid chirping in tokamaks and to resolve the disparity with respect to chirping observation in spherical and conventional tokamaks.

Electrochemical wall shear rate microscopy of collapsing bubbles

NASA Astrophysics Data System (ADS)

Reuter, Fabian; Mettin, Robert

2018-06-01

An electrochemical high-speed wall shear raster microscope is presented. It involves chronoamperometric measurements on a microelectrode that is flush-mounted in a submerged test specimen. Wall shear rates are derived from the measured microelectrode signal by numerically solving a convection-diffusion equation with an optimization approach. This way, the unsteady wall shear rates from the collapse of a laser pulse seeded cavitation bubble close to a substrate are measured. By planar scanning, they are resolved in high spatial resolution. The wall shear rates are related to the bubble dynamics via synchronized high-speed imaging of the bubble shape.

Spatially-resolved probing of biological phantoms by point-radiance spectroscopy

NASA Astrophysics Data System (ADS)

Grabtchak, Serge; Palmer, Tyler J.; Whelan, William M.

2011-03-01

Interstitial fiber-optic based strategies for therapy monitoring and assessment rely on detecting treatment-induced changes in the light distribution in biological tissues. We present an optical technique to identify spectrally and spatially specific tissue chromophores in highly scattering turbid media. Typical optical sensors measure non-directional light intensity (i.e. fluence) and require fiber translation (i.e. 3-5 positions), which is difficult to implement clinically. Point radiance spectroscopy is based on directional light collection (i.e. radiance) at a single point with a side-firing fiber that can be rotated up to 360°. A side firing fiber accepts light within a well-defined solid angle thus potentially providing an improved spatial resolution. Experimental measurements were performed using an 800-μm diameter isotropic spherical diffuser coupled to a halogen light source and a 600 μm, ~43° cleaved fiber (i.e. radiance detector). The background liquid-based scattering phantom was fabricated using 1% Intralipid (i.e. scattering medium). Light was collected at 1-5° increments through 360°-segment. Gold nanoparticles, placed into a 3.5 mm diameter capillary tube were used as localized scatterers and absorbers introduced into the liquid phantom both on- and off-axis between source and detector. The localized optical inhomogeneity was detectable as an angular-resolved variation in the radiance polar plots. This technique is being investigated as a non-invasive optical modality for prostate cancer monitoring.

Mesoscopic structural phase progression in photo-excited VO 2 revealed by time-resolved x-ray diffraction microscopy

DOE PAGES

Zhu, Yi; Cai, Zhonghou; Chen, Pice; ...

2016-02-26

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase seperated regions. The ability to simultanousely track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of- the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO 2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation ismore » initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO 2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, which is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO 2. Lastly, the direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.« less

Mesoscopic structural phase progression in photo-excited VO2 revealed by time-resolved x-ray diffraction microscopy

NASA Astrophysics Data System (ADS)

Zhu, Yi; Cai, Zhonghou; Chen, Pice; Zhang, Qingteng; Highland, Matthew J.; Jung, Il Woong; Walko, Donald A.; Dufresne, Eric M.; Jeong, Jaewoo; Samant, Mahesh G.; Parkin, Stuart S. P.; Freeland, John W.; Evans, Paul G.; Wen, Haidan

2016-02-01

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase separated regions. The ability to simultaneously track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of-the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation is initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, and is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO2. The direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.

Mesoscopic structural phase progression in photo-excited VO2 revealed by time-resolved x-ray diffraction microscopy.

PubMed

Zhu, Yi; Cai, Zhonghou; Chen, Pice; Zhang, Qingteng; Highland, Matthew J; Jung, Il Woong; Walko, Donald A; Dufresne, Eric M; Jeong, Jaewoo; Samant, Mahesh G; Parkin, Stuart S P; Freeland, John W; Evans, Paul G; Wen, Haidan

2016-02-26

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase separated regions. The ability to simultaneously track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of-the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation is initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, and is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO2. The direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.

Redox-dependent spatially resolved electrochemistry at graphene and graphite step edges.

PubMed

Güell, Aleix G; Cuharuc, Anatolii S; Kim, Yang-Rae; Zhang, Guohui; Tan, Sze-yin; Ebejer, Neil; Unwin, Patrick R

2015-04-28

The electrochemical (EC) behavior of mechanically exfoliated graphene and highly oriented pyrolytic graphite (HOPG) is studied at high spatial resolution in aqueous solutions using Ru(NH3)6(3+/2+) as a redox probe whose standard potential sits close to the intrinsic Fermi level of graphene and graphite. When scanning electrochemical cell microscopy (SECCM) data are coupled with that from complementary techniques (AFM, micro-Raman) applied to the same sample area, different time-dependent EC activity between the basal planes and step edges is revealed. In contrast, other redox couples (ferrocene derivatives) whose potential is further removed from the intrinsic Fermi level of graphene and graphite show uniform and high activity (close to diffusion-control). Macroscopic voltammetric measurements in different environments reveal that the time-dependent behavior after HOPG cleavage, peculiar to Ru(NH3)6(3+/2+), is not associated particularly with any surface contaminants but is reasonably attributed to the spontaneous delamination of the HOPG with time to create partially coupled graphene layers, further supported by conductive AFM measurements. This process has a major impact on the density of states of graphene and graphite edges, particularly at the intrinsic Fermi level to which Ru(NH3)6(3+/2+) is most sensitive. Through the use of an improved voltammetric mode of SECCM, we produce movies of potential-resolved and spatially resolved HOPG activity, revealing how enhanced activity at step edges is a subtle effect for Ru(NH3)6(3+/2+). These latter studies allow us to propose a microscopic model to interpret the EC response of graphene (basal plane and edges) and aged HOPG considering the nontrivial electronic band structure.

Spatially modulated ephrinA1:EphA2 signaling increases local contractility and global focal adhesion dynamics to promote cell motility.

PubMed

Chen, Zhongwen; Oh, Dongmyung; Biswas, Kabir H; Yu, Cheng-Han; Zaidel-Bar, Ronen; Groves, Jay T

2018-06-19

Recent studies have revealed pronounced effects of the spatial distribution of EphA2 receptors on cellular response to receptor activation. However, little is known about molecular mechanisms underlying this spatial sensitivity, in part due to lack of experimental systems. Here, we introduce a hybrid live-cell patterned supported lipid bilayer experimental platform in which the sites of EphA2 activation and integrin adhesion are spatially controlled. Using a series of live-cell imaging and single-molecule tracking experiments, we map the transmission of signals from ephrinA1:EphA2 complexes. Results show that ligand-dependent EphA2 activation induces localized myosin-dependent contractions while simultaneously increasing focal adhesion dynamics throughout the cell. Mechanistically, Src kinase is activated at sites of ephrinA1:EphA2 clustering and subsequently diffuses on the membrane to focal adhesions, where it up-regulates FAK and paxillin tyrosine phosphorylation. EphrinA1:EphA2 signaling triggers multiple cellular responses with differing spatial dependencies to enable a directed migratory response to spatially resolved contact with ephrinA1 ligands.

Tunable Reflective Spatial Heterodyne Spectrometer: A Technique for High Resolving Power, Wide Field Of View Observation Of Diffuse Emission Line Sources

NASA Astrophysics Data System (ADS)

Hosseini, Seyedeh Sona

The purpose of this dissertation is to discuss the need for new technology in broadband high-resolution spectroscopy based on the emerging technique of Spatial Heterodyne Spectroscopy (SHS) and to propose new solutions that should enhance and generalize this technology to other fields. Spectroscopy is a proven tool for determining compositional and other properties of remote objects. Narrow band imaging and low resolving spectroscopic measurements provide information about composition, photochemical evolution, energy distribution and density. The extension to high resolving power provides further access to temperature, velocity, isotopic ratios, separation of blended sources, and opacity effects. In current high resolving power devices, the drawback of high-resolution spectroscopy is bound to the instrumental limitations of lower throughput, the necessity of small entrance apertures, sensitivity, field of view, and large physical instrumental size. These limitations quickly become handicapping for observation of faint and/or extended targets and for spacecraft encounters. A technique with promise for the study of faint and extended sources at high resolving power is the reflective format of the Spatial Heterodyne Spectrometer (SHS). SHS instruments are compact and naturally tailored for both high etendue (defined in section 2.2.5) and high resolving power. In contrast, to achieve similar spectral grasp, grating spectrometers require large telescopes. For reference, SHS is a cyclical interferometer that produces Fizeau fringe pattern for all other wavelengths except the tuned wavelength. The large etendue obtained by SHS instruments makes them ideal for observations of extended, low surface brightness, isolated emission line sources, while their intrinsically high spectral resolution enables one to study the dynamical and physical properties described above. This document contains four chapters. Chapter 1, introduces a class of scientific targets that formerly have not been extensively observed due to absence of technical capabilities in current apparatus. We will introduce the concept of Special Heterodyne Spectrometers and address how it can fill the gap. Chapter 2 reports on the development of a new mathematical frame work for the Reflective SHS. Chapter 3 provides the details of the design and construction of a Tunable Reflective SHS at both UC Davis laboratory and Mt. Hamilton, Lick Observatory, CA. And chapter 4 contains an overview of the prospects of SHS instruments in future.

Time-resolved correlative optical microscopy of charge-carrier transport, recombination, and space-charge fields in CdTe heterostructures

DOE PAGES

Kuciauskas, Darius; Myers, Thomas H.; Barnes, Teresa M.; ...

2017-02-20

From time- and spatially resolved optical measurements, we show that extended defects can have a large effect on the charge-carrier recombination in II-VI semiconductors. In CdTe double heterostructures grown by molecular beam epitaxy on the InSb (100)-orientation substrates, we characterized the extended defects and found that near stacking faults the space-charge field extends by 2-5 μm. Charge carriers drift (with the space-charge field strength of 730-1,360 V cm -1) and diffuse (with the mobility of 260 ± 30 cm 2 V -1 s -1) toward the extended defects, where the minority-carrier lifetime is reduced from 560 ns to 0.25 ns.more » Furthermore, the extended defects are nonradiative recombination sinks that affect areas significantly larger than the typical crystalline grains in II-VI solar cells. From the correlative time-resolved photoluminescence and second-harmonic generation microscopy data, we developed a band-diagram model that can be used to analyze the impact of extended defects on solar cells and other electronic devices.« less

Spectrally resolving and scattering-compensated x-ray luminescence/fluorescence computed tomography

PubMed Central

Cong, Wenxiang; Shen, Haiou; Wang, Ge

2011-01-01

The nanophosphors, or other similar materials, emit near-infrared (NIR) light upon x-ray excitation. They were designed as optical probes for in vivo visualization and analysis of molecular and cellular targets, pathways, and responses. Based on the previous work on x-ray fluorescence computed tomography (XFCT) and x-ray luminescence computed tomography (XLCT), here we propose a spectrally-resolving and scattering-compensated x-ray luminescence/fluorescence computed tomography (SXLCT or SXFCT) approach to quantify a spatial distribution of nanophosphors (other similar materials or chemical elements) within a biological object. In this paper, the x-ray scattering is taken into account in the reconstruction algorithm. The NIR scattering is described in the diffusion approximation model. Then, x-ray excitations are applied with different spectra, and NIR signals are measured in a spectrally resolving fashion. Finally, a linear relationship is established between the nanophosphor distribution and measured NIR data using the finite element method and inverted using the compressive sensing technique. The numerical simulation results demonstrate the feasibility and merits of the proposed approach. PMID:21721815

Time-resolved correlative optical microscopy of charge-carrier transport, recombination, and space-charge fields in CdTe heterostructures

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

Kuciauskas, Darius; Myers, Thomas H.; Barnes, Teresa M.

From time- and spatially resolved optical measurements, we show that extended defects can have a large effect on the charge-carrier recombination in II-VI semiconductors. In CdTe double heterostructures grown by molecular beam epitaxy on the InSb (100)-orientation substrates, we characterized the extended defects and found that near stacking faults the space-charge field extends by 2-5 μm. Charge carriers drift (with the space-charge field strength of 730-1,360 V cm -1) and diffuse (with the mobility of 260 ± 30 cm 2 V -1 s -1) toward the extended defects, where the minority-carrier lifetime is reduced from 560 ns to 0.25 ns.more » Furthermore, the extended defects are nonradiative recombination sinks that affect areas significantly larger than the typical crystalline grains in II-VI solar cells. From the correlative time-resolved photoluminescence and second-harmonic generation microscopy data, we developed a band-diagram model that can be used to analyze the impact of extended defects on solar cells and other electronic devices.« less

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.

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

PubMed

Caprihan, A; Seymour, J D

2000-05-01

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

A Green's function method for simulation of time-dependent solute transport and reaction in realistic microvascular geometries

PubMed Central

Secomb, Timothy W.

2016-01-01

A novel theoretical method is presented for simulating the spatially resolved convective and diffusive transport of reacting solutes between microvascular networks and the surrounding tissues. The method allows for efficient computational solution of problems involving convection and non-linear binding of solutes in blood flowing through microvascular networks with realistic 3D geometries, coupled with transvascular exchange and diffusion and reaction in the surrounding tissue space. The method is based on a Green's function approach, in which the solute concentration distribution in the tissue is expressed as a sum of fields generated by time-varying distributions of discrete sources and sinks. As an example of the application of the method, the washout of an inert diffusible tracer substance from a tissue region perfused by a network of microvessels is simulated, showing its dependence on the solute's transvascular permeability and tissue diffusivity. Exponential decay of the washout concentration is predicted, with rate constants that are about 10–30% lower than the rate constants for a tissue cylinder model with the same vessel length, vessel surface area and blood flow rate per tissue volume. PMID:26443811

Lateral carrier diffusion in InGaAs/GaAs coupled quantum dot-quantum well system

NASA Astrophysics Data System (ADS)

Pieczarka, M.; Syperek, M.; Biegańska, D.; Gilfert, C.; Pavelescu, E. M.; Reithmaier, J. P.; Misiewicz, J.; Sek, G.

2017-05-01

The lateral carrier diffusion process is investigated in coupled InGaAs/GaAs quantum dot-quantum well (QD-QW) structures by means of spatially resolved photoluminescence spectroscopy at low temperature. Under non-resonant photo-excitation above the GaAs bandgap, the lateral carrier transport reflected in the distorted electron-hole pair emission profiles is found to be mainly governed by high energy carriers created within the 3D density of states of GaAs. In contrast, for the case of resonant excitation tuned to the QW-like ground state of the QD-QW system, the emission profiles remain unaffected by the excess kinetic energy of carriers and local phonon heating within the pump spot. The lateral diffusion lengths are determined and present certain dependency on the coupling strength between QW and QDs. While for a strongly coupled structure the diffusion length is found to be around 0.8 μm and monotonically increases up to 1.4 μm with the excitation power density, in weakly coupled structures, it is determined to ca. 1.6 μm and remained virtually independent of the pumping power density.

Development of a wearable CMOS-based contact imaging system for real-time skin condition diagnosis

NASA Astrophysics Data System (ADS)

Petitdidier, Nils; Koenig, Anne; Gerbelot, Rémi; Gioux, Sylvain; Dinten, Jean-Marc

2017-07-01

Diffuse reflectance spectroscopy has been widely used in the field of biological tissue characterization with various modalities [1-5,6]. One of these modalities consists in measuring the spatially resolved diffuse reflectance (SRDR). In this technique, light is collected at multiple distances from the excitation point. The obtained reflectance decay curve is used to determine scattering and absorption properties of the tissue [7], which are directly related to tissue content and structure. Existing systems usually use fiber optics to collect light reflected from the tissue and transfer it to an optical sensor [1,6]. Such devices make it possible to perform SRDR measurements directly in contact with the tissue. However, they offer poor spatial sampling of the reflectance and low light collection efficiency. We propose to overcome these limitations by using a CMOS sensor placed in contact with the tissue to achieve light collection with high spatial sampling over several millimeters and with increased fill factor. Our objective in this paper is to demonstrate the potential of our instrument to determine the optical properties of tissues from SRDR measurements. We first describe the instrument and the employed methodology. Then, preliminary results obtained on optical phantoms are presented. Finally, the potential of our system for SRDR measurements is evaluated through comparison with a fiber-optic probe previously developed in our laboratory [6,8].

Path-length-resolved dynamic light scattering in highly scattering random media: The transition to diffusing wave spectroscopy

NASA Astrophysics Data System (ADS)

Bizheva, Kostadinka K.; Siegel, Andy M.; Boas, David A.

1998-12-01

We used low coherence interferometry to measure Brownian motion within highly scattering random media. A coherence gate was applied to resolve the optical path-length distribution and to separate ballistic from diffusive light. Our experimental analysis provides details on the transition from single scattering to light diffusion and its dependence on the system parameters. We found that the transition to the light diffusion regime occurs at shorter path lengths for media with higher scattering anisotropy or for larger numerical aperture of the focusing optics.

Upscaling transport of a reacting solute through a peridocially converging-diverging channel at pre-asymptotic times

NASA Astrophysics Data System (ADS)

Sund, Nicole L.; Bolster, Diogo; Dawson, Clint

2015-11-01

In this study we extend the Spatial Markov model, which has been successfully used to upscale conservative transport across a diverse range of porous media flows, to test if it can accurately upscale reactive transport, defined by a spatially heterogeneous first order degradation rate. We test the model in a well known highly simplified geometry, commonly considered as an idealized pore or fracture structure, a periodic channel with wavy boundaries. The edges of the flow domain have a layer through which there is no flow, but in which diffusion of a solute still occurs. Reactions are confined to this region. We demonstrate that the Spatial Markov model, an upscaled random walk model that enforces correlation between successive jumps, can reproduce breakthrough curves measured from microscale simulations that explicitly resolve all pertinent processes. We also demonstrate that a similar random walk model that does not enforce successive correlations is unable to reproduce all features of the measured breakthrough curves.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Determination of the complex refractive index segments of turbid sample with multispectral spatially modulated structured light and models approximation

NASA Astrophysics Data System (ADS)

Meitav, Omri; Shaul, Oren; Abookasis, David

2017-09-01

Spectral data enabling the derivation of a biological tissue sample's complex refractive index (CRI) can provide a range of valuable information in the clinical and research contexts. Specifically, changes in the CRI reflect alterations in tissue morphology and chemical composition, enabling its use as an optical marker during diagnosis and treatment. In the present work, we report a method for estimating the real and imaginary parts of the CRI of a biological sample using Kramers-Kronig (KK) relations in the spatial frequency domain. In this method, phase-shifted sinusoidal patterns at single high spatial frequency are serially projected onto the sample surface at different near-infrared wavelengths while a camera mounted normal to the sample surface acquires the reflected diffuse light. In the offline analysis pipeline, recorded images at each wavelength are converted to spatial phase maps using KK analysis and are then calibrated against phase-models derived from diffusion approximation. The amplitude of the reflected light, together with phase data, is then introduced into Fresnel equations to resolve both real and imaginary segments of the CRI at each wavelength. The technique was validated in tissue-mimicking phantoms with known optical parameters and in mouse models of ischemic injury and heat stress. Experimental data obtained indicate variations in the CRI among brain tissue suffering from injury. CRI fluctuations correlated with alterations in the scattering and absorption coefficients of the injured tissue are demonstrated. This technique for deriving dynamic changes in the CRI of tissue may be further developed as a clinical diagnostic tool and for biomedical research applications. To the best of our knowledge, this is the first report of the estimation of the spectral CRI of a mouse head following injury obtained in the spatial frequency domain.

Sparse Solution of Fiber Orientation Distribution Function by Diffusion Decomposition

PubMed Central

Yeh, Fang-Cheng; Tseng, Wen-Yih Isaac

2013-01-01

Fiber orientation is the key information in diffusion tractography. Several deconvolution methods have been proposed to obtain fiber orientations by estimating a fiber orientation distribution function (ODF). However, the L 2 regularization used in deconvolution often leads to false fibers that compromise the specificity of the results. To address this problem, we propose a method called diffusion decomposition, which obtains a sparse solution of fiber ODF by decomposing the diffusion ODF obtained from q-ball imaging (QBI), diffusion spectrum imaging (DSI), or generalized q-sampling imaging (GQI). A simulation study, a phantom study, and an in-vivo study were conducted to examine the performance of diffusion decomposition. The simulation study showed that diffusion decomposition was more accurate than both constrained spherical deconvolution and ball-and-sticks model. The phantom study showed that the angular error of diffusion decomposition was significantly lower than those of constrained spherical deconvolution at 30° crossing and ball-and-sticks model at 60° crossing. The in-vivo study showed that diffusion decomposition can be applied to QBI, DSI, or GQI, and the resolved fiber orientations were consistent regardless of the diffusion sampling schemes and diffusion reconstruction methods. The performance of diffusion decomposition was further demonstrated by resolving crossing fibers on a 30-direction QBI dataset and a 40-direction DSI dataset. In conclusion, diffusion decomposition can improve angular resolution and resolve crossing fibers in datasets with low SNR and substantially reduced number of diffusion encoding directions. These advantages may be valuable for human connectome studies and clinical research. PMID:24146772

Characteristics of a Direct Current-driven plasma jet operated in open air

NASA Astrophysics Data System (ADS)

Li, Xuechen; Di, Cong; Jia, Pengying; Bao, Wenting

2013-09-01

A DC-driven plasma jet has been developed to generate a diffuse plasma plume by blowing argon into the ambient air. The plasma plume, showing a cup shape with a diameter of several centimeters at a higher voltage, is a pulsed discharge despite a DC voltage is applied. The pulse frequency is investigated as a function of the voltage under different gap widths and gas flow rates. Results show that plasma bullets propagate from the hollow needle to the plate electrode by spatially resolved measurement. A supposition about non-electroneutral trail of the streamer is proposed to interpret these experimental phenomena.

A transmission-grating-modulated pump-probe absorption spectroscopy and demonstration of diffusion dynamics of photoexcited carriers in bulk intrinsic GaAs film.

PubMed

Chen, Ke; Wang, Wenfang; Chen, Jianming; Wen, Jinhui; Lai, Tianshu

2012-02-13

A transmission-grating-modulated time-resolved pump-probe absorption spectroscopy is developed and formularized. The spectroscopy combines normal time-resolved pump-probe absorption spectroscopy with a binary transmission grating, is sensitive to the spatiotemporal evolution of photoinjected carriers, and has extensive applicability in the study of diffusion transport dynamics of photoinjected carriers. This spectroscopy has many advantages over reported optical methods to measure diffusion dynamics, such as simple experimental setup and operation, and high detection sensitivity. The measurement of diffusion dynamics is demonstrated on bulk intrinsic GaAs films. A carrier density dependence of carrier diffusion coefficient is obtained and agrees well with reported results.

Hybrid stochastic and deterministic simulations of calcium blips.

PubMed

Rüdiger, S; Shuai, J W; Huisinga, W; Nagaiah, C; Warnecke, G; Parker, I; Falcke, M

2007-09-15

Intracellular calcium release is a prime example for the role of stochastic effects in cellular systems. Recent models consist of deterministic reaction-diffusion equations coupled to stochastic transitions of calcium channels. The resulting dynamics is of multiple time and spatial scales, which complicates far-reaching computer simulations. In this article, we introduce a novel hybrid scheme that is especially tailored to accurately trace events with essential stochastic variations, while deterministic concentration variables are efficiently and accurately traced at the same time. We use finite elements to efficiently resolve the extreme spatial gradients of concentration variables close to a channel. We describe the algorithmic approach and we demonstrate its efficiency compared to conventional methods. Our single-channel model matches experimental data and results in intriguing dynamics if calcium is used as charge carrier. Random openings of the channel accumulate in bursts of calcium blips that may be central for the understanding of cellular calcium dynamics.

Development and experimental testing of an optical micro-spectroscopic technique incorporating true line-scan excitation.

PubMed

Biener, Gabriel; Stoneman, Michael R; Acbas, Gheorghe; Holz, Jessica D; Orlova, Marianna; Komarova, Liudmila; Kuchin, Sergei; Raicu, Valerică

2013-12-27

Multiphoton micro-spectroscopy, employing diffraction optics and electron-multiplying CCD (EMCCD) cameras, is a suitable method for determining protein complex stoichiometry, quaternary structure, and spatial distribution in living cells using Förster resonance energy transfer (FRET) imaging. The method provides highly resolved spectra of molecules or molecular complexes at each image pixel, and it does so on a timescale shorter than that of molecular diffusion, which scrambles the spectral information. Acquisition of an entire spectrally resolved image, however, is slower than that of broad-bandwidth microscopes because it takes longer times to collect the same number of photons at each emission wavelength as in a broad bandwidth. Here, we demonstrate an optical micro-spectroscopic scheme that employs a laser beam shaped into a line to excite in parallel multiple sample voxels. The method presents dramatically increased sensitivity and/or acquisition speed and, at the same time, has excellent spatial and spectral resolution, similar to point-scan configurations. When applied to FRET imaging using an oligomeric FRET construct expressed in living cells and consisting of a FRET acceptor linked to three donors, the technique based on line-shaped excitation provides higher accuracy compared to the point-scan approach, and it reduces artifacts caused by photobleaching and other undesired photophysical effects.

A Monte Carlo study of fluorescence generation probability in a two-layered tissue model

NASA Astrophysics Data System (ADS)

Milej, Daniel; Gerega, Anna; Wabnitz, Heidrun; Liebert, Adam

2014-03-01

It was recently reported that the time-resolved measurement of diffuse reflectance and/or fluorescence during injection of an optical contrast agent may constitute a basis for a technique to assess cerebral perfusion. In this paper, we present results of Monte Carlo simulations of the propagation of excitation photons and tracking of fluorescence photons in a two-layered tissue model mimicking intra- and extracerebral tissue compartments. Spatial 3D distributions of the probability that the photons were converted from excitation to emission wavelength in a defined voxel of the medium (generation probability) during their travel between source and detector were obtained for different optical properties in intra- and extracerebral tissue compartments. It was noted that the spatial distribution of the generation probability depends on the distribution of the fluorophore in the medium and is influenced by the absorption of the medium and of the fluorophore at excitation and emission wavelengths. Simulations were also carried out for realistic time courses of the dye concentration in both layers. The results of the study show that the knowledge of the absorption properties of the medium at excitation and emission wavelengths is essential for the interpretation of the time-resolved fluorescence signals measured on the surface of the head.

The Analytical Limits of Modeling Short Diffusion Timescales

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Quantitative experimental monitoring of molecular diffusion in clay with positron emission tomography

NASA Astrophysics Data System (ADS)

Kulenkampff, Johannes; Zakhnini, Abdelhamid; Gründig, Marion; Lippmann-Pipke, Johanna

2016-08-01

Clay plays a prominent role as barrier material in the geosphere. The small particle sizes cause extremely small pore sizes and induce low permeability and high sorption capacity. Transport of dissolved species by molecular diffusion, driven only by a concentration gradient, is less sensitive to the pore size. Heterogeneous structures on the centimetre scale could cause heterogeneous effects, like preferential transport zones, which are difficult to assess. Laboratory measurements with diffusion cells yield limited information on heterogeneity, and pore space imaging methods have to consider scale effects. We established positron emission tomography (PET), applying a high-resolution PET scanner as a spatially resolved quantitative method for direct laboratory observation of the molecular diffusion process of a PET tracer on the prominent scale of 1-100 mm. Although PET is rather insensitive to bulk effects, quantification required significant improvements of the image reconstruction procedure with respect to Compton scatter and attenuation. The experiments were conducted with 22Na and 124I over periods of 100 and 25 days, respectively. From the images we derived trustable anisotropic diffusion coefficients and, in addition, we identified indications of preferential transport zones. We thus demonstrated the unique potential of the PET imaging modality for geoscientific process monitoring under conditions where other methods fail, taking advantage of the extremely high detection sensitivity that is typical of radiotracer applications.

A Green's function method for simulation of time-dependent solute transport and reaction in realistic microvascular geometries.

PubMed

Secomb, Timothy W

2016-12-01

A novel theoretical method is presented for simulating the spatially resolved convective and diffusive transport of reacting solutes between microvascular networks and the surrounding tissues. The method allows for efficient computational solution of problems involving convection and non-linear binding of solutes in blood flowing through microvascular networks with realistic 3D geometries, coupled with transvascular exchange and diffusion and reaction in the surrounding tissue space. The method is based on a Green's function approach, in which the solute concentration distribution in the tissue is expressed as a sum of fields generated by time-varying distributions of discrete sources and sinks. As an example of the application of the method, the washout of an inert diffusible tracer substance from a tissue region perfused by a network of microvessels is simulated, showing its dependence on the solute's transvascular permeability and tissue diffusivity. Exponential decay of the washout concentration is predicted, with rate constants that are about 10-30% lower than the rate constants for a tissue cylinder model with the same vessel length, vessel surface area and blood flow rate per tissue volume. © The authors 2015. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

Spatial-temporal evolution of self-organized loop-patterns on a water surface and a diffuse discharge in the gap

NASA Astrophysics Data System (ADS)

Li, Xuechen; Geng, Jinling; Jia, Pengying; Zhang, Panpan; Zhang, Qi; Li, Yaru

2017-11-01

Excited by an alternating current voltage, a patterned discharge and a diffuse discharge are generated in a needle to liquid configuration. Using an intensified charge-coupled device (ICCD), temporal evolution of the discharge between the two electrodes is investigated for the diffuse mode and the patterned mode, respectively. For the diffuse mode, the positive discharge is in a glow regime, and the negative discharge is in a Townsend discharge regime. For the patterned mode, the discharge always belongs to the Townsend discharge regime. Moreover, in the patterned mode, various patterns including the single loop, single loop with the surrounding corona, triple loops, and concentric loops with a central spot are observed on the water surface with the increasing positive peak-value of the applied voltage (Upp). Temporally resolved images of the loop-patterns are captured on the water surface. From the electrical measurements and the ICCD imaging, it is found that the loop pattern emerges after the discharge bridges the two electrodes. Then, it begins to evolve and finally degenerates with the decrease in the discharge current. The pattern does not disappear until the discharge quenches. Formation of the loop-patterns is attributed to the role of negative ions.

Robust estimation of cerebral hemodynamics in neonates using multilayered diffusion model for normal and oblique incidences

NASA Astrophysics Data System (ADS)

Steinberg, Idan; Harbater, Osnat; Gannot, Israel

2014-07-01

The diffusion approximation is useful for many optical diagnostics modalities, such as near-infrared spectroscopy. However, the simple normal incidence, semi-infinite layer model may prove lacking in estimation of deep-tissue optical properties such as required for monitoring cerebral hemodynamics, especially in neonates. To answer this need, we present an analytical multilayered, oblique incidence diffusion model. Initially, the model equations are derived in vector-matrix form to facilitate fast and simple computation. Then, the spatiotemporal reflectance predicted by the model for a complex neonate head is compared with time-resolved Monte Carlo (TRMC) simulations under a wide range of physiologically feasible parameters. The high accuracy of the multilayer model is demonstrated in that the deviation from TRMC simulations is only a few percent even under the toughest conditions. We then turn to solve the inverse problem and estimate the oxygen saturation of deep brain tissues based on the temporal and spatial behaviors of the reflectance. Results indicate that temporal features of the reflectance are more sensitive to deep-layer optical parameters. The accuracy of estimation is shown to be more accurate and robust than the commonly used single-layer diffusion model. Finally, the limitations of such approaches are discussed thoroughly.

The Foggy EUV Corona and Coronal Heating by MHD Waves from Explosive Reconnection Events

NASA Technical Reports Server (NTRS)

Moore, Ron L.; Cirtain, Jonathan W.; Falconer, David A.

2008-01-01

In 0.5 arcsec/pixel TRACE coronal EUV images, the corona rooted in active regions that are at the limb and are not flaring is seen to consist of (1) a complex array of discrete loops and plumes embedded in (2) a diffuse ambient component that shows no fine structure and gradually fades with height. For each of two not-flaring active regions, found that the diffuse component is (1) approximately isothermal and hydrostatic and (2) emits well over half of the total EUV luminosity of the active-region corona. Here, from a TRACE Fe XII coronal image of another not-flaring active region, the large sunspot active region AR 10652 when it was at the west limb on 30 July 2004, we separate the diffuse component from the discrete loop component by spatial filtering, and find that the diffuse component has about 60% of the total luminosity. If under much higher spatial resolution than that of TRACE (e. g., the 0.1 arcsec/pixel resolution of the Hi-C sounding-rocket experiment proposed by J. W. Cirtain et al), most of the diffuse component remains diffuse rather being resolved into very narrow loops and plumes, this will raise the possibility that the EUV corona in active regions consists of two basically different but comparably luminous components: one being the set of discrete bright loops and plumes and the other being a truly diffuse component filling the space between the discrete loops and plumes. This dichotomy would imply that there are two different but comparably powerful coronal heating mechanisms operating in active regions, one for the distinct loops and plumes and another for the diffuse component. We present a scenario in which (1) each discrete bright loop or plume is a flux tube that was recently reconnected in a burst of reconnection, and (2) the diffuse component is heated by MHD waves that are generated by these reconnection events and by other fine-scale explosive reconnection events, most of which occur in and below the base of the corona where they are seen as UV explosive events, EUV blinkers, and type II spicules. These MHD waves propagate across field lines and dissipate, heating the plasma in the field between the bright loops and plumes.

Matching time and spatial scales of rapid solidification: dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

NASA Astrophysics Data System (ADS)

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.; Fattebert, Jean-Luc; McKeown, Joseph T.

2018-01-01

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu-Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid-liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu-Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying from ˜0.1 to ˜0.6 m s-1. After an ‘incubation’ time, the velocity of the planar solid-liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Finally, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid-liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).

Matching time and spatial scales of rapid solidification: Dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

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

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu–Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid–liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu–Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying frommore » ~0.1 to ~0.6 m s –1. After an 'incubation' time, the velocity of the planar solid–liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Lastly, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid–liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).« less

Matching time and spatial scales of rapid solidification: Dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

DOE PAGES

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.; ...

2017-12-05

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu–Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid–liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu–Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying frommore » ~0.1 to ~0.6 m s –1. After an 'incubation' time, the velocity of the planar solid–liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Lastly, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid–liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).« less

Investigating SWOT's capabilities to detect meso and submesoscale eddies in the western Mediterranean

NASA Astrophysics Data System (ADS)

Gomez-Navarro, Laura; Pascual, Ananda; Fablet, Ronan; Mason, Evan

2017-04-01

The primary oceanographic objective of the future Surface Water Ocean Topography (SWOT) altimetric satellite is to characterize the mesoscale and submesoscale ocean circulation. The aim of this study is to assess the capabilities of SWOT to resolve the meso and submesoscale in the western Mediterranean. With ROMS model data as inputs for the SWOT simulator, pseudo-SWOT data were generated. These data were compared with the original ROMS model data and ADT data from present day altimetric satellites to assess the temporal and spatial resolution of SWOT in the western Mediterranean. We then addressed the removal of the satellite's noise in the pseudo-SWOT data using a Laplacian diffusion. We investigated different parameters of the filter by looking at their impact on the spatial spectra and RMSEs calculated from the simulator outputs. To further assess the satellites capabilities, we derived absolute geostrophic velocities and relative vorticity. Our numerical experiments show that the noise patterns affect the spectral content of the pseudo-SWOT fields below 30 km. The Laplacian diffusion improves the recovery of the spectral signature of the altimetric field, especially down to 20 km. With the help of this filter, we manage to observe small scale oceanic features in pseudo-SWOT data, and in its derived variables.

Identifying Extraplanar Diffuse Ionized Gas in a Sample of MaNGA Galaxies

NASA Astrophysics Data System (ADS)

Hubbard, Ryan J.; Diamond-Stanic, Aleksandar M.; MaNGA Team

2016-01-01

The efficiency with which galaxies convert gas into stars is driven by the continuous cycle of accretion and feedback processes within the circumgalactic medium. Extraplanar diffuse ionized gas (eDIG) can provide insights into the tumultuous processes that govern the evolution of galactic disks because eDIG emission traces both inflowing and outflowing gas. With the help of state-of-the-art, spatially-resolved spectroscopy from MaNGA (Mapping Nearby Galaxies at Apache Point Observatory), we developed a computational method to identify eDIG based on the strength of and spatial extent of optical emission lines for a diverse sample of 550 nearby galaxies. This sample includes roughly half of the MaNGA galaxies that will become publicly available in summer 2016 as part of the Thirteenth Data Release of the Sloan Digital Sky Survey. We identified signatures of eDIG in 8% of the galaxies in this sample, and we found that these signatures are particularly common among galaxies with active star formation and inclination angles >45 degrees. Our analysis of the morphology, incidence, and kinematics of eDIG has important implications for current models of accretion and feedback processes that regulate star formation in galaxies. We acknowledge support from the Astrophysics REU program at the University of Wisconsin-Madison, the National Astronomy Consortium, and The Grainger Foundation.

OH and CH luminescence in opposed flow methane oxy-flames

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

De Leo, Maurizio; Saveliev, Alexei; Kennedy, Lawrence A.

Emission spectroscopy is a 2-D nonintrusive diagnostic technique that offers spatially resolved data for combustion optimization and control. The UV and visible chemiluminescence of the excited radicals CH(A{sup 2}{delta},B{sup 2}{sigma}{sup -}) and OH(A{sup 2}{sigma}{sup +}) is studied experimentally and numerically in opposed-flow diffusion flames of methane and oxygen-enriched air. The oxidized oxygen content is varied from 21 to 100% while the range of the studied strain rates spans from 20 to 40 s{sup -1}. The spectrally resolved imaging is obtained by two different methods: scattering through a grating monochromator and interposition of interference filters along the optical path. Absolute measuredmore » chemiluminescence intensities, coupled with a numerical model based on the opposed flow flame code, are used to evaluate the chemical kinetics of the excited species. The predictions of the selected model are in good agreement with the experimental data over the range of the studied flame conditions. (author)« less

Three-dimensional cathodoluminescence characterization of a semipolar GaInN based LED sample

NASA Astrophysics Data System (ADS)

Hocker, Matthias; Maier, Pascal; Tischer, Ingo; Meisch, Tobias; Caliebe, Marian; Scholz, Ferdinand; Mundszinger, Manuel; Kaiser, Ute; Thonke, Klaus

2017-02-01

A semipolar GaInN based light-emitting diode (LED) sample is investigated by three-dimensionally resolved cathodoluminescence (CL) mapping. Similar to conventional depth-resolved CL spectroscopy (DRCLS), the spatial resolution perpendicular to the sample surface is obtained by calibration of the CL data with Monte-Carlo-simulations (MCSs) of the primary electron beam scattering. In addition to conventional MCSs, we take into account semiconductor-specific processes like exciton diffusion and the influence of the band gap energy. With this method, the structure of the LED sample under investigation can be analyzed without additional sample preparation, like cleaving of cross sections. The measurement yields the thickness of the p-type GaN layer, the vertical position of the quantum wells, and a defect analysis of the underlying n-type GaN, including the determination of the free charge carrier density. The layer arrangement reconstructed from the DRCLS data is in good agreement with the nominal parameters defined by the growth conditions.

Experimental investigation of concentration and stable isotopes signals during organic contaminants back diffusion

NASA Astrophysics Data System (ADS)

Jin, Biao; Nika, Chrysanthi-Elisabeth; Rolle, Massimo

2017-04-01

Back diffusion of organic contaminants is often the cause of groundwater plumes' persistence and can significantly hinder cleanup interventions [1, 2]. In this study we perform a high-resolution investigation of back diffusion in a well-controlled flow-through laboratory setup. We considered cis-dichloroethene (cis-DCE) as model contaminant and we investigated its back diffusion from an impermeable source into a permeable saturated layer, in which advection-dominated flow conditions were established. We used concentration and stable chlorine isotope measurements to investigate the plumes originated by cis-DCE back diffusion in a series of flow-through experiments, performed in porous media with different hydraulic conductivity and at different seepage velocities (i.e., 0.4, 0.8 and 1.2 m/day). A two-centimeter thick agarose gel layer was placed at the bottom of the setup to simulate the source of cis-DCE back diffusion from an impervious layer. Intensive sampling (>1000 measurements) was carried out, including the withdrawal of aqueous samples at closely spaced (1 cm) outlet ports, as well as the high-resolution sampling of the source zone (agarose gel) at the end of each experiment. The transient behavior of the plumes originated by back diffusion was investigated by sampling the outlet ports at regular intervals in the experiments, each run for a total time corresponding to 15 pore volumes. The high-resolution sampling allowed us to resolve the spatial and temporal evolution of concentration and stable isotope gradients in the flow-through setup. In particular, steep concentration and stable isotope gradients were observed at the outlet. Lateral isotope gradients corresponding to chlorine isotope fractionation up to 20‰ were induced by cis-DCE back diffusion and subsequent advection-dominated transport in all flow-through experiments. A numerical modeling approach, tracking individually all chlorine isotopologues, based on the accurate parameterization of local dispersion, as well as on the values of aqueous diffusion coefficients and diffusion-induced isotope fractionation from a previous study [3], provided a good agreement with the experimental data. References [1] Mackay, D. M.; Cherry, J. A. Groundwater contamination: Pumpand-treat remediation. Environ. Sci. Technol. 1989, 23, 630-636. [2] Parker, B. L.; Chapman, S. W.; Guilbeault, M. A. Plume persistence caused by back diffusion from thin clay layers in a sand aquifer following TCE source-zone hydraulic isolation. J. Contam. Hydrol. 2008, 102, 19-19. [3] Jin, B., Rolle, M., Li, T., Haderlein, S.B., 2014. Diffusive fractionation of BTEX and chlorinated ethenes in aqueous solution: quantification of spatial isotope gradients. Environ. Sci. Technol. 48, 6141-6150.

High spatial variability of carbon dioxide and methane emission in three tropical reservoirs

NASA Astrophysics Data System (ADS)

Reinaldo Paranaiba, José; Barros, Nathan O.; Mendonça, Raquel F.; Linkhorst, Annika; Isidorova, Anastasija; Roland, Fabio; Sobek, Sebastian

2017-04-01

In the tropics, many new large hydropower dams are being built, in order to produce renewable energy for economic growth. Most inland waters, such as rivers, lakes and reservoirs, emit greenhouse gases to the atmosphere, and especially tropical reservoirs have been pointed out as strong sources of methane. However, present estimates of greenhouse gas emission from reservoirs are limited by the amount of available data. In particular, the spatial variability of greenhouse gas emission from reservoirs is insufficiently understood. In order to test the hypothesis that the diffusive emission of carbon dioxide (CO2) and methane (CH4) from tropical reservoirs is characterized by strong spatial variability and incorrectly represented by measurements at one site only, we studied three reservoirs situated in different tropical climates, during the dry period. We conducted spatially resolved measurements of surface water concentrations of dissolved carbon dioxide and methane using an on-line equilibration system, as well as of the gas exchange velocity using floating chambers. We found pronounced spatial variability of diffusive CO2 and CH4 emission in all three reservoirs. River inflow areas were more likely to have high concentrations of particularly CH4, but also CO2, than other areas in the reservoirs. Close to the dam, CH4 concentrations were comparatively low in each reservoir. The variability of CH4 concentration was linked to geographical position, which we ascribe to hot spots of methanogenesis at sites of high sediment deposition, such as river inflow areas. The variability of CO2 concentration seemed instead rather to be linked to in-situ metabolism. Also the gas exchange velocity varied pronouncedly in each reservoir, but without any detectable systematic patterns, calling for further studies. We conclude that accurate upscaling of reservoir greenhouse gas emissions requires accounting for within-reservoir spatial variability, and that the anthropogenic increase of sediment flux from catchments to downstream reservoirs may be linked to increased reservoir CH4 emission.

Spectral refractive index assessment of turbid samples by combining spatial frequency near-infrared spectroscopy with Kramers-Kronig analysis

NASA Astrophysics Data System (ADS)

Meitav, Omri; Shaul, Oren; Abookasis, David

2018-03-01

A practical algorithm for estimating the wavelength-dependent refractive index (RI) of a turbid sample in the spatial frequency domain with the aid of Kramers-Kronig (KK) relations is presented. In it, phase-shifted sinusoidal patterns (structured illumination) are serially projected at a high spatial frequency onto the sample surface (mouse scalp) at different near-infrared wavelengths while a camera mounted normally to the sample surface captures the reflected diffuse light. In the offline analysis pipeline, recorded images at each wavelength are converted to spatial absorption maps by logarithmic function, and once the absorption coefficient information is obtained, the imaginary part (k) of the complex RI (CRI), based on Maxell's equations, can be calculated. Using the data represented by k, the real part of the CRI (n) is then resolved by KK analysis. The wavelength dependence of n ( λ ) is then fitted separately using four standard dispersion models: Cornu, Cauchy, Conrady, and Sellmeier. In addition, three-dimensional surface-profile distribution of n is provided based on phase profilometry principles and a phase-unwrapping-based phase-derivative-variance algorithm. Experimental results demonstrate the capability of the proposed idea for sample's determination of a biological sample's RI value.

Beyond spatial correlation effect in micro-Raman light scattering: An example of zinc-blende GaN/GaAs hetero-interface

NASA Astrophysics Data System (ADS)

Ning, J. Q.; Zheng, C. C.; Zheng, L. X.; Xu, S. J.

2015-08-01

Spatially resolved Raman light scattering experiments were performed on a zinc-blende GaN/GaAs heterostructure with confocal micro-Raman scattering technique under the backscattering geometric configuration. By varying the illumination spot locations across the heterostructure interface, we found that the Raman light scattering spectral features change remarkably. The interface effect on the GaAs substrate manifested as a much broader lineshape of the transverse optical (TO) phonon mode. Two kinds of broadening mechanisms, namely, spatial correlation induced wave-vector relaxation effect and lattice-mismatch strain + compositional intermixing effect, have been identified. The former leads to the broadening of the TO mode at the low-energy side, whereas the latter accounts for the broadening at the high-energy side. The diffuse light scattering from the highly defective nucleation layer of GaN was found to produce a broad scattering background of the GaN TO mode. The methodology and conclusions of the present work could be applicable to Raman spectroscopic studies on other material interfaces.

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

Yamashita, G.; Nagai, M., E-mail: mnagai@mp.es.osaka-u.ac.jp, E-mail: ashida@mp.es.osaka-u.ac.jp; Ashida, M., E-mail: mnagai@mp.es.osaka-u.ac.jp, E-mail: ashida@mp.es.osaka-u.ac.jp

We estimated the carrier multiplication efficiency in the most common solar-cell material, Si, by using optical-pump/terahertz-probe spectroscopy. Through close analysis of time-resolved data, we extracted the exact number of photoexcited carriers from the sheet carrier density 10 ps after photoexcitation, excluding the influences of spatial diffusion and surface recombination in the time domain. For incident photon energies greater than 4.0 eV, we observed enhanced internal quantum efficiency due to carrier multiplication. The evaluated value of internal quantum efficiency agrees well with the results of photocurrent measurements. This optical method allows us to estimate the carrier multiplication and surface recombination of carriersmore » quantitatively, which are crucial for the design of the solar cells.« less

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

NASA Technical Reports Server (NTRS)

Straus, John; Lewis, John F.

2011-01-01

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

X-Ray-Based Imaging for Characterizing Heterogeneous Gas Diffusion Layers for Polymer Electrolyte Membrane Fuel Cells

NASA Astrophysics Data System (ADS)

George, Michael G.

Characterization of gas diffusion layers (GDLs) for polymer electrolyte membrane (PEM) fuel cells informs modeling studies and the manufacturers of next generation fuel cell materials. Identifying the physical properties related to the primary functions of the modern GDL (thermal, electrical, and mass transport) is necessary for understanding the impact of GDL design choices. X-ray micro-computed tomographic reconstructions of GDLs were studied to isolate GDL surface morphologies. Surface roughness was measured for a wide variety of samples and a sensitivity study highlighted the scale-dependence of surface roughness measurements. Furthermore, a spatially resolved distribution map of polytetrafluoroethylene (PTFE) in the microporous layer (MPL), critical for water management and mass transport, was identified and the existence of PTFE agglomerations was highlighted. Finally, the impact of accelerated degradation on GDL wettability and water transport increases in liquid water accumulation and oxygen mass transport resistance were quantified as a result of accelerated GDL degradation.

Magnetic resonance imaging of granular materials

NASA Astrophysics Data System (ADS)

Stannarius, Ralf

2017-05-01

Magnetic Resonance Imaging (MRI) has become one of the most important tools to screen humans in medicine; virtually every modern hospital is equipped with a Nuclear Magnetic Resonance (NMR) tomograph. The potential of NMR in 3D imaging tasks is by far greater, but there is only "a handful" of MRI studies of particulate matter. The method is expensive, time-consuming, and requires a deep understanding of pulse sequences, signal acquisition, and processing. We give a short introduction into the physical principles of this imaging technique, describe its advantages and limitations for the screening of granular matter, and present a number of examples of different application purposes, from the exploration of granular packing, via the detection of flow and particle diffusion, to real dynamic measurements. Probably, X-ray computed tomography is preferable in most applications, but fast imaging of single slices with modern MRI techniques is unmatched, and the additional opportunity to retrieve spatially resolved flow and diffusion profiles without particle tracking is a unique feature.

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 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

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.

Temporally and Spatially Resolved Plasma Spectroscopy in Pulsed Laser Deposition of Ultra-Thin Boron Nitride Films (Postprint)

DTIC Science & Technology

2015-04-24

AFRL-RX-WP-JA-2016-0196 TEMPORALLY AND SPATIALLY RESOLVED PLASMA SPECTROSCOPY IN PULSED LASER DEPOSITION OF ULTRA-THIN BORON NITRIDE...AND SPATIALLY RESOLVED PLASMA SPECTROSCOPY IN PULSED LASER DEPOSITION OF ULTRA-THIN BORON NITRIDE FILMS (POSTPRINT) 5a. CONTRACT NUMBER FA8650...distributions within a PVD plasma plume ablated from a boron nitride (BN) target by a KrF laser at different pressures of nitrogen gas were investigated

Control and measurement of the physical properties in acrylamide based photopolymer materials

NASA Astrophysics Data System (ADS)

Close, Ciara E.; Gleeson, Michael R.; O'Neill, Feidhlim T.; Kelly, John V.; Sheridan, John T.

2005-06-01

Recent improvements in holographic materials have led to advances in a variety of applications, including data storage and interferometry. To further increase the possibility of commercial applications in these areas it is necessary to have available an inexpensive, self-processing, environmentally stable material that has a good spatial frequency response. One promising type of material is Acrylamide-based photopolymer recording materials. The material can be made self-processing and can be sensitised to different recording wavelengths using different photosensitive dyes. The self-processing capability of this material simplifies the recording and testing processes and enables holographic interferometry to be carried out without the need for complex realignment procedures. Although this material has a lot of advantages over others it has significant disadvantages such as its spatial frequency response range (500-2500 lines/mm). Therefore, it is of ever-increasing importance to resolve uncertainties regarding optical and material properties, i.e. the refractive index and the diffusion constants. Using experimental diffraction efficiency measurements, a value for the refractive index modulation can be obtained. Then carrying out analysis using the Polymerisation Driven Diffusion model (PDD) values for the diffusion coefficients of various materials in the grating layer can be found. Applying the Lorentz-Lorenz relation, refractive index variations within the material can be more fully understood. With the resulting improved understanding it will be possible to improve the characteristics of photopolymer materials by altering the chemical composition, for example by controlling the crosslinker concentration or through the careful use of inhibitor and/or retarders to control the polymer chain growth.

MRI of chemical reactions and processes.

PubMed

Britton, Melanie M

2017-08-01

As magnetic resonance imaging (MRI) can spatially resolve a wealth of molecular information available from nuclear magnetic resonance (NMR), it is able to non-invasively visualise the composition, properties and reactions of a broad range of spatially-heterogeneous molecular systems. Hence, MRI is increasingly finding applications in the study of chemical reactions and processes in a diverse range of environments and technologies. This article will explain the basic principles of MRI and how it can be used to visualise chemical composition and molecular properties, providing an overview of the variety of information available. Examples are drawn from the disciplines of chemistry, chemical engineering, environmental science, physics, electrochemistry and materials science. The review introduces a range of techniques used to produce image contrast, along with the chemical and molecular insight accessible through them. Methods for mapping the distribution of chemical species, using chemical shift imaging or spatially-resolved spectroscopy, are reviewed, as well as methods for visualising physical state, temperature, current density, flow velocities and molecular diffusion. Strategies for imaging materials with low signal intensity, such as those containing gases or low sensitivity nuclei, using compressed sensing, para-hydrogen or polarisation transfer, are discussed. Systems are presented which encapsulate the diversity of chemical and physical parameters observable by MRI, including one- and two-phase flow in porous media, chemical pattern formation, phase transformations and hydrodynamic (fingering) instabilities. Lastly, the emerging area of electrochemical MRI is discussed, with studies presented on the visualisation of electrochemical deposition and dissolution processes during corrosion and the operation of batteries, supercapacitors and fuel cells. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Resolving complex fibre architecture by means of sparse spherical deconvolution in the presence of isotropic diffusion

NASA Astrophysics Data System (ADS)

Zhou, Q.; Michailovich, O.; Rathi, Y.

2014-03-01

High angular resolution diffusion imaging (HARDI) improves upon more traditional diffusion tensor imaging (DTI) in its ability to resolve the orientations of crossing and branching neural fibre tracts. The HARDI signals are measured over a spherical shell in q-space, and are usually used as an input to q-ball imaging (QBI) which allows estimation of the diffusion orientation distribution functions (ODFs) associated with a given region-of interest. Unfortunately, the partial nature of single-shell sampling imposes limits on the estimation accuracy. As a result, the recovered ODFs may not possess sufficient resolution to reveal the orientations of fibre tracts which cross each other at acute angles. A possible solution to the problem of limited resolution of QBI is provided by means of spherical deconvolution, a particular instance of which is sparse deconvolution. However, while capable of yielding high-resolution reconstructions over spacial locations corresponding to white matter, such methods tend to become unstable when applied to anatomical regions with a substantial content of isotropic diffusion. To resolve this problem, a new deconvolution approach is proposed in this paper. Apart from being uniformly stable across the whole brain, the proposed method allows one to quantify the isotropic component of cerebral diffusion, which is known to be a useful diagnostic measure by itself.

Spatially resolved Spectroscopy of Europa’s Large-scale Compositional Units at 3-4 μm with Keck NIRSPEC

NASA Astrophysics Data System (ADS)

Fischer, P. D.; Brown, M. E.; Trumbo, S. K.; Hand, K. P.

2017-01-01

We present spatially resolved spectroscopic observations of Europa’s surface at 3-4 μm obtained with the near-infrared spectrograph and adaptive optics system on the Keck II telescope. These are the highest quality spatially resolved reflectance spectra of Europa’s surface at 3-4 μm. The observations spatially resolve Europa’s large-scale compositional units at a resolution of several hundred kilometers. The spectra show distinct features and geographic variations associated with known compositional units; in particular, large-scale leading hemisphere chaos shows a characteristic longward shift in peak reflectance near 3.7 μm compared to icy regions. These observations complement previous spectra of large-scale chaos, and can aid efforts to identify the endogenous non-ice species.

Coupling temporal and spatial gradient information in high-density unstructured Lagrangian measurements

NASA Astrophysics Data System (ADS)

Wong, Jaime G.; Rosi, Giuseppe A.; Rouhi, Amirreza; Rival, David E.

2017-10-01

Particle tracking velocimetry (PTV) produces high-quality temporal information that is often neglected when computing spatial gradients. A method is presented here to utilize this temporal information in order to improve the estimation of spatial gradients for spatially unstructured Lagrangian data sets. Starting with an initial guess, this method penalizes any gradient estimate where the substantial derivative of vorticity along a pathline is not equal to the local vortex stretching/tilting. Furthermore, given an initial guess, this method can proceed on an individual pathline without any further reference to neighbouring pathlines. The equivalence of the substantial derivative and vortex stretching/tilting is based on the vorticity transport equation, where viscous diffusion is neglected. By minimizing the residual of the vorticity-transport equation, the proposed method is first tested to reduce error and noise on a synthetic Taylor-Green vortex field dissipating in time. Furthermore, when the proposed method is applied to high-density experimental data collected with `Shake-the-Box' PTV, noise within the spatial gradients is significantly reduced. In the particular test case investigated here of an accelerating circular plate captured during a single run, the method acts to delineate the shear layer and vortex core, as well as resolve the Kelvin-Helmholtz instabilities, which were previously unidentifiable without the use of ensemble averaging. The proposed method shows promise for improving PTV measurements that require robust spatial gradients while retaining the unstructured Lagrangian perspective.

Sensitivity of the mesosphere to the Lorenz energy cycle of the troposphere

NASA Astrophysics Data System (ADS)

Becker, Erich

The sensitivity of the mesosphere and lower thermosphere (MLT) to climate variability in the troposphere is largely controlled by the generation, propagation, and dissipation of gravity waves (GWs). Conventional climate models cannot fully describe this sensitivity since GWs must be parameterized by invoking strong assumptions. In particular, a fixed GW source at a single level in the troposphere is often assumed. Since the Eliassen-Palm flux (EPF) of low-frequency inertia GWs tends to vanish, the main contribution to the EPF divergence at high latitudes of the MLT is due to midand high-frequency GWs with periods of a few hours or less. In order to resolve at least a good portion of these waves in a GCM, a high spatial resolution from the boundary layer to the lower thermosphere is required. Furthermore, both the generation and dissipation of resolved GWs is expected to depend strongly on the details of the parameterization of turbulence. The present study proposes a new formulation of a mechanistic GCM with high spatial resolution and a sophisticated parameterization of turbulence. This model explicitly simulates the wave drag of the MLT that results from the dynamical GW sources in the troposphere. The Smagorinsky-type horizontal and vertical diffusion coefficients are scaled by the Richardson criterion such that no sponge layer is required for the GWs to dissipate in the MLT. A sensitivity experiment shows that a reduced static stability in the lower troposphere, which may be associated with climate change, leads to a stronger Lorenz energy cycle. The intensification of the tropospheric heat engine is accompanied by enhanced GW acitivity in the upper troposphere at middle latitudes. These changes induce the following remote effects in the summer MLT: downshift of the residual circulation, as well as stronger dissipation, lower temperatures, and reduced easterlies below the mesopause. The simulated sensitivity is consistent with enhanced turbulent diffusion at lower altitudes resulting from stronger GW amplitudes.

Land-Atmosphere Coupling in the Multi-Scale Modelling Framework

NASA Astrophysics Data System (ADS)

Kraus, P. M.; Denning, S.

2015-12-01

The Multi-Scale Modeling Framework (MMF), in which cloud-resolving models (CRMs) are embedded within general circulation model (GCM) gridcells to serve as the model's cloud parameterization, has offered a number of benefits to GCM simulations. The coupling of these cloud-resolving models directly to land surface model instances, rather than passing averaged atmospheric variables to a single instance of a land surface model, the logical next step in model development, has recently been accomplished. This new configuration offers conspicuous improvements to estimates of precipitation and canopy through-fall, but overall the model exhibits warm surface temperature biases and low productivity.This work presents modifications to a land-surface model that take advantage of the new multi-scale modeling framework, and accommodate the change in spatial scale from a typical GCM range of ~200 km to the CRM grid-scale of 4 km.A parameterization is introduced to apportion modeled surface radiation into direct-beam and diffuse components. The diffuse component is then distributed among the land-surface model instances within each GCM cell domain. This substantially reduces the number excessively low light values provided to the land-surface model when cloudy conditions are modeled in the CRM, associated with its 1-D radiation scheme. The small spatial scale of the CRM, ~4 km, as compared with the typical ~200 km GCM scale, provides much more realistic estimates of precipitation intensity, this permits the elimination of a model parameterization of canopy through-fall. However, runoff at such scales can no longer be considered as an immediate flow to the ocean. Allowing sub-surface water flow between land-surface instances within the GCM domain affords better realism and also reduces temperature and productivity biases.The MMF affords a number of opportunities to land-surface modelers, providing both the advantages of direct simulation at the 4 km scale and a much reduced conceptual gap between model resolution and parameterized processes.

Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T.

PubMed

Beaujoin, Justine; Palomero-Gallagher, Nicola; Boumezbeur, Fawzi; Axer, Markus; Bernard, Jeremy; Poupon, Fabrice; Schmitz, Daniel; Mangin, Jean-François; Poupon, Cyril

2018-06-01

The human hippocampus plays a key role in memory management and is one of the first structures affected by Alzheimer's disease. Ultra-high magnetic resonance imaging provides access to its inner structure in vivo. However, gradient limitations on clinical systems hinder access to its inner connectivity and microstructure. A major target of this paper is the demonstration of diffusion MRI potential, using ultra-high field (11.7 T) and strong gradients (750 mT/m), to reveal the extra- and intra-hippocampal connectivity in addition to its microstructure. To this purpose, a multiple-shell diffusion-weighted acquisition protocol was developed to reach an ultra-high spatio-angular resolution with a good signal-to-noise ratio. The MRI data set was analyzed using analytical Q-Ball Imaging, Diffusion Tensor Imaging (DTI), and Neurite Orientation Dispersion and Density Imaging models. High Angular Resolution Diffusion Imaging estimates allowed us to obtain an accurate tractography resolving more complex fiber architecture than DTI models, and subsequently provided a map of the cross-regional connectivity. The neurite density was akin to that found in the histological literature, revealing the three hippocampal layers. Moreover, a gradient of connectivity and neurite density was observed between the anterior and the posterior part of the hippocampus. These results demonstrate that ex vivo ultra-high field/ultra-high gradients diffusion-weighted MRI allows the mapping of the inner connectivity of the human hippocampus, its microstructure, and to accurately reconstruct elements of the polysynaptic intra-hippocampal pathway using fiber tractography techniques at very high spatial/angular resolutions.

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

PubMed Central

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

2010-01-01

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

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.

A LES-CMC formulation for premixed flames including differential diffusion

NASA Astrophysics Data System (ADS)

Farrace, Daniele; Chung, Kyoungseoun; Bolla, Michele; Wright, Yuri M.; Boulouchos, Konstantinos; Mastorakos, Epaminondas

2018-05-01

A finite volume large eddy simulation-conditional moment closure (LES-CMC) numerical framework for premixed combustion developed in a previous studyhas been extended to account for differential diffusion. The non-unity Lewis number CMC transport equation has an additional convective term in sample space proportional to the conditional diffusion of the progress variable, that in turn accounts for diffusion normal to the flame front and curvature-induced effects. Planar laminar simulations are first performed using a spatially homogeneous non-unity Lewis number CMC formulation and validated against physical-space fully resolved reference solutions. The same CMC formulation is subsequently used to numerically investigate the effects of curvature for laminar flames having different effective Lewis numbers: a lean methane-air flame with Leeff = 0.99 and a lean hydrogen-air flame with Leeff = 0.33. Results suggest that curvature does not affect the conditional heat release if the effective Lewis number tends to unity, so that curvature-induced transport may be neglected. Finally, the effect of turbulence on the flame structure is qualitatively analysed using LES-CMC simulations with and without differential diffusion for a turbulent premixed bluff body methane-air flame exhibiting local extinction behaviour. Overall, both the unity and the non-unity computations predict the characteristic M-shaped flame observed experimentally, although some minor differences are identified. The findings suggest that for the high Karlovitz number (from 1 to 10) flame considered, turbulent mixing within the flame weakens the differential transport contribution by reducing the conditional scalar dissipation rate and accordingly the conditional diffusion of the progress variable.

Spatial Modeling of Iron Transformations Within Artificial Soil Aggregates

NASA Astrophysics Data System (ADS)

Kausch, M.; Meile, C.; Pallud, C.

2008-12-01

Structured soils exhibit significant variations in transport characteristics at the aggregate scale. Preferential flow occurs through macropores while predominantly diffusive exchange takes place in intra-aggregate micropores. Such environments characterized by mass transfer limitations are conducive to the formation of small-scale chemical gradients and promote strong spatial variation in processes controlling the fate of redox-sensitive elements such as Fe. In this study, we present a reactive transport model used to spatially resolve iron bioreductive processes occurring within a spherical aggregate at the interface between advective and diffusive domains. The model is derived from current conceptual models of iron(hydr)oxide (HFO) transformations and constrained by literature and experimental data. Data were obtained from flow-through experiments on artificial soil aggregates inoculated with Shewanella putrefaciens strain CN32, and include the temporal evolution of the bulk solution composition, as well as spatial information on the final solid phase distribution within aggregates. With all iron initially in the form of ferrihydrite, spatially heterogeneous formation of goethite/lepidocrocite, magnetite and siderite was observed during the course of the experiments. These transformations were reproduced by the model, which ascribes a central role to divalent iron as a driver of HFO transformations and master variable in the rate laws of the considered reaction network. The predicted dissolved iron breakthrough curves also match the experimental ones closely. Thus, the computed chemical concentration fields help identify factors governing the observed trends in the solid phase distribution patterns inside the aggregate. Building on a mechanistic description of transformation reactions, fluid flow and solute transport, the model was able to describe the observations and hence illustrates the importance of small-scale gradients and dynamics of bioreductive processes for assessing bulk iron cycling. As HFOs are ubiquitous in soils, such process-level understanding of aggregate-scale iron dynamics has broad implications for the prediction of the subsurface fate of nutrients and contaminants that interact strongly with HFO surfaces.

SPATIALLY RESOLVED SPECTROSCOPY OF EUROPA’S LARGE-SCALE COMPOSITIONAL UNITS AT 3–4 μ m WITH KECK NIRSPEC

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

Fischer, P. D.; Brown, M. E.; Trumbo, S. K.

2017-01-01

We present spatially resolved spectroscopic observations of Europa’s surface at 3–4 μ m obtained with the near-infrared spectrograph and adaptive optics system on the Keck II telescope. These are the highest quality spatially resolved reflectance spectra of Europa’s surface at 3–4 μ m. The observations spatially resolve Europa’s large-scale compositional units at a resolution of several hundred kilometers. The spectra show distinct features and geographic variations associated with known compositional units; in particular, large-scale leading hemisphere chaos shows a characteristic longward shift in peak reflectance near 3.7 μ m compared to icy regions. These observations complement previous spectra of large-scalemore » chaos, and can aid efforts to identify the endogenous non-ice species.« less

Evaluation of positron-emission-tomography for visualisation of migration processes in geomaterials

NASA Astrophysics Data System (ADS)

Kulenkampff, J.; Gründig, M.; Richter, M.; Enzmann, F.

Positron-emission-tomography (PET) was applied for direct visualisation of solute transport in order to overcome the limitations of conventional methods for measuring advection and diffusion properties. At intervals from minutes to days the 3D-spatial distribution of the PET-tracer is determined. This spatiotemporal evolution of the tracer concentration can be used as experimental basis for clarification of the relevant transport processes, derivation of transport parameters, and model calibration. Here, 18F and 124I in 0.01 M carrier solution of KF and KI, respectively, have been chosen out of the limited number of available PET-tracers, primarily on account of their decay time and the time span of the experiments. The sample is a granite core from the Äspö Hard Rock Laboratory which carries an axial fracture with an aperture of ∼0.5 mm. Therefore, its permeability is high: high injection rates of 0.1 ml/min caused a pressure drop below 100 kPa. The experiments showed that the transport path through the fracture is modulated by the flow rate. The comparison of the experiments with different flow rates indicates diffusion into the matrix material at localized sites. However, the derived diffusion length falls below the resolution limits of the medical PET-scanner. With recently available dedicated high-resolution PET-scanners, which are usually applied in biomedical research, diffusion effects will be clearly resolvable.

Analytical approximations for spatial stochastic gene expression in single cells and tissues

PubMed Central

Smith, Stephen; Cianci, Claudia; Grima, Ramon

2016-01-01

Gene expression occurs in an environment in which both stochastic and diffusive effects are significant. Spatial stochastic simulations are computationally expensive compared with their deterministic counterparts, and hence little is currently known of the significance of intrinsic noise in a spatial setting. Starting from the reaction–diffusion master equation (RDME) describing stochastic reaction–diffusion processes, we here derive expressions for the approximate steady-state mean concentrations which are explicit functions of the dimensionality of space, rate constants and diffusion coefficients. The expressions have a simple closed form when the system consists of one effective species. These formulae show that, even for spatially homogeneous systems, mean concentrations can depend on diffusion coefficients: this contradicts the predictions of deterministic reaction–diffusion processes, thus highlighting the importance of intrinsic noise. We confirm our theory by comparison with stochastic simulations, using the RDME and Brownian dynamics, of two models of stochastic and spatial gene expression in single cells and tissues. PMID:27146686

Geometrical Patterning of Super-Hydrophobic Biosensing Transistors Enables Space and Time Resolved Analysis of Biological Mixtures.

PubMed

Gentile, Francesco; Ferrara, Lorenzo; Villani, Marco; Bettelli, Manuele; Iannotta, Salvatore; Zappettini, Andrea; Cesarelli, Mario; Di Fabrizio, Enzo; Coppedè, Nicola

2016-01-12

PSS is a conductive polymer that can be integrated into last generation Organic Electrochemical Transistor (OECT) devices for biological inspection, identification and analysis. While a variety of reports in literature demonstrated the chemical and biological sensitivity of these devices, still their ability in resolving complex mixtures remains controversial. Similar OECT devices display good time dynamics behavior but lack spatial resolution. In this work, we integrated PSS with patterns of super-hydrophobic pillars in which a finite number of those pillars is independently controlled for site-selective measurement of a solution. We obtained a multifunctional, hierarchical OECT device that bridges the micro- to the nano-scales for specific, combined time and space resolved analysis of the sample. Due to super-hydrophobic surface properties, the biological species in the drop are driven by convection, diffusion, and the externally applied electric field: the balance/unbalance between these forces will cause the molecules to be transported differently within its volume depending on particle size thus realizing a size-selective separation. Within this framework, the separation and identification of two different molecules, namely Cetyl Trimethyl Ammonium Bromid (CTAB) and adrenaline, in a biological mixture have been demonstrated, showing that geometrical control at the micro-nano scale impart unprecedented selectivity to the devices.

Geometrical Patterning of Super-Hydrophobic Biosensing Transistors Enables Space and Time Resolved Analysis of Biological Mixtures

PubMed Central

Gentile, Francesco; Ferrara, Lorenzo; Villani, Marco; Bettelli, Manuele; Iannotta, Salvatore; Zappettini, Andrea; Cesarelli, Mario; Di Fabrizio, Enzo; Coppedè, Nicola

2016-01-01

PEDOT:PSS is a conductive polymer that can be integrated into last generation Organic Electrochemical Transistor (OECT) devices for biological inspection, identification and analysis. While a variety of reports in literature demonstrated the chemical and biological sensitivity of these devices, still their ability in resolving complex mixtures remains controversial. Similar OECT devices display good time dynamics behavior but lack spatial resolution. In this work, we integrated PEDOT:PSS with patterns of super-hydrophobic pillars in which a finite number of those pillars is independently controlled for site-selective measurement of a solution. We obtained a multifunctional, hierarchical OECT device that bridges the micro- to the nano-scales for specific, combined time and space resolved analysis of the sample. Due to super-hydrophobic surface properties, the biological species in the drop are driven by convection, diffusion, and the externally applied electric field: the balance/unbalance between these forces will cause the molecules to be transported differently within its volume depending on particle size thus realizing a size-selective separation. Within this framework, the separation and identification of two different molecules, namely Cetyl Trimethyl Ammonium Bromid (CTAB) and adrenaline, in a biological mixture have been demonstrated, showing that geometrical control at the micro-nano scale impart unprecedented selectivity to the devices. PMID:26753611

Geometrical Patterning of Super-Hydrophobic Biosensing Transistors Enables Space and Time Resolved Analysis of Biological Mixtures

NASA Astrophysics Data System (ADS)

Gentile, Francesco; Ferrara, Lorenzo; Villani, Marco; Bettelli, Manuele; Iannotta, Salvatore; Zappettini, Andrea; Cesarelli, Mario; di Fabrizio, Enzo; Coppedè, Nicola

2016-01-01

PEDOT:PSS is a conductive polymer that can be integrated into last generation Organic Electrochemical Transistor (OECT) devices for biological inspection, identification and analysis. While a variety of reports in literature demonstrated the chemical and biological sensitivity of these devices, still their ability in resolving complex mixtures remains controversial. Similar OECT devices display good time dynamics behavior but lack spatial resolution. In this work, we integrated PEDOT:PSS with patterns of super-hydrophobic pillars in which a finite number of those pillars is independently controlled for site-selective measurement of a solution. We obtained a multifunctional, hierarchical OECT device that bridges the micro- to the nano-scales for specific, combined time and space resolved analysis of the sample. Due to super-hydrophobic surface properties, the biological species in the drop are driven by convection, diffusion, and the externally applied electric field: the balance/unbalance between these forces will cause the molecules to be transported differently within its volume depending on particle size thus realizing a size-selective separation. Within this framework, the separation and identification of two different molecules, namely Cetyl Trimethyl Ammonium Bromid (CTAB) and adrenaline, in a biological mixture have been demonstrated, showing that geometrical control at the micro-nano scale impart unprecedented selectivity to the devices.

X-ray Diffuse Scattering from Ultrafast Laser Excited Solids

NASA Astrophysics Data System (ADS)

Trigo, Mariano; Sheu, Yu-Miin; Chen, Jian; Reis, David; Fahy, Stephen; Murray, Eamonn; Graber, Timothy; Henning, Robert

2009-03-01

Intense, ultrashort laser pulses can be used to excite and detect coherent phonons in solids. However, optical experiments can only probe a reduced fraction of the Brillouin zone and hence most of the decay channels of such coherent phonons become invisible. In contrast, time-resolved x-ray diffuse scattering (TRXDS) has the potential to be the ultimate tool to study these phonon decay processes throughout the Brillouin-zone of the crystal. In our work, performed at the BioCARS beamline at the Advanced Photon Source, we use synchrotron time-resolved diffuse x-ray scattering to study Si and Bi under intense laser excitation with 100 ps resolution. We show that reasonable signal levels can be achieved with incident flux of 10^12 photons comparable to the flux that will be available at future 4th generation sources such as the LCLS in a single pulse. These sources will also provide three orders of magnitude shorter pulses; thus, this experiment serves as a test of the feasibility of time-resolved X-ray diffuse scattering as a tool for studying nonequilibrium phonon dynamics in solids.

ARGon{sup 3}: ''3D appearance robot-based gonioreflectometer'' at PTB

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

Hoepe, A.; Atamas, T.; Huenerhoff, D.

At the Physikalisch-Technische Bundesanstalt, the National Metrology Institute of Germany, a new facility for measuring visual appearance-related quantities has been built up. The acronym ARGon{sup 3} stands for ''3D appearance robot-based gonioreflectometer''. Compared to standard gonioreflectometers, there are two main new features within this setup. First, a photometric luminance camera with a spatial resolution of 28 {mu}m on the device under test (DUT) enables spatially high-resolved measurements of luminance and color coordinates. Second, a line-scan CCD-camera mounted to a spectrometer provides measurements of the radiance factor, respectively the bidirectional reflectance distribution function, in full V({lambda})-range (360 nm-830 nm) with arbitrarymore » angles of irradiation and detection relative to the surface normal, on a time scale of about 2 min. First goniometric measurements of diffuse reflection within 3D-space above the DUT with subsequent colorimetric representation of the obtained data of special effect pigments based on the interference effect are presented.« less

Dynamics of ultrathin V-oxide layers on Rh(111) in catalytic oxidation of ammonia and CO.

PubMed

von Boehn, B; Preiss, A; Imbihl, R

2016-07-20

Catalytic oxidation of ammonia and CO has been studied in the 10(-4) mbar range using a catalyst prepared by depositing ultra-thin vanadium oxide layers on Rh(111) (θV ≈ 0.2 MLE). Using photoemission electron microscopy (PEEM) as a spatially resolving method, we observe that upon heating in an atmosphere of NH3 and O2 the spatial homogeneity of the VOx layer is removed at 800 K and a pattern consisting of macroscopic stripes develops; at elevated temperatures this pattern transforms into a pattern of circular VOx islands. Under reaction conditions the neighboring VOx islands become attracted by each other and coalesce. Similar processes of pattern formation and island coalescence are observed in catalytic CO oxidation. Reoxidation of the reduced VOx catalyst proceeds via surface diffusion of oxygen adsorbed onto Rh(111). A pattern consisting of macroscopic circular VOx islands can also be obtained by heating a Rh(111)/VOx catalyst in pure O2.

Phase correlation imaging of unlabeled cell dynamics

NASA Astrophysics Data System (ADS)

Ma, Lihong; Rajshekhar, Gannavarpu; Wang, Ru; Bhaduri, Basanta; Sridharan, Shamira; Mir, Mustafa; Chakraborty, Arindam; Iyer, Rajashekar; Prasanth, Supriya; Millet, Larry; Gillette, Martha U.; Popescu, Gabriel

2016-09-01

We present phase correlation imaging (PCI) as a novel approach to study cell dynamics in a spatially-resolved manner. PCI relies on quantitative phase imaging time-lapse data and, as such, functions in label-free mode, without the limitations associated with exogenous markers. The correlation time map outputted in PCI informs on the dynamics of the intracellular mass transport. Specifically, we show that PCI can extract quantitatively the diffusion coefficient map associated with live cells, as well as standard Brownian particles. Due to its high sensitivity to mass transport, PCI can be applied to studying the integrity of actin polymerization dynamics. Our results indicate that the cyto-D treatment blocking the actin polymerization has a dominant effect at the large spatial scales, in the region surrounding the cell. We found that PCI can distinguish between senescent and quiescent cells, which is extremely difficult without using specific markers currently. We anticipate that PCI will be used alongside established, fluorescence-based techniques to enable valuable new studies of cell function.

Experimental Observation of Thin-shell Instability in a Collisionless Plasma

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

Ahmed, H.; Doria, D.; Sarri, G.

We report on the experimental observation of the instability of a plasma shell, which formed during the expansion of a laser-ablated plasma into a rarefied ambient medium. By means of a proton radiography technique, the evolution of the instability is temporally and spatially resolved on a timescale much shorter than the hydrodynamic one. The density of the thin shell exceeds that of the surrounding plasma, which lets electrons diffuse outward. An ambipolar electric field grows on both sides of the thin shell that is antiparallel to the density gradient. Ripples in the thin shell result in a spatially varying balancemore » between the thermal pressure force mediated by this field and the ram pressure force that is exerted on it by the inflowing plasma. This mismatch amplifies the ripples by the same mechanism that drives the hydrodynamic nonlinear thin-shell instability (NTSI). Our results thus constitute the first experimental verification that the NTSI can develop in colliding flows.« less

Experimental Observation of Thin-shell Instability in a Collisionless Plasma

NASA Astrophysics Data System (ADS)

Ahmed, H.; Doria, D.; Dieckmann, M. E.; Sarri, G.; Romagnani, L.; Bret, A.; Cerchez, M.; Giesecke, A. L.; Ianni, E.; Kar, S.; Notley, M.; Prasad, R.; Quinn, K.; Willi, O.; Borghesi, M.

2017-01-01

We report on the experimental observation of the instability of a plasma shell, which formed during the expansion of a laser-ablated plasma into a rarefied ambient medium. By means of a proton radiography technique, the evolution of the instability is temporally and spatially resolved on a timescale much shorter than the hydrodynamic one. The density of the thin shell exceeds that of the surrounding plasma, which lets electrons diffuse outward. An ambipolar electric field grows on both sides of the thin shell that is antiparallel to the density gradient. Ripples in the thin shell result in a spatially varying balance between the thermal pressure force mediated by this field and the ram pressure force that is exerted on it by the inflowing plasma. This mismatch amplifies the ripples by the same mechanism that drives the hydrodynamic nonlinear thin-shell instability (NTSI). Our results thus constitute the first experimental verification that the NTSI can develop in colliding flows.

Extracting spatial information from large aperture exposures of diffuse sources

NASA Technical Reports Server (NTRS)

Clarke, J. T.; Moos, H. W.

1981-01-01

The spatial properties of large aperture exposures of diffuse emission can be used both to investigate spatial variations in the emission and to filter out camera noise in exposures of weak emission sources. Spatial imaging can be accomplished both parallel and perpendicular to dispersion with a resolution of 5-6 arc sec, and a narrow median filter running perpendicular to dispersion across a diffuse image selectively filters out point source features, such as reseaux marks and fast particle hits. Spatial information derived from observations of solar system objects is presented.

Baryons at the edge of the X-ray-brightest galaxy cluster.

PubMed

Simionescu, Aurora; Allen, Steven W; Mantz, Adam; Werner, Norbert; Takei, Yoh; Morris, R Glenn; Fabian, Andrew C; Sanders, Jeremy S; Nulsen, Paul E J; George, Matthew R; Taylor, Gregory B

2011-03-25

Studies of the diffuse x-ray-emitting gas in galaxy clusters have provided powerful constraints on cosmological parameters and insights into plasma astrophysics. However, measurements of the faint cluster outskirts have become possible only recently. Using data from the Suzaku x-ray telescope, we determined an accurate, spatially resolved census of the gas, metals, and dark matter out to the edge of the Perseus Cluster. Contrary to previous results, our measurements of the cluster baryon fraction are consistent with the expected universal value at half of the virial radius. The apparent baryon fraction exceeds the cosmic mean at larger radii, suggesting a clumpy distribution of the gas, which is important for understanding the ongoing growth of clusters from the surrounding cosmic web.

Spatially and momentum resolved energy electron loss spectra from an ultra-thin PrNiO{sub 3} layer

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

Kinyanjui, M. K., E-mail: michael.kinyanjui@uni-ulm.de; Kaiser, U.; Benner, G.

2015-05-18

We present an experimental approach which allows for the acquisition of spectra from ultra-thin films at high spatial, momentum, and energy resolutions. Spatially and momentum (q) resolved electron energy loss spectra have been obtained from a 12 nm ultra-thin PrNiO{sub 3} layer using a nano-beam electron diffraction based approach which enabled the acquisition of momentum resolved spectra from individual, differently oriented nano-domains and at different positions of the PrNiO{sub 3} thin layer. The spatial and wavelength dependence of the spectral excitations are obtained and characterized after the analysis of the experimental spectra using calculated dielectric and energy loss functions. The presentedmore » approach makes a contribution towards obtaining momentum-resolved spectra from nanostructures, thin film, heterostructures, surfaces, and interfaces.« less

Performance of Orbital Neutron Instruments for Spatially Resolved Hydrogen Measurements of Airless Planetary Bodies

PubMed Central

Elphic, Richard C.; Feldman, William C.; Funsten, Herbert O.; Prettyman, Thomas H.

2010-01-01

Abstract Orbital neutron spectroscopy has become a standard technique for measuring planetary surface compositions from orbit. While this technique has led to important discoveries, such as the deposits of hydrogen at the Moon and Mars, a limitation is its poor spatial resolution. For omni-directional neutron sensors, spatial resolutions are 1–1.5 times the spacecraft's altitude above the planetary surface (or 40–600 km for typical orbital altitudes). Neutron sensors with enhanced spatial resolution have been proposed, and one with a collimated field of view is scheduled to fly on a mission to measure lunar polar hydrogen. No quantitative studies or analyses have been published that evaluate in detail the detection and sensitivity limits of spatially resolved neutron measurements. Here, we describe two complementary techniques for evaluating the hydrogen sensitivity of spatially resolved neutron sensors: an analytic, closed-form expression that has been validated with Lunar Prospector neutron data, and a three-dimensional modeling technique. The analytic technique, called the Spatially resolved Neutron Analytic Sensitivity Approximation (SNASA), provides a straightforward method to evaluate spatially resolved neutron data from existing instruments as well as to plan for future mission scenarios. We conclude that the existing detector—the Lunar Exploration Neutron Detector (LEND)—scheduled to launch on the Lunar Reconnaissance Orbiter will have hydrogen sensitivities that are over an order of magnitude poorer than previously estimated. We further conclude that a sensor with a geometric factor of ∼ 100 cm2 Sr (compared to the LEND geometric factor of ∼ 10.9 cm2 Sr) could make substantially improved measurements of the lunar polar hydrogen spatial distribution. Key Words: Planetary instrumentation—Planetary science—Moon—Spacecraft experiments—Hydrogen. Astrobiology 10, 183–200. PMID:20298147

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

PubMed

Marquez-Lago, Tatiana T; Burrage, Kevin

2007-09-14

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spatial heterogeneity can all affect the cellular dynamics. However, there are ways in which important effects can be accounted without going to the extent of using highly resolved spatial simulators (such as single-particle software), hence reducing the overall computation time significantly. We present a new coarse grained modified version of the next subvolume method that allows the user to consider both diffusion and reaction events in relatively long simulation time spans as compared with the original method and other commonly used fully stochastic computational methods. Benchmarking of the simulation algorithm was performed through comparison with the next subvolume method and well mixed models (MATLAB), as well as stochastic particle reaction and transport simulations (CHEMCELL, Sandia National Laboratories). Additionally, we construct a model based on a set of chemical reactions in the epidermal growth factor receptor pathway. For this particular application and a bistable chemical system example, we analyze and outline the advantages of our presented binomial tau-leap spatial stochastic simulation algorithm, in terms of efficiency and accuracy, in scenarios of both molecular homogeneity and heterogeneity.

Characterization of Secondary Mineral Grain Coatings and their Role as Diffusion-controlled Sinks and Sources for Metal Contaminants

NASA Astrophysics Data System (ADS)

Davis, J. A.; Guo, H.; Lai, B.; Kemner, K. M.; Ercius, P.; Fox, P. M.; Singer, D. M.; Minor, A.; Waychunas, G.

2012-12-01

Many important geochemical reactions occur at the mineral-water interface, including sorption and desorption reactions of contaminants. Fundamental knowledge of the kinetics of these processes is based primarily on experimental observations of reactions at faces of single crystals or macroscopic data from pure mineral powder suspensions. Sorption reactions at crystal faces are generally very fast, on the order of microseconds or less, with reaction times often limited only by film diffusion at the mineral-water interface. In well-stirred suspensions of aquifer sediments, however, sorptive equilibrium can take many hours or days to achieve steady-state concentrations. We have examined the potential reasons for sorption rate limitation using uranium(VI) sorption by sediments from a sandy aquifer in Savannah River, South Carolina (USA). U(VI) sorption by sand-sized grains from the aquifer is dominated by reaction with secondary mineral coatings on quartz and feldspar grains. The coatings studied were on the order of 15 microns in thickness (i.e., from quartz grain to aqueous solution) and composed primarily of clay minerals and hematite of varying particle size. Microfocused-XRF imaging of elemental concentrations (e.g., U, Fe) of polished cross-sections of the grain/coating contact showed strong spatial correlations of U and Fe within the coatings, regardless of the length of reaction time (30 minutes to 4 weeks). The spatial resolution of the μ-XRF technique is of the order of 2 microns in horizontal directions, but the uncertainty of the observed spatial gradients is high due to grain curvature away from the polished surface and fluorescence contributed from the entire 30 micron thickness of a typical grain/epoxy thin section. TEM characterization of focused-ion-beam (FIB), vertically-extracted samples of the grain-coating contact shows that complex pore networks exist within the coatings of variable dimensions and unknown connectivity. Using scanning TEM (STEM) tomography, it can be seen that there are large numbers of pore throat sizes less than 10 nm within the coatings. We hypothesize that diffusion through these pores, which likely have electrically charged surfaces, controls the observed macroscopic rates of U(VI) sorption in batch experiments with sand grains. Evidence to support this hypothesis was observed by studying U and Fe fluorescence spatial variation within FIB samples (1 micron thick) at 200 nm spatial resolution. With this greater spatial resolution, it is possible to see U concentration variations within the coatings that are dependent on the time of sorption reaction, and illustrates how the coating environment constitutes a diffusion constraint to achieve adsorptive equilibrium between an aqueous phase and the mineral surfaces. Including this diffusion constraint within conceptual models for reactive contaminant transport may be significant at the field scale, because secondary mineral coatings are potentially both sinks and sources of contaminants depending on the history of a contaminated site. This is important in resolving long-term transport predictions at DOE sites, such as Hanford and Savannah River, where equilibrium versus kinetic reactive transport models are being evaluated.

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.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Spatially Resolved Isotopic Source Signatures of Wetland Methane Emissions

NASA Astrophysics Data System (ADS)

Ganesan, A. L.; Stell, A. C.; Gedney, N.; Comyn-Platt, E.; Hayman, G.; Rigby, M.; Poulter, B.; Hornibrook, E. R. C.

2018-04-01

We present the first spatially resolved wetland δ13C(CH4) source signature map based on data characterizing wetland ecosystems and demonstrate good agreement with wetland signatures derived from atmospheric observations. The source signature map resolves a latitudinal difference of 10‰ between northern high-latitude (mean -67.8‰) and tropical (mean -56.7‰) wetlands and shows significant regional variations on top of the latitudinal gradient. We assess the errors in inverse modeling studies aiming to separate CH4 sources and sinks by comparing atmospheric δ13C(CH4) derived using our spatially resolved map against the common assumption of globally uniform wetland δ13C(CH4) signature. We find a larger interhemispheric gradient, a larger high-latitude seasonal cycle, and smaller trend over the period 2000-2012. The implication is that erroneous CH4 fluxes would be derived to compensate for the biases imposed by not utilizing spatially resolved signatures for the largest source of CH4 emissions. These biases are significant when compared to the size of observed signals.

Imaging White Matter in Human Brainstem

PubMed Central

Ford, Anastasia A.; Colon-Perez, Luis; Triplett, William T.; Gullett, Joseph M.; Mareci, Thomas H.; FitzGerald, David B.

2013-01-01

The human brainstem is critical for the control of many life-sustaining functions, such as consciousness, respiration, sleep, and transfer of sensory and motor information between the brain and the spinal cord. Most of our knowledge about structure and organization of white and gray matter within the brainstem is derived from ex vivo dissection and histology studies. However, these methods cannot be applied to study structural architecture in live human participants. Tractography from diffusion-weighted magnetic resonance imaging (MRI) may provide valuable insights about white matter organization within the brainstem in vivo. However, this method presents technical challenges in vivo due to susceptibility artifacts, functionally dense anatomy, as well as pulsatile and respiratory motion. To investigate the limits of MR tractography, we present results from high angular resolution diffusion imaging of an intact excised human brainstem performed at 11.1 T using isotropic resolution of 0.333, 1, and 2 mm, with the latter reflecting resolution currently used clinically. At the highest resolution, the dense fiber architecture of the brainstem is evident, but the definition of structures degrades as resolution decreases. In particular, the inferred corticopontine/corticospinal tracts (CPT/CST), superior (SCP) and middle cerebellar peduncle (MCP), and medial lemniscus (ML) pathways are clearly discernable and follow known anatomical trajectories at the highest spatial resolution. At lower resolutions, the CST/CPT, SCP, and MCP pathways are artificially enlarged due to inclusion of collinear and crossing fibers not inherent to these three pathways. The inferred ML pathways appear smaller at lower resolutions, indicating insufficient spatial information to successfully resolve smaller fiber pathways. Our results suggest that white matter tractography maps derived from the excised brainstem can be used to guide the study of the brainstem architecture using diffusion MRI in vivo. PMID:23898254

Imaging white matter in human brainstem.

PubMed

Ford, Anastasia A; Colon-Perez, Luis; Triplett, William T; Gullett, Joseph M; Mareci, Thomas H; Fitzgerald, David B

2013-01-01

The human brainstem is critical for the control of many life-sustaining functions, such as consciousness, respiration, sleep, and transfer of sensory and motor information between the brain and the spinal cord. Most of our knowledge about structure and organization of white and gray matter within the brainstem is derived from ex vivo dissection and histology studies. However, these methods cannot be applied to study structural architecture in live human participants. Tractography from diffusion-weighted magnetic resonance imaging (MRI) may provide valuable insights about white matter organization within the brainstem in vivo. However, this method presents technical challenges in vivo due to susceptibility artifacts, functionally dense anatomy, as well as pulsatile and respiratory motion. To investigate the limits of MR tractography, we present results from high angular resolution diffusion imaging of an intact excised human brainstem performed at 11.1 T using isotropic resolution of 0.333, 1, and 2 mm, with the latter reflecting resolution currently used clinically. At the highest resolution, the dense fiber architecture of the brainstem is evident, but the definition of structures degrades as resolution decreases. In particular, the inferred corticopontine/corticospinal tracts (CPT/CST), superior (SCP) and middle cerebellar peduncle (MCP), and medial lemniscus (ML) pathways are clearly discernable and follow known anatomical trajectories at the highest spatial resolution. At lower resolutions, the CST/CPT, SCP, and MCP pathways are artificially enlarged due to inclusion of collinear and crossing fibers not inherent to these three pathways. The inferred ML pathways appear smaller at lower resolutions, indicating insufficient spatial information to successfully resolve smaller fiber pathways. Our results suggest that white matter tractography maps derived from the excised brainstem can be used to guide the study of the brainstem architecture using diffusion MRI in vivo.

Reference-free spectroscopic determination of fat and protein in milk in the visible and near infrared region below 1000nm using spatially resolved diffuse reflectance fiber probe.

PubMed

Bogomolov, Andrey; Belikova, Valeria; Galyanin, Vladislav; Melenteva, Anastasiia; Meyer, Hans

2017-05-15

New technique of diffuse reflectance spectroscopic analysis of milk fat and total protein content in the visible (Vis) and adjacent near infrared (NIR) region (400-995nm) has been developed and tested. Sample analysis was performed through a probe having eight 200-µm fiber channels forming a linear array. One of the end fibers was used for the illumination and other seven - for the spectroscopic detection of diffusely reflected light. One of the detection channels was used as a reference to normalize the spectra and to convert them into absorbance-equivalent units. The method has been tested experimentally using a designed sample set prepared from industrial raw milk standards with widely varying fat and protein content. To increase the modelling robustness all milk samples were measured in three different homogenization degrees. Comprehensive data analysis has shown the advantage of combining both spectral and spatial resolution in the same measurement and revealed the most relevant channels and wavelength regions. The modelling accuracy was further improved using joint variable selection and preprocessing optimization method based on the genetic algorithm. The root mean-square errors of different validation methods were below 0.10% for fat and below 0.08% for total protein content. Based on the present experimental data, it was computationally shown that the full-spectrum analysis in this method can be replaced by a sensor measurement at several specific wavelengths, for instance, using light-emitting diodes (LEDs) for illumination. Two optimal sensor configurations have been suggested: with nine LEDs for the analysis of fat and seven - for protein content. Both simulated sensors exhibit nearly the same component determination accuracy as corresponding full-spectrum analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Kinetic D/H fractionation during hydration and dehydration of silicate glasses, melts and nominally anhydrous minerals

NASA Astrophysics Data System (ADS)

Roskosz, M.; Deloule, E.; Ingrin, J.; Depecker, C.; Laporte, D.; Merkel, S.; Remusat, L.; Leroux, H.

2018-07-01

The distribution of hydrogen isotopes during diffusion-driven aqueous processes in silicate glasses, melts and crystals was investigated. Hydration/dehydration experiments were performed on silica glasses at 1000 °C and 1 bar total pressure. Dehydration triggered by decompression-driven bubble nucleation and growth was performed on rhyolitic melts at 800 °C and a few hundred MPa. Hydrogen extraction from a nominally anhydrous mineral (grossular) single crystal was carried out at 800 °C and ambient pressure. After these three series of experiments, pronounced water (sensu lato) concentration profiles were observed in all recovered samples. In the grossular single-crystal, a large spatial variation in H isotopes (δD variation > 550‰) was measured across the sample. This isotopic distribution correlates with the hydrogen extraction profile. The fit to the data suggests an extreme decoupling between hydrogen and deuterium diffusion coefficients (DH and DD respectively), akin to the decoupling expected in a dilute ideal gas (DH/DD ≈ 1.41). Conversely, no measurable spatially- and time-resolved isotopic variations were measured in silicate glasses and melts. This contrasted behavior of hydrogen isotopes likely stands in the different water speciation and solution mechanisms in the three different materials. Glasses and melts contain essentially hydroxyl and molecular water groups but the mobile species is molecular water in both cases. Protonated defects make up most of the water accommodated in grossular and other nominally anhydrous minerals (NAM). These defects are also the mobile species that diffuse against polarons. These results are crucial to accurately model the degassing behavior of terrestrial and lunar magmas and to derive the initial D/H of water trapped in fluid inclusions commonly analyzed in mantle NAMs, which suffered complex geological histories.

Towards a more consistent picture of isopycnal mixing in climate models

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Unified path integral approach to theories of diffusion-influenced reactions

NASA Astrophysics Data System (ADS)

Prüstel, Thorsten; Meier-Schellersheim, Martin

2017-08-01

Building on mathematical similarities between quantum mechanics and theories of diffusion-influenced reactions, we develop a general approach for computational modeling of diffusion-influenced reactions that is capable of capturing not only the classical Smoluchowski picture but also alternative theories, as is here exemplified by a volume reactivity model. In particular, we prove the path decomposition expansion of various Green's functions describing the irreversible and reversible reaction of an isolated pair of molecules. To this end, we exploit a connection between boundary value and interaction potential problems with δ - and δ'-function perturbation. We employ a known path-integral-based summation of a perturbation series to derive a number of exact identities relating propagators and survival probabilities satisfying different boundary conditions in a unified and systematic manner. Furthermore, we show how the path decomposition expansion represents the propagator as a product of three factors in the Laplace domain that correspond to quantities figuring prominently in stochastic spatially resolved simulation algorithms. This analysis will thus be useful for the interpretation of current and the design of future algorithms. Finally, we discuss the relation between the general approach and the theory of Brownian functionals and calculate the mean residence time for the case of irreversible and reversible reactions.

Study of the Formation and Evolution of Precipitation Induced Sea Surface Salinity Minima in the Tropical Pacific Using HYCOM

NASA Astrophysics Data System (ADS)

Gallagher, R. L.

2016-02-01

During heavy rain events in the tropics, areas of relatively low salinity water collect on the ocean surface. Rainfall events increase the buoyancy of the ocean surface and impact upper ocean salinity and temperature profiles. This resists downward mixing and as a result can persist (SPURS II planning group, 2012; Oceanography 28(1) 150-159). Salinity at the surface adjusts through advective and diffusive mixing processes (Scott, J. et al, 2013; AGU Fall meeting abstracts). This project investigates the upper ocean salinity response in both advection and diffusion dominated regions. The changes in ocean surface salinity are tracked before, during, and after rainfall events. Data from a standard oceanographic model, HYCOM, are used to identify areas where each surface process is significant. Rainfall events are identified using a TRMM dataset. It provides a tropical rainfall analysis which uses amalgamated satellite data to develop detailed global precipitation grids between 50 o north and south latitude. TRMM is useful due its high temporal and spatial resolutions. The salinity response in HYCOM is tested against simple theoretical advective and diffusive mixing models. The magnitude of sea surface salinity minima, their persistence and the precision by which HYCOM can resolve these phenomena are of interest.

Spread spectrum time-resolved diffuse optical measurement system for enhanced sensitivity in detecting human brain activity

NASA Astrophysics Data System (ADS)

Mehta, Kalpesh; Hasnain, Ali; Zhou, Xiaowei; Luo, Jianwen; Penney, Trevor B.; Chen, Nanguang

2017-04-01

Diffuse optical spectroscopy (DOS) and imaging methods have been widely applied to noninvasive detection of brain activity. We have designed and implemented a low cost, portable, real-time one-channel time-resolved DOS system for neuroscience studies. Phantom experiments were carried out to test the performance of the system. We further conducted preliminary human experiments and demonstrated that enhanced sensitivity in detecting neural activity in the cortex could be achieved by the use of late arriving photons.

Quantification of joint inflammation in rheumatoid arthritis by time-resolved diffuse optical spectroscopy and tracer kinetic modeling

NASA Astrophysics Data System (ADS)

Ioussoufovitch, Seva; Morrison, Laura B.; Lee, Ting-Yim; St. Lawrence, Keith; Diop, Mamadou

2015-03-01

Rheumatoid arthritis (RA) is characterized by chronic synovial inflammation, which can cause progressive joint damage and disability. Diffuse optical spectroscopy (DOS) and imaging have the potential to become potent monitoring tools for RA. We devised a method that combined time-resolved DOS and tracer kinetics modeling to rapidly and reliably quantify blood flow in the joint. Preliminary results obtained from two animals show that the technique can detect joint inflammation as early as 5 days after onset.

Stochastic downscaling of numerically simulated spatial rain and cloud fields using a transient multifractal approach

NASA Astrophysics Data System (ADS)

Nogueira, M.; Barros, A. P.; Miranda, P. M.

2012-04-01

Atmospheric fields can be extremely variable over wide ranges of spatial scales, with a scale ratio of 109-1010 between largest (planetary) and smallest (viscous dissipation) scale. Furthermore atmospheric fields with strong variability over wide ranges in scale most likely should not be artificially split apart into large and small scales, as in reality there is no scale separation between resolved and unresolved motions. Usually the effects of the unresolved scales are modeled by a deterministic bulk formula representing an ensemble of incoherent subgrid processes on the resolved flow. This is a pragmatic approach to the problem and not the complete solution to it. These models are expected to underrepresent the small-scale spatial variability of both dynamical and scalar fields due to implicit and explicit numerical diffusion as well as physically based subgrid scale turbulent mixing, resulting in smoother and less intermittent fields as compared to observations. Thus, a fundamental change in the way we formulate our models is required. Stochastic approaches equipped with a possible realization of subgrid processes and potentially coupled to the resolved scales over the range of significant scale interactions range provide one alternative to address the problem. Stochastic multifractal models based on the cascade phenomenology of the atmosphere and its governing equations in particular are the focus of this research. Previous results have shown that rain and cloud fields resulting from both idealized and realistic numerical simulations display multifractal behavior in the resolved scales. This result is observed even in the absence of scaling in the initial conditions or terrain forcing, suggesting that multiscaling is a general property of the nonlinear solutions of the Navier-Stokes equations governing atmospheric dynamics. Our results also show that the corresponding multiscaling parameters for rain and cloud fields exhibit complex nonlinear behavior depending on large scale parameters such as terrain forcing and mean atmospheric conditions at each location, particularly mean wind speed and moist stability. A particularly robust behavior found is the transition of the multiscaling parameters between stable and unstable cases, which has a clear physical correspondence to the transition from stratiform to organized (banded) convective regime. Thus multifractal diagnostics of moist processes are fundamentally transient and should provide a physically robust basis for the downscaling and sub-grid scale parameterizations of moist processes. Here, we investigate the possibility of using a simplified computationally efficient multifractal downscaling methodology based on turbulent cascades to produce statistically consistent fields at scales higher than the ones resolved by the model. Specifically, we are interested in producing rainfall and cloud fields at spatial resolutions necessary for effective flash flood and earth flows forecasting. The results are examined by comparing downscaled field against observations, and tendency error budgets are used to diagnose the evolution of transient errors in the numerical model prediction which can be attributed to aliasing.

Impedance Spectroscopic Investigation of Proton Conductivity in Nafion Using Transient Electrochemical Atomic Force Microscopy (AFM)

PubMed Central

Hink, Steffen; Wagner, Norbert; Bessler, Wolfgang G.; Roduner, Emil

2012-01-01

Spatially resolved impedance spectroscopy of a Nafion polyelectrolyte membrane is performed employing a conductive and Pt-coated tip of an atomic force microscope as a point-like contact and electrode. The experiment is conducted by perturbing the system by a rectangular voltage step and measuring the incurred current, followed by Fourier transformation and plotting the impedance against the frequency in a conventional Bode diagram. To test the potential and limitations of this novel method, we present a feasibility study using an identical hydrogen atmosphere at a well-defined relative humidity on both sides of the membrane. It is demonstrated that good quality impedance spectra are obtained in a frequency range of 0.2–1000 Hz. The extracted polarization curves exhibit a maximum current which cannot be explained by typical diffusion effects. Simulation based on equivalent circuits requires a Nernst element for restricted diffusion in the membrane which suggests that this effect is based on the potential dependence of the electrolyte resistance in the high overpotential region. PMID:24958175

Rationalizing long-lived photo-excited carriers in photocatalyst (La5Ti2CuS5O7) in terms of one-dimensional carrier transport

NASA Astrophysics Data System (ADS)

Suzuki, Yohichi; Singh, Rupashree Balia; Matsuzaki, Hiroyuki; Furube, Akihiro; Ma, Guijun; Hisatomi, Takashi; Domen, Kazunari; Seki, Kazuhiko

2016-09-01

The semiconductor La5Ti2CuS5O7 (LTC) is a potential photocatalyst capable of operating under visible light irradiation and behaves both as a photocathode and anode when embedded onto metal layers. Time-resolved diffuse reflectance (TRDR) measurements were carried out on LTC powder and LTC deposited on Au as the back contact using the particle-transfer method. Results of TRDR measurements of powdered LTC indicated the existence of long-lived photo-excited carriers, and suggested the existence of a mechanism for preventing carrier loss in LTC. Prior research has reported that LTC has a rod-shaped crystal structure and that electrons and holes are transported through different, spatially separated channels. Based on this, we introduced a one-dimensional carrier transport model. By analyzing TRDR data, we extracted material parameters such as the diffusion coefficient of LTC. Theoretical results indicated that a micron-sized LTC particle would be preferable if carriers trapped at the top-surface do contribute to photocatalytic gas generation.

Computationally efficient approach for solving time dependent diffusion equation with discrete temporal convolution applied to granular particles of battery electrodes

NASA Astrophysics Data System (ADS)

Senegačnik, Jure; Tavčar, Gregor; Katrašnik, Tomaž

2015-03-01

The paper presents a computationally efficient method for solving the time dependent diffusion equation in a granule of the Li-ion battery's granular solid electrode. The method, called Discrete Temporal Convolution method (DTC), is based on a discrete temporal convolution of the analytical solution of the step function boundary value problem. This approach enables modelling concentration distribution in the granular particles for arbitrary time dependent exchange fluxes that do not need to be known a priori. It is demonstrated in the paper that the proposed method features faster computational times than finite volume/difference methods and Padé approximation at the same accuracy of the results. It is also demonstrated that all three addressed methods feature higher accuracy compared to the quasi-steady polynomial approaches when applied to simulate the current densities variations typical for mobile/automotive applications. The proposed approach can thus be considered as one of the key innovative methods enabling real-time capability of the multi particle electrochemical battery models featuring spatial and temporal resolved particle concentration profiles.

A versatile optical profilometer based on conoscopic holography sensors for acquisition of specular and diffusive surfaces in artworks

NASA Astrophysics Data System (ADS)

Gaburro, Nicola; Marchioro, Giacomo; Daffara, Claudia

2017-07-01

Surface metrology of artworks requires the design of suitable devices for in-situ non-destructive measurement together with reliable procedures for an effective analysis of such non-engineered variegate objects. To advance the state-of-the-art it has been implemented a versatile optical micro-profilometry taking advantage of the adapt- ability of conoscopic holography sensors, able to operate with irregular shapes and composite materials (diffusive, specular, and polychrome) of artworks. The scanning technique is used to obtain wide field and high spatially resolved areal profilometry. The prototype has a modular scheme based on a set of conoscopic sensors, extending the typical design based on a scanning stage and a single probe with a limited bandwidth, thus allowing the collection of heights data from surface with different scales and materials with variegate optical response. The system was optimized by characterizing the quality of the measurement with the probes triggered in continuous scanning modality. The results obtained on examples of cultural heritage objects (2D paintings, 3D height-relief) and materials (pictorial, metallic) demonstrate the versatility of the implemented device.

Broadband interferometric characterization of divergence and spatial chirp.

PubMed

Meier, Amanda K; Iliev, Marin; Squier, Jeff A; Durfee, Charles G

2015-09-01

We demonstrate a spectral interferometric method to characterize lateral and angular spatial chirp to optimize intensity localization in spatio-temporally focused ultrafast beams. Interference between two spatially sheared beams in an interferometer will lead to straight fringes if the wavefronts are curved. To produce reference fringes, we delay one arm relative to another in order to measure fringe rotation in the spatially resolved spectral interferogram. With Fourier analysis, we can obtain frequency-resolved divergence. In another arrangement, we spatially flip one beam relative to the other, which allows the frequency-dependent beamlet direction (angular spatial chirp) to be measured. Blocking one beam shows the spatial variation of the beamlet position with frequency (i.e., the lateral spatial chirp).

Spatially Resolved Mid-IR Spectra from Meteorites; Linking Composition, Crystallographic Orientation and Spectra on the Micro-Scale

NASA Astrophysics Data System (ADS)

Stephen, N. R.

2016-08-01

IR spectroscopy is used to infer composition of extraterrestrial bodies, comparing bulk spectra to databases of separate mineral phases. We extract spatially resolved meteorite-specific spectra from achondrites with respect to zonation and orientation.

Emergent spatial synaptic structure from diffusive plasticity.

PubMed

Sweeney, Yann; Clopath, Claudia

2017-04-01

Some neurotransmitters can diffuse freely across cell membranes, influencing neighbouring neurons regardless of their synaptic coupling. This provides a means of neural communication, alternative to synaptic transmission, which can influence the way in which neural networks process information. Here, we ask whether diffusive neurotransmission can also influence the structure of synaptic connectivity in a network undergoing plasticity. We propose a form of Hebbian synaptic plasticity which is mediated by a diffusive neurotransmitter. Whenever a synapse is modified at an individual neuron through our proposed mechanism, similar but smaller modifications occur in synapses connecting to neighbouring neurons. The effects of this diffusive plasticity are explored in networks of rate-based neurons. This leads to the emergence of spatial structure in the synaptic connectivity of the network. We show that this spatial structure can coexist with other forms of structure in the synaptic connectivity, such as with groups of strongly interconnected neurons that form in response to correlated external drive. Finally, we explore diffusive plasticity in a simple feedforward network model of receptive field development. We show that, as widely observed across sensory cortex, the preferred stimulus identity of neurons in our network become spatially correlated due to diffusion. Our proposed mechanism of diffusive plasticity provides an efficient mechanism for generating these spatial correlations in stimulus preference which can flexibly interact with other forms of synaptic organisation. © 2016 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Spherical Deconvolution of Multichannel Diffusion MRI Data with Non-Gaussian Noise Models and Spatial Regularization

PubMed Central

Canales-Rodríguez, Erick J.; Caruyer, Emmanuel; Aja-Fernández, Santiago; Radua, Joaquim; Yurramendi Mendizabal, Jesús M.; Iturria-Medina, Yasser; Melie-García, Lester; Alemán-Gómez, Yasser; Thiran, Jean-Philippe; Sarró, Salvador; Pomarol-Clotet, Edith; Salvador, Raymond

2015-01-01

Spherical deconvolution (SD) methods are widely used to estimate the intra-voxel white-matter fiber orientations from diffusion MRI data. However, while some of these methods assume a zero-mean Gaussian distribution for the underlying noise, its real distribution is known to be non-Gaussian and to depend on many factors such as the number of coils and the methodology used to combine multichannel MRI signals. Indeed, the two prevailing methods for multichannel signal combination lead to noise patterns better described by Rician and noncentral Chi distributions. Here we develop a Robust and Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD) technique, intended to deal with realistic MRI noise, based on a Richardson-Lucy (RL) algorithm adapted to Rician and noncentral Chi likelihood models. To quantify the benefits of using proper noise models, RUMBA-SD was compared with dRL-SD, a well-established method based on the RL algorithm for Gaussian noise. Another aim of the study was to quantify the impact of including a total variation (TV) spatial regularization term in the estimation framework. To do this, we developed TV spatially-regularized versions of both RUMBA-SD and dRL-SD algorithms. The evaluation was performed by comparing various quality metrics on 132 three-dimensional synthetic phantoms involving different inter-fiber angles and volume fractions, which were contaminated with noise mimicking patterns generated by data processing in multichannel scanners. The results demonstrate that the inclusion of proper likelihood models leads to an increased ability to resolve fiber crossings with smaller inter-fiber angles and to better detect non-dominant fibers. The inclusion of TV regularization dramatically improved the resolution power of both techniques. The above findings were also verified in human brain data. PMID:26470024

Thermal Pressure in Diffuse H2 Gas Measured by Herschel [C II] Emission and FUSE UV H2 Absorption

NASA Astrophysics Data System (ADS)

Velusamy, T.; Langer, W. D.; Goldsmith, P. F.; Pineda, J. L.

2017-04-01

UV absorption studies with the Far Ultraviolet Spectroscopic Explorer (FUSE) satellite have made important observations of H2 molecular gas in Galactic interstellar translucent and diffuse clouds. Observations of the 158 μm [C II] fine-structure line with Herschel trace the same H2 molecular gas in emission. We present [C II] observations along 27 lines of sight (LOSs) toward target stars of which 25 have FUSE H2 UV absorption. Two stars have only HST STIS C II λ2325 absorption data. We detect [C II] 158 μm emission features in all but one target LOS. For three target LOSs that are close to the Galactic plane, | {\\text{}}b| < 1°, we also present position-velocity maps of [C II] emission observed by Herschel Heterodyne Instrument in the Far Infrared (HIFI) in on-the-fly spectral-line mapping. We use the velocity-resolved [C II] spectra observed by the HIFI instrument toward the target LOSs observed by FUSE to identify [C II] velocity components associated with the H2 clouds. We analyze the observed velocity integrated [C II] spectral-line intensities in terms of the densities and thermal pressures in the H2 gas using the H2 column densities and temperatures measured by the UV absorption data. We present the H2 gas densities and thermal pressures for 26 target LOSs and from the [C II] intensities derive a mean thermal pressure in the range of ˜6100-7700 K cm-3 in diffuse H2 clouds. We discuss the thermal pressures and densities toward 14 targets, comparing them to results obtained using the UV absorption data for two other tracers C I and CO. Our results demonstrate the richness of the far-IR [C II] spectral data which is a valuable complement to the UV H2 absorption data for studying diffuse H2 molecular clouds. While the UV absorption is restricted to the directions of the target star, far-IR [C II] line emission offers an opportunity to employ velocity-resolved spectral-line mapping capability to study in detail the clouds’ spatial and velocity structures.

A Spatially Resolved Study of the GRB 020903 Host Galaxy

NASA Astrophysics Data System (ADS)

Thorp, Mallory D.; Levesque, Emily M.

2018-03-01

GRB 020903 is a long-duration gamma-ray burst with a host galaxy close enough and extended enough for spatially resolved observations, making it one of less than a dozen GRBs where such host studies are possible. GRB 020903 lies in a galaxy host complex that appears to consist of four interacting components. Here we present the results of spatially resolved spectroscopic observations of the GRB 020903 host. By taking observations at two different position angles, we were able to obtain optical spectra (3600–9000 Å) of multiple regions in the galaxy. We confirm redshifts for three regions of the host galaxy that match that of GRB 020903. We measure the metallicity of these regions, and find that the explosion site and the nearby star-forming regions both have comparable subsolar metallicities. We conclude that, in agreement with past spatially resolved studies of GRBs, the GRB explosion site is representative of the host galaxy as a whole rather than localized in a metal-poor region of the galaxy.

Space- and time-resolved raman and breakdown spectroscopy: advanced lidar techniques

NASA Astrophysics Data System (ADS)

Silviu, Gurlui; Marius Mihai, Cazacu; Adrian, Timofte; Oana, Rusu; Georgiana, Bulai; Dimitriu, Dan

2018-04-01

DARLIOES - the advanced LIDAR is based on space- and time-resolved RAMAN and breakdown spectroscopy, to investigate chemical and toxic compounds, their kinetics and physical properties at high temporal (2 ns) and spatial (1 cm) resolution. The high spatial and temporal resolution are needed to resolve a large variety of chemical troposphere compounds, emissions from aircraft, the self-organization space charges induced light phenomena, temperature and humidity profiles, ice nucleation, etc.

Diffusion tensor imaging in children with tuberous sclerosis complex: tract-based spatial statistics assessment of brain microstructural changes.

PubMed

Zikou, Anastasia K; Xydis, Vasileios G; Astrakas, Loukas G; Nakou, Iliada; Tzarouchi, Loukia C; Tzoufi, Meropi; Argyropoulou, Maria I

2016-07-01

There is evidence of microstructural changes in normal-appearing white matter of patients with tuberous sclerosis complex. To evaluate major white matter tracts in children with tuberous sclerosis complex using tract-based spatial statistics diffusion tensor imaging (DTI) analysis. Eight children (mean age ± standard deviation: 8.5 ± 5.5 years) with an established diagnosis of tuberous sclerosis complex and 8 age-matched controls were studied. The imaging protocol consisted of T1-weighted high-resolution 3-D spoiled gradient-echo sequence and a spin-echo, echo-planar diffusion-weighted sequence. Differences in the diffusion indices were evaluated using tract-based spatial statistics. Tract-based spatial statistics showed increased axial diffusivity in the children with tuberous sclerosis complex in the superior and anterior corona radiata, the superior longitudinal fascicle, the inferior fronto-occipital fascicle, the uncinate fascicle and the anterior thalamic radiation. No significant differences were observed in fractional anisotropy, mean diffusivity and radial diffusivity between patients and control subjects. No difference was found in the diffusion indices between the baseline and follow-up examination in the patient group. Patients with tuberous sclerosis complex have increased axial diffusivity in major white matter tracts, probably related to reduced axonal integrity.

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.

A novel approach to in-situ rutile petrochronology

NASA Astrophysics Data System (ADS)

Kooijman, Ellen; Smit, Matthijs; Kylander-Clark, Andrew

2017-04-01

Rutile petrochronology has become an increasingly important tool for deciphering the timing and conditions of petrological processes. Rutile provides a reliable single-mineral thermometer, capable of retaining temperature information during high and ultra-high temperature metamorphism. Its HFSE contents can be used to investigate the geochemical environment in which rutile crystallized. Most importantly, rutile strongly fractionates U/Pb and enables U-Pb thermochronology in the intermediate temperature range. Here we present a novel approach to using U-Pb thermochronology of rutile by exploring the use of Pb as a diffusive species in kinetics-based thermometry. We performed high spatial and analytical resolution micro-analysis of rutile by laser ablation multi-collector ICPMS to constrain Pb diffusion profiles in rutile from high-grade metamorphic rocks of the Western Gneiss Complex (WGC), Norway. The age and thermometric results from this analysis are used to constrain a full thermal history from single grains. Millimeter-sized single crystals of rutile from a rutile-rich phlogopitite vein in eclogite were mounted and polished to expose their geometric cores. The grains were analyzed in transects using rectangular spots (c. 15x45 μm). This ensures ablation of a significant volume while maintaining the required radial spatial resolution. The transects yielded well-defined Pb diffusion profiles, with U-Pb ages ranging from c. 415 Ma in the cores to c. 380 Ma in the outermost rims (±2%, 2σ on individual spots). Diffusion zoning length was used with well-established Pb diffusion parameters [1] to determine peak temperature conditions following the approach of [2]. The result, c. 810 ± 25 ˚ C, is consistent with 800 ± 25 ˚ C and c. 780 ˚ C estimated for the same sample using conventional and Zr-in-rutile thermometry, respectively. The cooling history that is reconstructed through age zoning analysis and diffusion modeling shows remarkable consistency with that established for the WGC through decades of 40Ar/39Ar dating. The data presented here demonstrate that in-situ rutile U-Pb analysis yields reliable and precise temperature and age information that can be combined to resolve full thermal histories from single crystals. This novel approach to the toolbox of rutile petrochronology has great potential for research into the tectonics and dynamics of the lithosphere. References [1] Cherniak (2000) Contrib. Mineral. Petrol. 139. 198-207. [2] Smit et al. (2013) J. Metamorph. Geol. 31. 339-358.

Gint2D-T2 correlation NMR of porous media

NASA Astrophysics Data System (ADS)

Zhang, Yan; Blümich, Bernhard

2015-03-01

The internal magnetic field gradient induced in porous media by magnetic susceptibility differences at material interfaces impacts diffusion measurements in particular at high magnetic field and can be used to probe the pore structure. Insight about the relationship between pore space and internal gradient Gint can be obtained from 2D Laplace NMR experiments. When measuring distributions of transverse relaxation times T2 in fluid filled porous media, relaxation and diffusion in internal gradients arise simultaneously and data are often interpreted with the assumption that one or the other parameter be constant throughout the sample. To examine this assumption we measure correlations of the distributions of Gint2D and T2 by 2D Laplace NMR for three different kinds of samples, glass beads with different bead diameters saturated with water, glass beads filled with oil and water, and a wet mortar sample. For the first two samples the cases where either the internal gradient or diffusion dominates were examined separately in order to better understand the relationship between Gint and D. These results are useful for assessing the impact of internal gradients and diffusion in unknown samples, such as the mortar sample. The experiments were performed at different magnetic field strengths corresponding to 300 MHz and 700 MHz 1H Larmor frequency to identify the impact of the magnetic field on the internal gradient. Subsequently, spatially resolved Gint2D-T2 maps were obtained to study the sample heterogeneity.

Nonlinear diffusion and viral spread through the leaf of a plant

NASA Astrophysics Data System (ADS)

Edwards, Maureen P.; Waterhouse, Peter M.; Munoz-Lopez, María Jesús; Anderssen, Robert S.

2016-10-01

The spread of a virus through the leaf of a plant is both spatially and temporally causal in that the present status depends on the past and the spatial spread is compactly supported and progresses outwards. Such spatial spread is known to occur for certain nonlinear diffusion processes. The first compactly supported solution for nonlinear diffusion equations appears to be that of Pattle published in 1959. In that paper, no explanation is given as to how the solution was derived. Here, we show how the solution can be derived using Lie symmetry analysis. This lays a foundation for exploring the behavior of other choices for nonlinear diffusion and exploring the addition of reaction terms which do not eliminate the compactly supported structure. The implications associated with using the reaction-diffusion equation to model the spatial-temporal spread of a virus through the leaf of a plant are discussed.

Chandra Observations of the M31

NASA Technical Reports Server (NTRS)

Garcia, Michael; Lavoie, Anthony R. (Technical Monitor)

2000-01-01

We report on Chandra observations of the nearest Spiral Galaxy, M3l, The nuclear source seen with previous X-ray observatories is resolved into five point sources. One of these sources is within 1 arc-sec of the M31 central super-massive black hole. As compared to the other point sources in M3l. this nuclear source has an unusually soft spectrum. Based on the spatial coincidence and the unusual spectrum. we identify this source with the central black hole. A bright transient is detected 26 arc-sec to the west of the nucleus, which may be associated with a stellar mass black hole. We will report on a comparison of the x-ray spectrum of the diffuse emission and point sources seen in the central few arcmin

Spatially unresolved SED fitting can underestimate galaxy masses: a solution to the missing mass problem

NASA Astrophysics Data System (ADS)

Sorba, Robert; Sawicki, Marcin

2018-05-01

We perform spatially resolved, pixel-by-pixel Spectral Energy Distribution (SED) fitting on galaxies up to z ˜ 2.5 in the Hubble eXtreme Deep Field (XDF). Comparing stellar mass estimates from spatially resolved and spatially unresolved photometry we find that unresolved masses can be systematically underestimated by factors of up to 5. The ratio of the unresolved to resolved mass measurement depends on the galaxy's specific star formation rate (sSFR): at low sSFRs the bias is small, but above sSFR ˜ 10-9.5 yr-1 the discrepancy increases rapidly such that galaxies with sSFRs ˜ 10-8 yr-1 have unresolved mass estimates of only one-half to one-fifth of the resolved value. This result indicates that stellar masses estimated from spatially unresolved data sets need to be systematically corrected, in some cases by large amounts, and we provide an analytic prescription for applying this correction. We show that correcting stellar mass measurements for this bias changes the normalization and slope of the star-forming main sequence and reduces its intrinsic width; most dramatically, correcting for the mass bias increases the stellar mass density of the Universe at high redshift and can resolve the long-standing discrepancy between the directly measured cosmic SFR density at z ≳ 1 and that inferred from stellar mass densities (`the missing mass problem').

Origin and z-distribution of Galactic diffuse [C II] emission

NASA Astrophysics Data System (ADS)

Velusamy, T.; Langer, W. D.

2014-12-01

Context. The [C ii] emission is an important probe of star formation in the Galaxy and in external galaxies. The GOT C+ survey and its follow up observations of spectrally resolved 1.9 THz [C ii] emission using Herschel HIFI provides the data needed to quantify the Galactic interstellar [C ii] gas components as tracers of star formation. Aims: We determine the source of the diffuse [C ii] emission by studying its spatial (radial and vertical) distributions by separating and evaluating the fractions of [C ii] and CO emissions in the Galactic ISM gas components. Methods: We used the HIFI [C ii] Galactic survey (GOT C+), along with ancillary H i, 12CO, 13CO, and C18O data toward 354 lines of sight, and several HIFI [C ii] and [C i] position-velocity maps. We quantified the emission in each spectral line profile by evaluating the intensities in 3 km s-1 wide velocity bins, "spaxels". Using the detection of [C ii] with CO or [C i], we separated the dense and diffuse gas components. We derived 2D Galactic disk maps using the spaxel velocities for kinematic distances. We separated the warm and cold H2 gases by comparing CO emissions with and without associated [C ii]. Results: We find evidence of widespread diffuse [C ii] emission with a z-scale distribution larger than that for the total [C ii] or CO. The diffuse [C ii] emission consists of (i) diffuse molecular (CO-faint) H2 clouds and (ii) diffuse H i clouds and/or WIM. In the inner Galaxy we find a lack of [C ii] detections in a majority (~62%) of H i spaxels and show that the diffuse component primarily comes from the WIM (~21%) and that the H i gas is not a major contributor to the diffuse component (~6%). The warm-H2 radial profile shows an excess in the range 4 to 7 kpc, consistent with enhanced star formation there. Conclusions: We derive, for the first time, the 2D [C ii] spatial distribution in the plane and the z-distributions of the individual [C ii] gas component. From the GOT C+ detections we estimate the fractional [C ii] emission tracing (i) H2 gas in dense and diffuse molecular clouds as ~48% and ~14%, respectively, (ii) in the H i gas ~18%, and (iii) in the WIM ~21%. Including non-detections from H i increases the [C ii] in H i to ~27%. The z-scale distributions FWHM from smallest to largest are [C ii] sources with CO, ~130 pc, (CO-faint) diffuse H2 gas, ~200 pc, and the diffuse H i and WIM, ~330 pc. When combined with [C ii], CO observations probe the warm-H2 gas, tracing star formation. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Effect of Azospirillum brasilense and Burkholderia unamae Bacteria on Maize Photosynthetic Activity Evaluated Using the Photoacoustic Technique

NASA Astrophysics Data System (ADS)

Gordillo-Delgado, F.; Marín, E.; Calderón, A.

2016-09-01

In this work, the photosynthetic process of maize plants ( Zea mays), which were grown using seeds inoculated with plant growth promoting bacteria Azospirillum brasilense and Burkholderia unamae, was monitored. Photothermal and photobaric signals obtained by a time-resolved photoacoustic measurement configuration were used for measuring the oxygen evolution rate in situ. A frequency-resolved configuration of the method was utilized to determine the oxygen diffusion coefficient and the thermal diffusivity of the maize leaves. The latter parameters, which can be used as indicators of the photosynthetic activity of maize, are found to vary according to the plant-microbe interaction. Treatment with plant growth promoting bacteria induced a decrease in the oxygen diffusion coefficient of about 20 %.

Development and applications of laser-induced incandescence

NASA Technical Reports Server (NTRS)

Vanderwal, Randy L.; Dietrich, Daniel L.; Zhou, Zhiquang; Choi, Mun Y.

1995-01-01

Several NASA-funded investigations focus on soot processes and radiative influences of soot in diffusion flames given their simplicity, practical significance, and potential for theoretical modeling. Among the physical parameters characterizing soot, soot volume fraction, f(sub v), a function of particle size and number density, is often of chief practical interest in these investigations, as this is the geometrical property that directly impacts radiative characteristics and the temperature field of the flame and is basic to understanding soot growth and oxidation processes. Diffusion flames, however, present a number of challenges to the determination of f(sub v) via traditional extinction measurements. Laser-induced incandescence (LII) possesses several advantages compared to line-of-sight extinction techniques for determination of f(sub v). Since LII is not a line-of-sight technique, similar to fluorescence, it possesses geometric versatility allowing spatially resolved measurements of f(sub v) in real time in nonaxisymmetric systems without using deconvolution techniques. The spatial resolution of LII is determined by the detector and imaging magnification used. Neither absorption by polycyclic aromatic hydrocarbons (PAH's) nor scattering contributes to the signal. Temporal capabilities are limited only by the laser pulse and camera gate duration, with measurements having been demonstrated with 10 ns resolution. Because of these advantages, LII should be applicable to a variety of combustion processes involving both homogeneous and heterogeneous phases. Our work has focussed on characterization of the technique as well as exploration of its capabilities and is briefly described.

Modelling and testing the x-ray performance of CCD and CMOS APS detectors using numerical finite element simulations

NASA Astrophysics Data System (ADS)

Weatherill, Daniel P.; Stefanov, Konstantin D.; Greig, Thomas A.; Holland, Andrew D.

2014-07-01

Pixellated monolithic silicon detectors operated in a photon-counting regime are useful in spectroscopic imaging applications. Since a high energy incident photon may produce many excess free carriers upon absorption, both energy and spatial information can be recovered by resolving each interaction event. The performance of these devices in terms of both the energy and spatial resolution is in large part determined by the amount of diffusion which occurs during the collection of the charge cloud by the pixels. Past efforts to predict the X-ray performance of imaging sensors have used either analytical solutions to the diffusion equation or simplified monte carlo electron transport models. These methods are computationally attractive and highly useful but may be complemented using more physically detailed models based on TCAD simulations of the devices. Here we present initial results from a model which employs a full transient numerical solution of the classical semiconductor equations to model charge collection in device pixels under stimulation from initially Gaussian photogenerated charge clouds, using commercial TCAD software. Realistic device geometries and doping are included. By mapping the pixel response to different initial interaction positions and charge cloud sizes, the charge splitting behaviour of the model sensor under various illuminations and operating conditions is investigated. Experimental validation of the model is presented from an e2v CCD30-11 device under varying substrate bias, illuminated using an Fe-55 source.

Decay and Spatial Diffusion of Turbulent Kinetic Energy In The Presence of a Linear Kinetic Energy Gradient

NASA Astrophysics Data System (ADS)

Meneveau, Charles

2015-11-01

A topic that elicited the interest of John Lumley is pressure transport in turbulence. In 1978 (JL, in Advances in Applied Mechanics, pages 123-176) he showed that pressure transport likely acts in the opposite direction to the spatial flux of kinetic energy due to triple velocity correlations. Here we examine a flow in which the interplay of turbulent decay and spatial transport is particularly relevant. Specifically, using a specially designed active grid and screens placed in the Corrsin wind tunnel, such a flow is realized. Data are acquired using X-wire thermal anemometry at different spanwise and downstream locations. In order to resolve the dissipation rate accurately, measurements are also acquired using the NSTAP probe developed and manufactured by Princeton researchers and kindly provided to us (M. Hultmark, Y. Fan, L. Smits). The results show power-law decay with downstream distance, with a decay exponent that becomes larger in the high kinetic energy side of the flow. Measurements of the dissipation enable us to obtain the spanwise gradient of the spatial flux. One possible explanation for the observations is upgrading transport of kinetic energy due to pressure-velocity correlations, although its magnitude required to close the budget appears very large. Absence of simultaneous pressure velocity measurement preclude us to fully elucidate the observed trends. In collaboration with Adrien Thormann, Johns Hopkins University. Financial support: National Science Foundation.

Dusty Pair Plasma—Wave Propagation and Diffusive Transition of Oscillations

NASA Astrophysics Data System (ADS)

Atamaniuk, Barbara; Turski, Andrzej J.

2011-11-01

The crucial point of the paper is the relation between equilibrium distributions of plasma species and the type of propagation or diffusive transition of plasma response to a disturbance. The paper contains a unified treatment of disturbance propagation (transport) in the linearized Vlasov electron-positron and fullerene pair plasmas containing charged dust impurities, based on the space-time convolution integral equations. Electron-positron-dust/ion (e-p-d/i) plasmas are rather widespread in nature. Space-time responses of multi-component linearized Vlasov plasmas on the basis of multiple integral equations are invoked. An initial-value problem for Vlasov-Poisson/Ampère equations is reduced to the one multiple integral equation and the solution is expressed in terms of forcing function and its space-time convolution with the resolvent kernel. The forcing function is responsible for the initial disturbance and the resolvent is responsible for the equilibrium velocity distributions of plasma species. By use of resolvent equations, time-reversibility, space-reflexivity and the other symmetries are revealed. The symmetries carry on physical properties of Vlasov pair plasmas, e.g., conservation laws. Properly choosing equilibrium distributions for dusty pair plasmas, we can reduce the resolvent equation to: (i) the undamped dispersive wave equations, (ii) and diffusive transport equations of oscillations.

Depth-resolved monitoring of diffusion of hyperosmotic agents in normal and malignant human esophagus tissues using optical coherence tomography in-vitro

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

Zhao Qingliang; Guo Zhouyi; Wei Huajiang

2011-10-31

Depth-resolved monitoring with differentiation and quantification of glucose diffusion in healthy and abnormal esophagus tissues has been studied in vitro. Experiments have been performed using human normal esophagus and esophageal squamous cell carcinoma (ESCC) tissues by the optical coherence tomography (OCT). The images have been continuously acquired for 120 min in the experiments, and the depth-resolved and average permeability coefficients of the 40 % glucose solution have been calculated by the OCT amplitude (OCTA) method. We demonstrate the capability of the OCT technique for depth-resolved monitoring, differentiation, and quantifying of glucose diffusion in normal esophagus and ESCC tissues. It ismore » found that the permeability coefficients of the 40 % glucose solution are not uniform throughout the normal esophagus and ESCC tissues and increase from (3.30 {+-} 0.09) Multiplication-Sign 10{sup -6} and (1.57 {+-} 0.05) Multiplication-Sign 10{sup -5} cm s{sup -1} at the mucous membrane of normal esophagus and ESCC tissues to (1.82 {+-} 0.04) Multiplication-Sign 10{sup -5} and (3.53 {+-} 0.09) Multiplication-Sign 10{sup -5} cm s{sup -1} at the submucous layer approximately 742 {mu}m away from the epithelial surface of normal esophagus and ESCC tissues, respectively. (optical coherence tomography)« less

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

PubMed

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

2014-03-01

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

Measurements and modelling of fast-ion redistribution due to resonant MHD instabilities in MAST

NASA Astrophysics Data System (ADS)

Jones, O. M.; Cecconello, M.; McClements, K. G.; Klimek, I.; Akers, R. J.; Boeglin, W. U.; Keeling, D. L.; Meakins, A. J.; Perez, R. V.; Sharapov, S. E.; Turnyanskiy, M.; the MAST Team

2015-12-01

The results of a comprehensive investigation into the effects of toroidicity-induced Alfvén eigenmodes (TAE) and energetic particle modes on the NBI-generated fast-ion population in MAST plasmas are reported. Fast-ion redistribution due to frequency-chirping TAE in the range 50 kHz-100 kHz and frequency-chirping energetic particle modes known as fishbones in the range 20 kHz-50 kHz, is observed. TAE and fishbones are also observed to cause losses of fast ions from the plasma. The spatial and temporal evolution of the fast-ion distribution is determined using a fission chamber, a radially-scanning collimated neutron flux monitor, a fast-ion deuterium alpha spectrometer and a charged fusion product detector. Modelling using the global transport analysis code Transp, with ad hoc anomalous diffusion and fishbone loss models introduced, reproduces the coarsest features of the affected fast-ion distribution in the presence of energetic particle-driven modes. The spectrally and spatially resolved measurements show, however, that these models do not fully capture the effects of chirping modes on the fast-ion distribution.

A discussion on validity of the diffusion theory by Monte Carlo method

NASA Astrophysics Data System (ADS)

Peng, Dong-qing; Li, Hui; Xie, Shusen

2008-12-01

Diffusion theory was widely used as a basis of the experiments and methods in determining the optical properties of biological tissues. A simple analytical solution could be obtained easily from the diffusion equation after a series of approximations. Thus, a misinterpret of analytical solution would be made: while the effective attenuation coefficient of several semi-infinite bio-tissues were the same, the distribution of light fluence in the tissues would be the same. In order to assess the validity of knowledge above, depth resolved internal fluence of several semi-infinite biological tissues which have the same effective attenuation coefficient were simulated with wide collimated beam in the paper by using Monte Carlo method in different condition. Also, the influence of bio-tissue refractive index on the distribution of light fluence was discussed in detail. Our results showed that, when the refractive index of several bio-tissues which had the same effective attenuation coefficient were the same, the depth resolved internal fluence would be the same; otherwise, the depth resolved internal fluence would be not the same. The change of refractive index of tissue would have affection on the light depth distribution in tissue. Therefore, the refractive index is an important optical property of tissue, and should be taken in account while using the diffusion approximation theory.

A spatially resolved pyrometer for measuring the blackbody temperature of a warm dense plasma

DOE PAGES

Coleman, Joshua Eugene

2016-12-30

A pyrometer has been developed to spatially resolve the blackbody temperature of a radiatively cooling warm dense plasma. The pyrometer is composed of a lens coupled fiber array, Czerny-Turner visible spectrometer, and an intensified gated CCD for the detector. The radiatively cooling warm dense plasma is generated by a ~100-ns-long intense relativistic electron bunch with an energy of 19.1 MeV and a current of 0.2 kA interacting with 100-μm-thick low-Z foils. The continuum spectrum is measured over 250 nm with a low groove density grating. These plasmas emit visible light or blackbody radiation on relatively long time scales (~0.1 tomore » 100 μs). Finally, we presented the diagnostic layout, calibration, and proof-of-principle measurement of a radiatively cooling aluminum plasma, which includes a spatially resolved temperature gradient and the ability to temporally resolve it also.« less

An online, energy-resolving beam profile detector for laser-driven proton beams

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

Metzkes, J.; Rehwald, M.; Obst, L.

In this paper, a scintillator-based online beam profile detector for the characterization of laser-driven proton beams is presented. Using a pixelated matrix with varying absorber thicknesses, the proton beam is spatially resolved in two dimensions and simultaneously energy-resolved. A thin plastic scintillator placed behind the absorber and read out by a CCD camera is used as the active detector material. The spatial detector resolution reaches down to ∼4 mm and the detector can resolve proton beam profiles for up to 9 proton threshold energies. With these detector design parameters, the spatial characteristics of the proton distribution and its cut-off energymore » can be analyzed online and on-shot under vacuum conditions. The paper discusses the detector design, its characterization and calibration at a conventional proton source, as well as the first detector application at a laser-driven proton source.« less

An online, energy-resolving beam profile detector for laser-driven proton beams.

PubMed

Metzkes, J; Zeil, K; Kraft, S D; Karsch, L; Sobiella, M; Rehwald, M; Obst, L; Schlenvoigt, H-P; Schramm, U

2016-08-01

In this paper, a scintillator-based online beam profile detector for the characterization of laser-driven proton beams is presented. Using a pixelated matrix with varying absorber thicknesses, the proton beam is spatially resolved in two dimensions and simultaneously energy-resolved. A thin plastic scintillator placed behind the absorber and read out by a CCD camera is used as the active detector material. The spatial detector resolution reaches down to ∼4 mm and the detector can resolve proton beam profiles for up to 9 proton threshold energies. With these detector design parameters, the spatial characteristics of the proton distribution and its cut-off energy can be analyzed online and on-shot under vacuum conditions. The paper discusses the detector design, its characterization and calibration at a conventional proton source, as well as the first detector application at a laser-driven proton source.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Multiwavelength analysis of the Lyman-α emitting galaxy Haro 2: relation between the diffuse Lyman-α and soft X-ray emissions

NASA Astrophysics Data System (ADS)

Otí-Floranes, H.; Mas-Hesse, J. M.; Jiménez-Bailón, E.; Schaerer, D.; Hayes, M.; Östlin, G.; Atek, H.; Kunth, D.

2012-10-01

Context. Lyman-α emission is commonly used as star formation tracer in cosmological studies. Nevertheless, resonant scattering strongly affects the resulting luminosity, leading to variable and unpredictable escape fractions in different objects. Aims: To understand how the Lyα escape fraction depends on the properties of the star-forming regions, we need high spatial resolution multiwavelength studies of nearby Lyα emitters, like Haro 2. Methods: We study the Lyα emission of Haro 2 in connection with the properties of the young stellar population, the characteristics of the interstellar medium, the distribution and intensity of the Balmer emission lines and the properties of the X-ray emission. We have used HST-STIS spectral images along the major and minor axes of Haro 2 to characterize the Lyα emission, as well as FOC UV, WFPC-2 optical and NICMOS near infrared broadband-filter images to analyze the properties of the stellar population. WFPC-2 Hα image and ground-based spectroscopy allow us to study the Balmer emission lines. Finally, Chandra/ACIS X-ray images provide resolved distribution of the X-ray emission at various energy bands. The observational data are analyzed by comparison with the predictions from evolutionary synthesis models to constrain the properties of the star formation episode. Results: The UV, Hα and far infrared luminosities of the Haro 2 nuclear starburst are well reproduced assuming a young stellar population with ages ~3.5-5.0 Myr, affected by differential intestellar extinctions. A significant fraction of the stars are completely obscured in the UV, being identifiable only indirectly by their contribution to the ionization of the gas and to the far infrared emission. The diffuse soft X-ray emission extending over the whole source is attributed to gas heated by the mechanical energy released by the starburst. A compact hard X-ray emission (likely an UltraLuminous X-ray source) has been identified in a star-forming condensation to the southeast. Both compact and diffuse Lyα emission components are observed along the major and minor axes in STIS spectral images. Lyα is spatially decoupled from Balmer lines emission, Balmer decrement and UV continuum. However, the diffuse Lyα component is spatially correlated with the diffuse soft X-ray emission. Moreover, unlike the compact Lyα emission, diffuse Lyα shows luminosities larger than predicted from Hα, assuming case B recombination and considering the dust extinction as derived from Hα/Hβ. Conclusions: The Lyα emission closely associated to the massive stellar clusters is strongly affected by the properties of the surrounding neutral gas (presence of outflows, dust abundance), leading to even a range of escape fractions at different locations within the same starburst. On the other hand, we propose that the diffuse Lyα emission originates in gas ionized by the hot plasma responsible for the soft X-ray radiation, as suggested by their spatial correlation and by the measured L(Hα)/L0.4-2.4 keV ratios. Calibration of Lyα as star formation rate tracer should therefore include both effects (destruction vs. enhancement) to avoid biases in the study of galaxies at cosmological distances.

Carrying capacity in a heterogeneous environment with habitat connectivity.

PubMed

Zhang, Bo; Kula, Alex; Mack, Keenan M L; Zhai, Lu; Ryce, Arrix L; Ni, Wei-Ming; DeAngelis, Donald L; Van Dyken, J David

2017-09-01

A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non-diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K. Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments. © 2017 John Wiley & Sons Ltd/CNRS.

Carrying capacity in a heterogeneous environment with habitat connectivity

USGS Publications Warehouse

Zhang, Bo; Kula, Alex; Mack, Keenan M.L.; Zhai, Lu; Ryce, Arrix L.; Ni, Wei-Ming; DeAngelis, Donald L.; Van Dyken, J. David

2017-01-01

A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non-diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K. Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments.

Optical coherence tomography in estimating molecular diffusion of drugs and analytes in ocular tissues

NASA Astrophysics Data System (ADS)

Ghosn, Mohamad G.; Tuchin, Valery V.; Larin, Kirill V.

2009-02-01

Aside from other ocular drug delivery methods, topical application and follow up drug diffusion through the cornea and sclera of the eye remain the favored method, as they impose the least pain and discomfort to the patient. However, this delivery route suffers from the low permeability of epithelial tissues and drug washout, thus reducing the effectiveness of the drug and ability to reach its target in effective concentrations. In order to better understand the behavioral characteristics of diffusion in ocular tissue, a method for noninvasive imaging of drug diffusion is needed. Due to its high resolution and depth-resolved imaging capabilities, optical coherence tomography (OCT) has been utilized in quantifying the molecular transport of different drugs and analytes in vitro in the sclera and the cornea. Diffusion of Metronidazole (0.5%), Dexamethasone (0.2%), Ciprofloxacin (0.3%), Mannitol (20%), and glucose solution (20%) in rabbit sclera and cornea were examined. Their permeability coefficients were calculated by using OCT signal slope and depth-resolved amplitude methods as function of time and tissue depth. For instance, mannitol was found to have a permeability coefficient of (8.99 +/- 1.43) × 10-6 cm/s in cornea (n=4) and (6.18 +/- 1.08) × 10-6 cm/s in sclera (n=5). We also demonstrate the capability of OCT technique for depth-resolved monitoring and quantifying of glucose diffusion in different layers of the sclera. We found that the glucose diffusion rate is not uniform throughout the tissue and is increased from approximately (2.39 +/- 0.73) × 10-6 cm/s at the epithelial side to (8.63 +/- 0.27) × 10-6 cm/s close to the endothelial side of the sclera. In addition, discrepancy in the permeability rates of glucose solutions with different concentrations was observed. Such diffusion studies could enhance our knowledge and potentially pave the way for advancements of therapeutic and diagnostic techniques in the treatment of ocular diseases.

Spatially Different Tissue-Scale Diffusivity Shapes ANGUSTIFOLIA3 Gradient in Growing Leaves.

PubMed

Kawade, Kensuke; Tanimoto, Hirokazu; Horiguchi, Gorou; Tsukaya, Hirokazu

2017-09-05

The spatial gradient of signaling molecules is pivotal for establishing developmental patterns of multicellular organisms. It has long been proposed that these gradients could arise from the pure diffusion process of signaling molecules between cells, but whether this simplest mechanism establishes the formation of the tissue-scale gradient remains unclear. Plasmodesmata are unique channel structures in plants that connect neighboring cells for molecular transport. In this study, we measured cellular- and tissue-scale kinetics of molecular transport through plasmodesmata in Arabidopsis thaliana developing leaf primordia by fluorescence recovery assays. These trans-scale measurements revealed biophysical properties of diffusive molecular transport through plasmodesmata and revealed that the tissue-scale diffusivity, but not the cellular-scale diffusivity, is spatially different along the leaf proximal-to-distal axis. We found that the gradient in cell size along the developmental axis underlies this spatially different tissue-scale diffusivity. We then asked how this diffusion-based framework functions in establishing a signaling gradient of endogenous molecules. ANGUSTIFOLIA3 (AN3) is a transcriptional co-activator, and as we have shown here, it forms a long-range signaling gradient along the leaf proximal-to-distal axis to determine a cell-proliferation domain. By genetically engineering AN3 mobility, we assessed each contribution of cell-to-cell movement and tissue growth to the distribution of the AN3 gradient. We constructed a diffusion-based theoretical model using these quantitative data to analyze the AN3 gradient formation and demonstrated that it could be achieved solely by the diffusive molecular transport in a growing tissue. Our results indicate that the spatially different tissue-scale diffusivity is a core mechanism for AN3 gradient formation. This provides evidence that the pure diffusion process establishes the formation of the long-range signaling gradient in leaf development. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Disease Spread and Its Effect on Population Dynamics in Heterogeneous Environment

NASA Astrophysics Data System (ADS)

Upadhyay, Ranjit Kumar; Roy, Parimita

In this paper, an eco-epidemiological model in which both species diffuse along a spatial gradient has been shown to exhibit temporal chaos at a fixed point in space. The proposed model is a modification of the model recently presented by Upadhyay and Roy [2014]. The spatial interactions among the species have been represented in the form of reaction-diffusion equations. The model incorporates the intrinsic growth rate of fish population which varies linearly with the depth of water. Numerical results show that diffusion can drive otherwise stable system into aperiodic behavior with sensitivity to initial conditions. We show that spatially induced chaos plays an important role in spatial pattern formation in heterogeneous environment. Spatiotemporal distributions of species have been simulated using the diffusivity assumptions realistic for natural eco-epidemic systems. We found that in heterogeneous environment, the temporal dynamics of both the species are drastically different and show chaotic behavior. It was also found that the instability observed in the model is due to spatial heterogeneity and diffusion-driven. Cumulative death rate of predator has an appreciable effect on model dynamics as the spatial distribution of all constituent populations exhibit significant changes when this model parameter is changed and it acts as a regularizing factor.

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

NASA Astrophysics Data System (ADS)

Guo, Yi-Qing; Yuan, Qiang

2018-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

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

PubMed Central

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

2017-01-01

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

Scaling Soil Microbe-Water Interactions from Pores to Ecosystems

NASA Astrophysics Data System (ADS)

Manzoni, S.; Katul, G. G.

2014-12-01

The spatial scales relevant to soil microbial activity are much finer than scales relevant to whole-ecosystem function and biogeochemical cycling. On the one hand, how to link such different scales and develop scale-aware biogeochemical and ecohydrological models remains a major challenge. On the other hand, resolving these linkages is becoming necessary for testing ecological hypotheses and resolving data-theory inconsistencies. Here, the relation between microbial respiration and soil moisture expressed in water potential is explored. Such relation mediates the water availability effects on ecosystem-level heterotrophic respiration and is of paramount importance for understanding CO2 emissions under increasingly variable rainfall regimes. Respiration has been shown to decline as the soil dries in a remarkably consistent way across climates and soil types (open triangles in Figure). Empirical models based on these respiration-moisture relations are routinely used in Earth System Models to predict moisture effects on ecosystem respiration. It has been hypothesized that this consistency in microbial respiration decline is due to breakage of water film continuity causing in turn solute diffusion limitations in dry conditions. However, this hypothesis appears to be at odds with what is known about soil hydraulic properties. Water film continuity estimated from soil water retention (SWR) measurements at the 'Darcy' scale breaks at far less negative water potential (<-0.1 MPa) levels than where microbial respiration ceases (approximately -15 MPa) as shown in the Figure (violet frequency distribution). Also, this threshold point inferred from SWR shows strong texture dependence, in contrast to the respiration curves. Employing theoretical tools from percolation theory, it is demonstrated that hydrological measurements can be spatially downscaled at a micro-level relevant to microbial activity. Such downscaling resolves the inconsistency between respiration thresholds and hydrological thresholds. This result, together with observations of residual microbial activity well below -15 MPa (dashed back curve in Figure), lends support to the hypothesis that soil microbes are substrate-limited in dry conditions.

RESOLVING GIANT MOLECULAR CLOUDS IN NGC 300: A FIRST LOOK WITH THE SUBMILLIMETER ARRAY

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

Faesi, Christopher M.; Lada, Charles J.; Forbrich, Jan

2016-04-20

We present the first high angular resolution study of giant molecular clouds (GMCs) in the nearby spiral galaxy NGC 300, based on observations from the Submillimeter Array (SMA). We target eleven 500 pc sized regions of active star formation within the galaxy in the {sup 12}CO( J = 2-1) line at 40 pc spatial and 1 km s{sup −1} spectral resolution and identify 45 individual GMCs. We characterize the physical properties of these GMCs, and find that they are similar to GMCs in the disks of the Milky Way and other nearby spiral galaxies. For example, the GMC mass spectrummore » in our sample has a slope of 1.80 ± 0.07. Twelve clouds are spatially resolved by our observations, of which ten have virial mass estimates that agree to within a factor of two with mass estimates derived directly from {sup 12}CO integrated intensity, suggesting that the majority of these GMCs are bound. The resolved clouds show consistency with Larson’s fundamental relations between size, linewidth, and mass observed in the Milky Way. We find that the linewidth scales with the size as Δ V ∝ R {sup 0.52±0.20}, and the median surface density in the subsample is 54 M {sub ⊙} pc{sup −2}. We detect {sup 13}CO in four GMCs and find a mean {sup 12}CO/{sup 13}CO flux ratio of 6.2. Our interferometric observations recover between 30% and 100% of the integrated intensity from the APEX single dish {sup 12}CO observations of Faesi et al., suggesting the presence of low-mass GMCs and/or diffuse gas below our sensitivity limit. The fraction of APEX emission recovered increases with the SMA total intensity, as well as with the star formation rate.« less

S{sub 2}SA preconditioning for the S{sub n} equations with strictly non negative spatial discretization

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

Bruss, D. E.; Morel, J. E.; Ragusa, J. C.

2013-07-01

Preconditioners based upon sweeps and diffusion-synthetic acceleration have been constructed and applied to the zeroth and first spatial moments of the 1-D S{sub n} transport equation using a strictly non negative nonlinear spatial closure. Linear and nonlinear preconditioners have been analyzed. The effectiveness of various combinations of these preconditioners are compared. In one dimension, nonlinear sweep preconditioning is shown to be superior to linear sweep preconditioning, and DSA preconditioning using nonlinear sweeps in conjunction with a linear diffusion equation is found to be essentially equivalent to nonlinear sweeps in conjunction with a nonlinear diffusion equation. The ability to use amore » linear diffusion equation has important implications for preconditioning the S{sub n} equations with a strictly non negative spatial discretization in multiple dimensions. (authors)« less

Diffuse idiopathic hyperplasia of the sternocleidomastoid muscle in a child

PubMed Central

Pal, Kamalesh; Bhat, Nisar; Moghazy, Khaled; Mitra, DK; Hegazi, Mohammed

2009-01-01

Unilateral diffuse or localized enlargement of the sternocleidomastoid muscle (SCM) is an event commonly seen in infancy, and is popularly known as ‘sternocleidomastoid tumor’. The condition, which usually spontaneously resolves with or without physiotherapy, is due to a hematoma following a difficult labor. The muscle regains its elasticity and complete function. In some infants it resolves with fibromatous changes in the muscle leading to shortening, fibrosis and finally culminating in torticollis. We describe a case of idiopathic diffuse enlargement of unilateral SCM in a 12-year-old child without any functional compromise or torticollis. The histopathological and clinical characteristics differentiating it from more commonly described sternocleidomastoid tumor or fibromatosis coli are described. We believe this is the first case report of idiopathic hyperplasia of SCM. PMID:19847086

Evolution and enabling capabilities of spatially resolved techniques for the characterization of heterogeneously catalyzed reactions

DOE PAGES

Morgan, Kevin; Touitou, Jamal; Choi, Jae -Soon; ...

2016-01-15

The development and optimization of catalysts and catalytic processes requires knowledge of reaction kinetics and mechanisms. In traditional catalyst kinetic characterization, the gas composition is known at the inlet, and the exit flow is measured to determine changes in concentration. As such, the progression of the chemistry within the catalyst is not known. Technological advances in electromagnetic and physical probes have made visualizing the evolution of the chemistry within catalyst samples a reality, as part of a methodology commonly known as spatial resolution. Herein, we discuss and evaluate the development of spatially resolved techniques, including the evolutions and achievements ofmore » this growing area of catalytic research. The impact of such techniques is discussed in terms of the invasiveness of physical probes on catalytic systems, as well as how experimentally obtained spatial profiles can be used in conjunction with kinetic modeling. Moreover, some aims and aspirations for further evolution of spatially resolved techniques are considered.« less

The spatial resolving power of earth resources satellites: A review

NASA Technical Reports Server (NTRS)

Townshend, J. R. G.

1980-01-01

The significance of spatial resolving power on the utility of current and future Earth resources satellites is critically discussed and the relative merits of different approaches in defining and estimating spatial resolution are outlined. It is shown that choice of a particular measure of spatial resolution depends strongly on the particular needs of the user. Several experiments have simulated the capabilities of future satellite systems by degradation of aircraft images. Surprisingly, many of these indicated that improvements in resolution may lead to a reduction in the classification accuracy of land cover types using computer assisted methods. However, where the frequency of boundary pixels is high, the converse relationship is found. Use of imagery dependent upon visual interpretation is likely to benefit more consistently from higher resolutions. Extraction of information from images will depend upon several other factors apart from spatial resolving power: these include characteristics of the terrain being sensed, the image processing methods that are applied as well as certain sensor characteristics.

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

Zhu, Yi; Cai, Zhonghou; Chen, Pice

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase seperated regions. The ability to simultanousely track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of- the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO 2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation ismore » initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO 2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, which is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO 2. Lastly, the direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.« less

Recording High Resolution 3D Lagrangian Motions In Marine Dinoflagellates using Digital Holographic Microscopic Cinematography

NASA Astrophysics Data System (ADS)

Sheng, J.; Malkiel, E.; Katz, J.; Place, A. R.; Belas, R.

2006-11-01

Detailed data on swimming behavior and locomotion for dense population of dinoflagellates constitutes a key component to understanding cell migration, cell-cell interactions and predator-prey dynamics, all of which affect algae bloom dynamics. Due to the multi-dimensional nature of flagellated cell motions, spatial-temporal Lagrangian measurements of multiple cells in high concentration are very limited. Here we present detailed data on 3D Lagrangian motions for three marine dinoflagellates: Oxyrrhis marina, Karlodinium veneficum, and Pfiesteria piscicida, using digital holographic microscopic cinematography. The measurements are performed in a 5x5x25mm cuvette with cell densities varying from 50,000 ˜ 90,000 cells/ml. Approximately 200-500 cells are tracked simultaneously for 12s at 60fps in a sample volume of 1x1x5 mm at a spatial resolution of 0.4x0.4x2 μm. We fully resolve the longitudinal flagella (˜200nm) along with the Lagrangian trajectory of each organism. Species dependent swimming behavior are identified and categorized quantitatively by velocities, radii of curvature, and rotations of pitch. Statistics on locomotion, temporal & spatial scales, and diffusion rate show substantial differences between species. The scaling between turning radius and cell dimension can be explained by a distributed stokeslet model for a self-propelled body.

Indium diffusion through high-k dielectrics in high-k/InP stacks

NASA Astrophysics Data System (ADS)

Dong, H.; Cabrera, W.; Galatage, R. V.; Santosh KC, Brennan, B.; Qin, X.; McDonnell, S.; Zhernokletov, D.; Hinkle, C. L.; Cho, K.; Chabal, Y. J.; Wallace, R. M.

2013-08-01

Evidence of indium diffusion through high-k dielectric (Al2O3 and HfO2) films grown on InP (100) by atomic layer deposition is observed by angle resolved X-ray photoelectron spectroscopy and low energy ion scattering spectroscopy. The analysis establishes that In-out diffusion occurs and results in the formation of a POx rich interface.

A passive physical model for DnaK chaperoning

NASA Astrophysics Data System (ADS)

Uhl, Lionel; Dumont, Audrey; Dukan, Sam

2018-03-01

Almost all living organisms use protein chaperones with a view to preventing proteins from misfolding or aggregation either spontaneously or during cellular stress. This work uses a reaction-diffusion stochastic model to describe the dynamic localization of the Hsp70 chaperone DnaK in Escherichia coli cells during transient proteotoxic collapse characterized by the accumulation of insoluble proteins. In the model, misfolded (‘abnormal’) proteins are produced during alcoholic stress and have the propensity to aggregate with a polymerization-like kinetics. When aggregates diffuse more slowly they grow larger. According to Michaelis-Menten-type kinetics, DnaK has the propensity to bind with misfolded proteins or aggregates in order to catalyse refolding. To match experimental fluorescence microscopy data showing clusters of DnaK-GFP localized in multiple foci, the model includes spatial zones with local reduced diffusion rates to generate spontaneous assemblies of DnaK called ‘foci’. Numerical simulations of our model succeed in reproducing the kinetics of DnaK localization experimentally observed. DnaK starts from foci, moves to large aggregates during acute stress, resolves those aggregates during recovery and finally returns to its initial punctate localization pattern. Finally, we compare real biological events with hypothetical repartitions of the protein aggregates or DnaK. We then notice that DnaK action is more efficient on protein aggregates than on protein homogeneously distributed.

Fluorescence imaging of single-molecule retention trajectories in reversed-phase chromatographic particles.

PubMed

Cooper, Justin T; Peterson, Eric M; Harris, Joel M

2013-10-01

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. The simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.

Using light transmission to watch hydrogen diffuse

PubMed Central

Pálsson, Gunnar K.; Bliersbach, Andreas; Wolff, Max; Zamani, Atieh; Hjörvarsson, Björgvin

2012-01-01

Because of its light weight and small size, hydrogen exhibits one of the fastest diffusion rates in solid materials, comparable to the diffusion rate of liquid water molecules at room temperature. The diffusion rate is determined by an intricate combination of quantum effects and dynamic interplay with the displacement of host atoms that is still only partially understood. Here we present direct observations of the spatial and temporal changes in the diffusion-induced concentration profiles in a vanadium single crystal and we show that the results represent the experimental counterpart of the full time and spatial solution of Fick's diffusion equation. We validate the approach by determining the diffusion rate of hydrogen in a single crystal vanadium (001) film, with net diffusion in the [110] direction. PMID:22692535

Using light transmission to watch hydrogen diffuse

NASA Astrophysics Data System (ADS)

Pálsson, Gunnar K.; Bliersbach, Andreas; Wolff, Max; Zamani, Atieh; Hjörvarsson, Björgvin

2012-06-01

Because of its light weight and small size, hydrogen exhibits one of the fastest diffusion rates in solid materials, comparable to the diffusion rate of liquid water molecules at room temperature. The diffusion rate is determined by an intricate combination of quantum effects and dynamic interplay with the displacement of host atoms that is still only partially understood. Here we present direct observations of the spatial and temporal changes in the diffusion-induced concentration profiles in a vanadium single crystal and we show that the results represent the experimental counterpart of the full time and spatial solution of Fick's diffusion equation. We validate the approach by determining the diffusion rate of hydrogen in a single crystal vanadium (001) film, with net diffusion in the [110] direction.

Holographic grating relaxation technique for soft matter science

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

Lesnichii, Vasilii, E-mail: vasilii.lesnichii@physchem.uni-freiburg.de; ITMO University, Kronverksky prospekt 49, Saint-Petersburg 197101; Kiessling, Andy

2016-06-17

The holographic grating relaxation technique also known as forced Rayleigh scattering consists basically in writing a holographic grating in the specimen of interest and monitoring its diffraction efficiency as a function of time, from which valuable information on mass or heat transfer and photoinduced transformations can be extracted. In a more detailed view, the shape of the relaxation curve and the relaxation rate as a function of the grating period were found to be affected by the architecture of diffusing species (molecular probes) that constitute the grating, as well as that of the environment they diffuse in, thus making itmore » possible to access and study spatial heterogeneity of materials and different modes of e.g., polymer motion. Minimum displacements and spatial domains approachable by the technique are in nanometer range, well below spatial periods of holographic gratings. In the present paper, several cases of holographic relaxation in heterogeneous media and complex motions are exemplified. Nano- to micro-structures or inhomogeneities comparable in spatial scale with holographic gratings manifest themselves in relaxation experiments via non-exponential decay (stepwise or stretched), spatial-period-dependent apparent diffusion coefficient, or unusual dependence of diffusion coefficient on molecular volume of diffusing probes.« less

Efficient kinetic Monte Carlo method for reaction-diffusion problems with spatially varying annihilation rates

NASA Astrophysics Data System (ADS)

Schwarz, Karsten; Rieger, Heiko

2013-03-01

We present an efficient Monte Carlo method to simulate reaction-diffusion processes with spatially varying particle annihilation or transformation rates as it occurs for instance in the context of motor-driven intracellular transport. Like Green's function reaction dynamics and first-passage time methods, our algorithm avoids small diffusive hops by propagating sufficiently distant particles in large hops to the boundaries of protective domains. Since for spatially varying annihilation or transformation rates the single particle diffusion propagator is not known analytically, we present an algorithm that generates efficiently either particle displacements or annihilations with the correct statistics, as we prove rigorously. The numerical efficiency of the algorithm is demonstrated with an illustrative example.

Role of density modulation in the spatially resolved dynamics of strongly confined liquids

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

Saw, Shibu, E-mail: shibu.saw@sydney.edu.au; Dasgupta, Chandan, E-mail: cdgupta@physics.iisc.ernet.in

Confinement by walls usually produces a strong modulation in the density of dense liquids near the walls. Using molecular dynamics simulations, we examine the effects of the density modulation on the spatially resolved dynamics of a liquid confined between two parallel walls, using a resolution of a fraction of the interparticle distance in the liquid. The local dynamics is quantified by the relaxation time associated with the temporal autocorrelation function of the local density. We find that this local relaxation time varies in phase with the density modulation. The amplitude of the spatial modulation of the relaxation time can bemore » quite large, depending on the characteristics of the wall and thermodynamic parameters of the liquid. To disentangle the effects of confinement and density modulation on the spatially resolved dynamics, we compare the dynamics of a confined liquid with that of an unconfined one in which a similar density modulation is induced by an external potential. We find several differences indicating that density modulation alone cannot account for all the features seen in the spatially resolved dynamics of confined liquids. We also examine how the dynamics near a wall depends on the separation between the two walls and show that the features seen in our simulations persist in the limit of large wall separation.« less

Spatially Resolved Analysis of Amines Using a Fluorescence Molecular Probe: Molecular Analysis of IDPs

NASA Technical Reports Server (NTRS)

Clemett, S. J.; Messenger, S.; Thomas-Keprta, K. L.; Wentworth, S. J.; Robinson, G. A.; McKay, D. S.

2002-01-01

Some Interplanetary Dust Particles (IDPs) have large isotope anomalies in H and N. To address the nature of the carrier phase, we are developing a procedure to spatially resolve the distribution of organic species on IDP thin sections utilizing fluorescent molecular probes. Additional information is contained in the original extended abstract.

Rapid resolution of diffusion weighted MRI abnormality in a patient with a stuttering stroke

PubMed Central

Peters, Jurriaan M; MacLean, Ainsley V; Young, Geoffrey S

2010-01-01

We report the unusually rapid and spontaneous normalisation of low diffusivity that accompanied resolution of acute neurological deficits in a stroke patient who underwent two magnetic resonance imaging examinations within 24 h of symptom onset. Diffusion weighted imaging obtained within hours of onset of left sided weakness demonstrated a focal right capsular area of low diffusivity that resolved within 24 h, coinciding with resolution of the patient’s symptoms. PMID:22315635

Micro-Mirrors for Nanoscale Three-Dimensional Microscopy

PubMed Central

Seale, Kevin; Janetopoulos, Chris; Wikswo, John

2013-01-01

A research-grade optical microscope is capable of resolving fine structures in two-dimensional images. However, three-dimensional resolution, or the ability of the microscope to distinguish between objects lying above or below the focal plane from in-focus objects, is not nearly as good as in-plane resolution. In this issue of ACS Nano, McMahon et al. report the use of mirrored pyramidal wells with a conventional microscope for rapid, 3D localization and tracking of nanoparticles. Mirrors have been used in microscopy before, but recent work with MPWs is unique because it enables the rapid determination of the x-, y-, and z-position of freely diffusing nanoparticles and cellular nanostructures with unprecedented speed and spatial accuracy. As inexpensive tools for 3D visualization, mirrored pyramidal wells may prove to be invaluable aids in nanotechnology and engineering of nanomaterials. PMID:19309167

Quantitative 3D evolution of colloidal nanoparticle oxidation in solution

DOE PAGES

Sun, Yugang; Zuo, Xiaobing; Sankaranarayanan, Subramanian K. R. S.; ...

2017-04-21

Real-time tracking three-dimensional (3D) evolution of colloidal nanoparticles in solution is essential for understanding complex mechanisms involved in nanoparticle growth and transformation. We simultaneously use time-resolved small-angle and wide-angle x-ray scattering to monitor oxidation of highly uniform colloidal iron nanoparticles, enabling the reconstruction of intermediate 3D morphologies of the nanoparticles with a spatial resolution of ~5 Å. The in-situ probing combined with large-scale reactive molecular dynamics simulations reveals the transformational details from the solid metal nanoparticles to hollow metal oxide nanoshells via nanoscale Kirkendall process, for example, coalescence of voids upon their growth, reversing of mass diffusion direction depending onmore » crystallinity, and so forth. In conclusion, our results highlight the complex interplay between defect chemistry and defect dynamics in determining nanoparticle transformation and formation.« less

Quantitative 3D evolution of colloidal nanoparticle oxidation in solution

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

Sun, Yugang; Zuo, Xiaobing; Sankaranarayanan, Subramanian K. R. S.

Real-time tracking three-dimensional (3D) evolution of colloidal nanoparticles in solution is essential for understanding complex mechanisms involved in nanoparticle growth and transformation. We simultaneously use time-resolved small-angle and wide-angle x-ray scattering to monitor oxidation of highly uniform colloidal iron nanoparticles, enabling the reconstruction of intermediate 3D morphologies of the nanoparticles with a spatial resolution of ~5 Å. The in-situ probing combined with large-scale reactive molecular dynamics simulations reveals the transformational details from the solid metal nanoparticles to hollow metal oxide nanoshells via nanoscale Kirkendall process, for example, coalescence of voids upon their growth, reversing of mass diffusion direction depending onmore » crystallinity, and so forth. In conclusion, our results highlight the complex interplay between defect chemistry and defect dynamics in determining nanoparticle transformation and formation.« less

A radially resolved kinetic model for nonlocal electron ripple diffusion losses in tokamaks

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

Robertson, Scott

A relatively simple radially resolved kinetic model is applied to the ripple diffusion problem for electrons in tokamaks. The distribution function f(r,v) is defined on a two-dimensional grid, where r is the radial coordinate and v is the velocity coordinate. Particle transport in the radial direction is from ripple and banana diffusion and transport in the velocity direction is described by the Fokker-Planck equation. Particles and energy are replaced by source functions that are adjusted to maintain a constant central density and temperature. The relaxed profiles of f(r,v) show that the electron distribution function at the wall contains suprathermal electronsmore » that have diffused from the interior that enhance ripple transport. The transport at the periphery is therefore nonlocal. The energy replacement times from the computational model are near to the experimental replacement times for tokamak discharges in the compilation by Pfeiffer and Waltz [Nucl. Fusion 19, 51 (1979)].« less

Excitation-dependent carrier lifetime and diffusion length in bulk CdTe determined by time-resolved optical pump-probe techniques

NASA Astrophysics Data System (ADS)

Ščajev, Patrik; Miasojedovas, Saulius; Mekys, Algirdas; Kuciauskas, Darius; Lynn, Kelvin G.; Swain, Santosh K.; JarašiÅ«nas, Kestutis

2018-01-01

We applied time-resolved pump-probe spectroscopy based on free carrier absorption and light diffraction on a transient grating for direct measurements of the carrier lifetime and diffusion coefficient D in high-resistivity single crystal CdTe (codoped with In and Er). The bulk carrier lifetime τ decreased from 670 ± 50 ns to 60 ± 10 ns with increase of excess carrier density N from 1016 to 5 × 1018 cm-3 due to the excitation-dependent radiative recombination rate. In this N range, the carrier diffusion length dropped from 14 μm to 6 μm due to lifetime decrease. Modeling of in-depth (axial) and in-plane (lateral) carrier diffusion provided the value of surface recombination velocity S = 6 × 105 cm/s for the untreated surface. At even higher excitations, in the 1019-3 × 1020 cm-3 density range, D increase from 5 to 20 cm2/s due to carrier degeneracy was observed.

The diffuse soft X-ray background as seen with the Einstein Observatory

NASA Technical Reports Server (NTRS)

Micela, G.; Sciortino, S.; Vaiana, G. S.; Harnden, F. R., Jr.; Rosner, R.

1991-01-01

A systematic survey of the diffuse soft X-ray background as seen directly with the Einstein Observatory is presented. With the aid of 1633 selected 1 x 1 deg fields of view obtained by the IPC to provide about 5-percent sky coverage, with some bias toward the Galactic plane, the background in the 0.16-3.5 keV spectral region was spatially resolved on this angular scale. Maps of the background are characterized and produced at different energies within the Einstein passband. It is confirmed that the Galactic ridge is not present at energies below 0.33 keV and it is demonstrated that the appearance of the ridge above this energy is not due to hard Galactic sources with a flux above 10 exp -13 ergs/sq cm/s. A southern Galactic region is identified, with l between 80 and 180 deg and b less than -5 deg, where the mean background intensity has the lowest value and is homogeneous within better than 9 percent. The implications of these results for the Galactic structure and for the nature of the extragalactic X-ray background are discussed.

Freehand diffuse optical spectroscopy imaging for intraoperative identification of major venous and arterial vessels underlying peritoneal fat: an in vivo demonstration in a pig model

NASA Astrophysics Data System (ADS)

Piao, Daqing; Ramadan, Mohammad; Park, Aaron; Bartels, Kenneth E.; Patel, Sanjay G.

2017-10-01

Inadvertent injury to important anatomic structures is a significant risk in minimally invasive surgery (MIS) that potentially requires conversion to an open procedure, which results in increased morbidity and mortality. Surgeons operating minimal-invasively currently do not have an easy-to-use, real-time device to aid in intraoperative identification of important anatomic structures that underlie tissue planes. We demonstrate freehand diffuse optical spectroscopy (DOS) imaging for intraoperatively identifying major underlying veins and arteries. An applicator probe that can be affixed to and detached from an 8-mm laparoscopic instrument has been developed. The 10-mm DOS source-detector separation renders sampling of tissue heterogeneities a few millimeters deep. DOS spectra acquired consecutively during freehand movement of the applicator probe on the tissue surface are displayed as a temporal and spectral image to assist in spatially resolved identification of the underlying structures. Open surgery identifications of the vena cava and aorta underlying peritoneal fat of ˜4 mm in thickness using the applicator probe under room light were demonstrated repeatedly in multiple pigs in vivo.

Time of flight imaging through scattering environments (Conference Presentation)

NASA Astrophysics Data System (ADS)

Le, Toan H.; Breitbach, Eric C.; Jackson, Jonathan A.; Velten, Andreas

2017-02-01

Light scattering is a primary obstacle to imaging in many environments. On small scales in biomedical microscopy and diffuse tomography scenarios scattering is caused by tissue. On larger scales scattering from dust and fog provide challenges to vision systems for self driving cars and naval remote imaging systems. We are developing scale models for scattering environments and investigation methods for improved imaging particularly using time of flight transient information. With the emergence of Single Photon Avalanche Diode detectors and fast semiconductor lasers, illumination and capture on picosecond timescales are becoming possible in inexpensive, compact, and robust devices. This opens up opportunities for new computational imaging techniques that make use of photon time of flight. Time of flight or range information is used in remote imaging scenarios in gated viewing and in biomedical imaging in time resolved diffuse tomography. In addition spatial filtering is popular in biomedical scenarios with structured illumination and confocal microscopy. We are presenting a combination analytical, computational, and experimental models that allow us develop and test imaging methods across scattering scenarios and scales. This framework will be used for proof of concept experiments to evaluate new computational imaging methods.

Measuring joint cartilage thickness using reflectance spectroscopy non-invasively and in real-time

NASA Astrophysics Data System (ADS)

Canpolat, Murat; Denkceken, Tuba; Karagol, Cosar; Aydin, Ahmet T.

2011-03-01

Joint cartilage thickness has been estimated using spatially resolved steady-state reflectance spectroscopy noninvasively and in-real time. The system consists of a miniature UV-VIS spectrometer, a halogen tungsten light source, and an optical fiber probe with six 400 um diameter fibers. The first fiber was used to deliver the light to the cartilage and the other five were used to detect back-reflected diffused light. Distances from the detector fibers to the source fiber were 0.8 mm, 1.6 mm, 2.4 mm, 3.2 mm and 4 mm. Spectra of back-reflected diffused light were taken on 40 bovine patella cartilages. The samples were grouped into four; the first group was the control group with undamaged cartilages, in the 2nd, 3rd and 4th groups cartilage thickness was reduced approximately 25%, 50% and 100%, respectively. A correlation between cartilage thicknesses and hemoglobin absorption of light in the wavelength range of 500 nm- 600 nm for source-detector pairs was found. The proposed system with an optical fiber probe less than 4 mm in diameter has the potential for cartilage thickness assessment through an arthroscopy channel in real-time without damaging the cartilage.

Helium-3 MR q-space imaging with radial acquisition and iterative highly constrained back-projection.

PubMed

O'Halloran, Rafael L; Holmes, James H; Wu, Yu-Chien; Alexander, Andrew; Fain, Sean B

2010-01-01

An undersampled diffusion-weighted stack-of-stars acquisition is combined with iterative highly constrained back-projection to perform hyperpolarized helium-3 MR q-space imaging with combined regional correction of radiofrequency- and T1-related signal loss in a single breath-held scan. The technique is tested in computer simulations and phantom experiments and demonstrated in a healthy human volunteer with whole-lung coverage in a 13-sec breath-hold. Measures of lung microstructure at three different lung volumes are evaluated using inhaled gas volumes of 500 mL, 1000 mL, and 1500 mL to demonstrate feasibility. Phantom results demonstrate that the proposed technique is in agreement with theoretical values, as well as with a fully sampled two-dimensional Cartesian acquisition. Results from the volunteer study demonstrate that the root mean squared diffusion distance increased significantly from the 500-mL volume to the 1000-mL volume. This technique represents the first demonstration of a spatially resolved hyperpolarized helium-3 q-space imaging technique and shows promise for microstructural evaluation of lung disease in three dimensions. Copyright (c) 2009 Wiley-Liss, Inc.

Permeation across hydrated DPPC lipid bilayers: simulation of the titrable amphiphilic drug valproic acid.

PubMed

Ulander, Johan; Haymet, A D J

2003-12-01

Valproic acid is a short branched fatty acid used as an anticonvulsant drug whose therapeutic action has been proposed to arise from membrane-disordering properties. Static and kinetic properties of valproic acid interacting with fully hydrated dipalmitoyl phosphatidylcholine lipid bilayers are studied using molecular-dynamics simulations. We calculate spatially resolved free energy profiles and local diffusion coefficients using the distance between the bilayer and valproic acid respective centers-of-mass along the bilayer normal as reaction coordinate. To investigate the pH dependence, we calculate profiles for the neutral valproic acid as well as its water-soluble anionic conjugate base valproate. The local diffusion constants for valproate/valproic acid along the bilayer normal are found to be approximately 10(-6) to 10(-5) cm2 s(-1). Assuming protonation of valproic acid upon association with--or insertion into--the lipid bilayer, we calculate the permeation coefficient to be approximately 2.0 10(-3) cm s(-1), consistent with recent experimental estimates of fast fatty acid transport. The ability of the lipid bilayer to sustain local defects such as water intrusions stresses the importance of going beyond mean field and taking into account correlation effects in theoretical descriptions of bilayer translocation processes.

A Huygens principle for diffusion and anomalous diffusion in spatially extended systems

PubMed Central

Gottwald, Georg A.; Melbourne, Ian

2013-01-01

We present a universal view on diffusive behavior in chaotic spatially extended systems for anisotropic and isotropic media. For anisotropic systems, strong chaos leads to diffusive behavior (Brownian motion with drift) and weak chaos leads to superdiffusive behavior (Lévy processes with drift). For isotropic systems, the drift term vanishes and strong chaos again leads to Brownian motion. We establish the existence of a nonlinear Huygens principle for weakly chaotic systems in isotropic media whereby the dynamics behaves diffusively in even space dimension and exhibits superdiffusive behavior in odd space dimensions. PMID:23653481

Consequences of using nonlinear particle trajectories to compute spatial diffusion coefficients. [for cosmic ray propagation in interstellar and interplanetary space

NASA Technical Reports Server (NTRS)

Goldstein, M. L.

1977-01-01

In a study of cosmic ray propagation in interstellar and interplanetary space, a perturbed orbit resonant scattering theory for pitch angle diffusion in a slab model of magnetostatic turbulence is slightly generalized and used to compute the diffusion coefficient for spatial propagation parallel to the mean magnetic field. This diffusion coefficient has been useful for describing the solar modulation of the galactic cosmic rays, and for explaining the diffusive phase in solar flares in which the initial anisotropy of the particle distribution decays to isotropy.

Investigation of dissimilar metal welds by energy-resolved neutron imaging.

PubMed

Tremsin, Anton S; Ganguly, Supriyo; Meco, Sonia M; Pardal, Goncalo R; Shinohara, Takenao; Feller, W Bruce

2016-08-01

A nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participating alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al-steel weld is clearly resolved and could be used to optimize the welding process. A highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption.

An interactive ocean surface albedo scheme (OSAv1.0): formulation and evaluation in ARPEGE-Climat (V6.1) and LMDZ (V5A)

NASA Astrophysics Data System (ADS)

Séférian, Roland; Baek, Sunghye; Boucher, Olivier; Dufresne, Jean-Louis; Decharme, Bertrand; Saint-Martin, David; Roehrig, Romain

2018-01-01

Ocean surface represents roughly 70 % of the Earth's surface, playing a large role in the partitioning of the energy flow within the climate system. The ocean surface albedo (OSA) is an important parameter in this partitioning because it governs the amount of energy penetrating into the ocean or reflected towards space. The old OSA schemes in the ARPEGE-Climat and LMDZ models only resolve the latitudinal dependence in an ad hoc way without an accurate representation of the solar zenith angle dependence. Here, we propose a new interactive OSA scheme suited for Earth system models, which enables coupling between Earth system model components like surface ocean waves and marine biogeochemistry. This scheme resolves spectrally the various contributions of the surface for direct and diffuse solar radiation. The implementation of this scheme in two Earth system models leads to substantial improvements in simulated OSA. At the local scale, models using the interactive OSA scheme better replicate the day-to-day distribution of OSA derived from ground-based observations in contrast to old schemes. At global scale, the improved representation of OSA for diffuse radiation reduces model biases by up to 80 % over the tropical oceans, reducing annual-mean model-data error in surface upwelling shortwave radiation by up to 7 W m-2 over this domain. The spatial correlation coefficient between modeled and observed OSA at monthly resolution has been increased from 0.1 to 0.8. Despite its complexity, this interactive OSA scheme is computationally efficient for enabling precise OSA calculation without penalizing the elapsed model time.

Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Spatial heterodyne interferometry of VY Canis Major's, alpha Orionis, alpha Scorpii, and R leonis at 11 microns

NASA Technical Reports Server (NTRS)

Sutton, E. C.; Storey, J. W. V.; Betz, A. L.; Townes, C. H.; Spears, D. L.

1977-01-01

Using the technique of heterodyne interferometry, measurements were made of the spatial distribution of 11 micron radiation from four late type stars. The circumstellar shells surrounding VY Canis Majoris, alpha Orionis, and alpha Scorpii were resolved, whereas that of R Leonis was only partially resolved at a fringe spacing of 0.4 sec.

Determination of Spatially Resolved Tablet Density and Hardness Using Near-Infrared Chemical Imaging (NIR-CI).

PubMed

Talwar, Sameer; Roopwani, Rahul; Anderson, Carl A; Buckner, Ira S; Drennen, James K

2017-08-01

Near-infrared chemical imaging (NIR-CI) combines spectroscopy with digital imaging, enabling spatially resolved analysis and characterization of pharmaceutical samples. Hardness and relative density are critical quality attributes (CQA) that affect tablet performance. Intra-sample density or hardness variability can reveal deficiencies in formulation design or the tableting process. This study was designed to develop NIR-CI methods to predict spatially resolved tablet density and hardness. The method was implemented using a two-step procedure. First, NIR-CI was used to develop a relative density/solid fraction (SF) prediction method for pure microcrystalline cellulose (MCC) compacts only. A partial least squares (PLS) model for predicting SF was generated by regressing the spectra of certain representative pixels selected from each image against the compact SF. Pixel selection was accomplished with a threshold based on the Euclidean distance from the median tablet spectrum. Second, micro-indentation was performed on the calibration compacts to obtain hardness values. A univariate model was developed by relating the empirical hardness values to the NIR-CI predicted SF at the micro-indented pixel locations: this model generated spatially resolved hardness predictions for the entire tablet surface.

Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes.

PubMed

Chevalier, Michael W; El-Samad, Hana

2012-08-28

Diffusion of biological molecules on 2D biological membranes can play an important role in the behavior of stochastic biochemical reaction systems. Yet, we still lack a fundamental understanding of circumstances where explicit accounting of the diffusion and spatial coordinates of molecules is necessary. In this work, we illustrate how time-dependent, non-exponential reaction probabilities naturally arise when explicitly accounting for the diffusion of molecules. We use the analytical expression of these probabilities to derive a novel algorithm which, while ignoring the exact position of the molecules, can still accurately capture diffusion effects. We investigate the regions of validity of the algorithm and show that for most parameter regimes, it constitutes an accurate framework for studying these systems. We also document scenarios where large spatial fluctuation effects mandate explicit consideration of all the molecules and their positions. Taken together, our results derive a fundamental understanding of the role of diffusion and spatial fluctuations in these systems. Simultaneously, they provide a general computational methodology for analyzing a broad class of biological networks whose behavior is influenced by diffusion on membranes.

Metamaterial devices for molding the flow of diffuse light (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wegener, Martin

2016-09-01

Much of optics in the ballistic regime is about designing devices to mold the flow of light. This task is accomplished via specific spatial distributions of the refractive index or the refractive-index tensor. For light propagating in turbid media, a corresponding design approach has not been applied previously. Here, we review our corresponding recent work in which we design spatial distributions of the light diffusivity or the light-diffusivity tensor to accomplish specific tasks. As an application, we realize cloaking of metal contacts on large-area OLEDs, eliminating the contacts' shadows, thereby homogenizing the diffuse light emission. In more detail, metal contacts on large-area organic light-emitting diodes (OLEDs) are mandatory electrically, but they cast optical shadows, leading to unwanted spatially inhomogeneous diffuse light emission. We show that the contacts can be made invisible either by (i) laminate metamaterials designed by coordinate transformations of the diffusion equation or by (ii) triangular-shaped regions with piecewise constant diffusivity, hence constant concentration of scattering centers. These structures are post-optimized in regard to light throughput by Monte-Carlo ray-tracing simulations and successfully validated by model experiments.

A Bayesian approach to distinguishing interdigitated tongue muscles from limited diffusion magnetic resonance imaging.

PubMed

Ye, Chuyang; Murano, Emi; Stone, Maureen; Prince, Jerry L

2015-10-01

The tongue is a critical organ for a variety of functions, including swallowing, respiration, and speech. It contains intrinsic and extrinsic muscles that play an important role in changing its shape and position. Diffusion tensor imaging (DTI) has been used to reconstruct tongue muscle fiber tracts. However, previous studies have been unable to reconstruct the crossing fibers that occur where the tongue muscles interdigitate, which is a large percentage of the tongue volume. To resolve crossing fibers, multi-tensor models on DTI and more advanced imaging modalities, such as high angular resolution diffusion imaging (HARDI) and diffusion spectrum imaging (DSI), have been proposed. However, because of the involuntary nature of swallowing, there is insufficient time to acquire a sufficient number of diffusion gradient directions to resolve crossing fibers while the in vivo tongue is in a fixed position. In this work, we address the challenge of distinguishing interdigitated tongue muscles from limited diffusion magnetic resonance imaging by using a multi-tensor model with a fixed tensor basis and incorporating prior directional knowledge. The prior directional knowledge provides information on likely fiber directions at each voxel, and is computed with anatomical knowledge of tongue muscles. The fiber directions are estimated within a maximum a posteriori (MAP) framework, and the resulting objective function is solved using a noise-aware weighted ℓ1-norm minimization algorithm. Experiments were performed on a digital crossing phantom and in vivo tongue diffusion data including three control subjects and four patients with glossectomies. On the digital phantom, effects of parameters, noise, and prior direction accuracy were studied, and parameter settings for real data were determined. The results on the in vivo data demonstrate that the proposed method is able to resolve interdigitated tongue muscles with limited gradient directions. The distributions of the computed fiber directions in both the controls and the patients were also compared, suggesting a potential clinical use for this imaging and image analysis methodology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Compressive hyperspectral time-resolved wide-field fluorescence lifetime imaging

NASA Astrophysics Data System (ADS)

Pian, Qi; Yao, Ruoyang; Sinsuebphon, Nattawut; Intes, Xavier

2017-07-01

Spectrally resolved fluorescence lifetime imaging and spatial multiplexing have offered information content and collection-efficiency boosts in microscopy, but efficient implementations for macroscopic applications are still lacking. An imaging platform based on time-resolved structured light and hyperspectral single-pixel detection has been developed to perform quantitative macroscopic fluorescence lifetime imaging (MFLI) over a large field of view (FOV) and multiple spectral bands simultaneously. The system makes use of three digital micromirror device (DMD)-based spatial light modulators (SLMs) to generate spatial optical bases and reconstruct N by N images over 16 spectral channels with a time-resolved capability (∼40 ps temporal resolution) using fewer than N2 optical measurements. We demonstrate the potential of this new imaging platform by quantitatively imaging near-infrared (NIR) Förster resonance energy transfer (FRET) both in vitro and in vivo. The technique is well suited for quantitative hyperspectral lifetime imaging with a high sensitivity and paves the way for many important biomedical applications.

Dynamics of Phenanthrenequinone on Carbon Nano-Onion Surfaces Probed by Quasielastic Neutron Scattering

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

Anjos, Daniela M; Mamontov, Eugene; Brown, Gilbert M

We used quasielastic neutron scattering (QENS) to study the dynamics of phenanthrenequinone (PQ) on the surface of onion-like carbon (OLC), or so called carbon onions, as a function of surface coverage and temperature. For both the high- and low-coverage samples, we observed two diffusion processes; a faster process and nearly an order of magnitude slower process. On the high-coverage surface, the slow diffusion process is of long-range translational character, whereas the fast diffusion process is spatially localized on the length scale of ~ 4.7 . On the low-coverage surface, both diffusion processes are spatially localized; on the same length scalemore » of ~ 4.7 for the fast diffusion and a somewhat larger length scale for the slow diffusion. Arrhenius temperature dependence is observed except for the long-range diffusion on the high-coverage surface. We attribute the fast diffusion process to the generic localized in-cage dynamics of PQ molecules, and the slow diffusion process to the long-range translational dynamics of PQ molecules, which, depending on the coverage, may be either spatially restricted, or long-range. On the low-coverage surface, uniform surface coverage is not attained, and the PQ molecules experience the effect of spatial constraints on their long-range translational dynamics. Unexpectedly, the dynamics of PQ molecules on OLC as a function of temperature and surface coverage bears qualitative resemblance to the dynamics of water molecules on oxide surfaces, including practically temperature-independent residence times for the low-coverage surface. The dynamics features that we observed may be universal across different classes of surface adsorbates.« less

Model-Based Design of Biochemical Microreactors

PubMed Central

Elbinger, Tobias; Gahn, Markus; Neuss-Radu, Maria; Hante, Falk M.; Voll, Lars M.; Leugering, Günter; Knabner, Peter

2016-01-01

Mathematical modeling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation, and optimization of metabolic processes in biochemical microreactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first microreactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments of the reactor multienzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions. The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multienzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the microreactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P) was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns, which differ for different experimental arrangements. Furthermore, the total output of G6P increases for scenarios where microcompartimentation of enzymes occurs. These results show that spatially resolved models are needed in the description of the conversion processes. Finally, the enzyme stoichiometry on the nano-beads is determined, which maximizes the production of glucose-6-phosphate. PMID:26913283

Mapping UV properties throughout the Cosmic Horseshoe: lessons from VLT-MUSE

NASA Astrophysics Data System (ADS)

James, Bethan L.; Auger, Matt; Pettini, Max; Stark, Daniel P.; Belokurov, V.; Carniani, Stefano

2018-05-01

We present the first spatially resolved rest-frame ultraviolet (UV) study of the gravitationally lensed galaxy, the `Cosmic Horseshoe' (J1148+1930) at z = 2.38. Our gravitational lens model shows that the system is made up of four star-forming regions, each ˜4-8 kpc2 in size, from which we extract four spatially exclusive regional spectra. We study the interstellar and wind absorption lines, along with C III] doublet emission lines, in each region to investigate any variation in emission/absorption line properties. The mapped C III] emission shows distinct kinematical structure, with velocity offsets of ˜±50 km s-1 between regions suggestive of a merging system, and a variation in equivalent width that indicates a change in ionization parameter and/or metallicity between the regions. Absorption line velocities reveal a range of outflow strengths, with gas outflowing in the range -200 ≲ v (km s-1) ≲ -50 relative to the systemic velocity of that region. Interestingly, the strongest gas outflow appears to emanate from the most diffuse star-forming region. The star formation rates remain relatively constant (˜8-16 M⊙ yr-1), mostly due to large uncertainties in reddening estimates. As such, the outflows appear to be `global' rather than `locally' sourced. We measure electron densities with a range of log (Ne) = 3.92-4.36 cm-3, and point out that such high densities may be common when measured using the C III] doublet due to its large critical density. Overall, our observations demonstrate that while it is possible to trace variations in large-scale gas kinematics, detecting inhomogeneities in physical gas properties and their effects on the outflowing gas may be more difficult. This study provides important lessons for the spatially resolved rest-frame UV studies expected with future observatories, such as James Webb Space Telescope.

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.

Determining biological tissue optical properties via integrating sphere spatial measurements

DOEpatents

Baba, Justin S [Knoxville, TN; Letzen, Brian S [Coral Springs, FL

2011-01-11

An optical sample is mounted on a spatial-acquisition apparatus that is placed in or on an enclosure. An incident beam is irradiated on a surface of the sample and the specular reflection is allowed to escape from the enclosure through an opening. The spatial-acquisition apparatus is provided with a light-occluding slider that moves in front of the sample to block portions of diffuse scattering from the sample. As the light-occluding slider moves across the front of the sample, diffuse light scattered into the area of the backside of the light-occluding slider is absorbed by back side surface of the light-occluding slider. By measuring a baseline diffuse reflectance without a light-occluding slider and subtracting measured diffuse reflectance with a light-occluding slider therefrom, diffuse reflectance for the area blocked by the light-occluding slider can be calculated.

Multi-Algorithm Particle Simulations with Spatiocyte.

PubMed

Arjunan, Satya N V; Takahashi, Koichi

2017-01-01

As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle simulator for biochemical reaction and diffusion processes. Simulations can be performed at single molecule and compartment spatial scales simultaneously. Molecules can diffuse and react in 1D (filament), 2D (membrane), and 3D (cytosol) compartments. The implications of crowded regions in the cell can be investigated because each diffusing molecule has spatial dimensions. Spatiocyte adopts multi-algorithm and multi-timescale frameworks to simulate models that simultaneously employ deterministic, stochastic, and particle reaction-diffusion algorithms. Comparison of light microscopy images to simulation snapshots is supported by Spatiocyte microscopy visualization and molecule tagging features. Spatiocyte is open-source software and is freely available at http://spatiocyte.org .

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.

Spatially resolved scatter measurement of diffractive micromirror arrays.

PubMed

Sicker, Cornelius; Heber, Jörg; Berndt, Dirk

2016-06-01

Spatial light modulators (SLMs) support flexible system concepts in modern optics and especially phase-only SLMs such as micromirror arrays (MMAs) appear attractive for many applications. In order to achieve a precise phase modulation, which is crucial for optical performance, careful characterization and calibration of SLM devices is required. We examine an intensity-based measurement concept, which promises distinct advantages by means of a spatially resolved scatter measurement that is combined with the MMA's diffractive principle. Measurements yield quantitative results, which are consistent with measurements of micromirror roughness components, by white-light interferometry. They reveal relative scatter as low as 10^-4, which corresponds to contrast ratios up to 10,000. The potential of the technique to resolve phase changes in the subnanometer range is experimentally demonstrated.

A Spatially Resolving X-ray Crystal Spectrometer for Measurement of Ion-temperature and Rotation-velocity Profiles on the AlcatorC-Mod Tokamak

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

Hill, K. W.; Bitter, M. L.; Scott, S. D.

2009-03-24

A new spatially resolving x-ray crystal spectrometer capable of measuring continuous spatial profiles of high resolution spectra (λ/dλ > 6000) of He-like and H-like Ar Kα lines with good spatial (~1 cm) and temporal (~10 ms) resolutions has been installed on the Alcator C-Mod tokamak. Two spherically bent crystals image the spectra onto four two-dimensional Pilatus II pixel detectors. Tomographic inversion enables inference of local line emissivity, ion temperature (Ti), and toroidal plasma rotation velocity (vφ) from the line Doppler widths and shifts. The data analysis techniqu

Determination of the diffusivity, dispersion, skewness and kurtosis in heterogeneous porous flow. Part I: Analytical solutions with the extended method of moments.

NASA Astrophysics Data System (ADS)

Ginzburg, Irina; Vikhansky, Alexander

2018-05-01

The extended method of moments (EMM) is elaborated in recursive algorithmic form for the prediction of the effective diffusivity, the Taylor dispersion dyadic and the associated longitudinal high-order coefficients in mean-concentration profiles and residence-time distributions. The method applies in any streamwise-periodic stationary d-dimensional velocity field resolved in the piecewise continuous heterogeneous porosity field. It is demonstrated that EMM reduces to the method of moments and the volume-averaging formulation in microscopic velocity field and homogeneous soil, respectively. The EMM simultaneously constructs two systems of moments, the spatial and the temporal, without resorting to solving of the high-order upscaled PDE. At the same time, the EMM is supported with the reconstruction of distribution from its moments, allowing to visualize the deviation from the classical ADE solution. The EMM can be handled by any linear advection-diffusion solver with explicit mass-source and diffusive-flux jump condition on the solid boundary and permeable interface. The prediction of the first four moments is decisive in the optimization of the dispersion, asymmetry, peakedness and heavy-tails of the solute distributions, through an adequate design of the composite materials, wetlands, chemical devices or oil recovery. The symbolic solutions for dispersion, skewness and kurtosis are constructed in basic configurations: diffusion process and Darcy flow through two porous blocks in "series", straight and radial Poiseuille flow, porous flow governed by the Stokes-Brinkman-Darcy channel equation and a fracture surrounded by penetrable diffusive matrix or embedded in porous flow. We examine the moments dependency upon porosity contrast, aspect ratio, Péclet and Darcy numbers, but also for their response on the effective Brinkman viscosity applied in flow modeling. Two numerical Lattice Boltzmann algorithms, a direct solver of the microscopic ADE in heterogeneous structure and a novel scheme for EMM numerical formulation, are called for validation of the constructed analytical predictions.

Analysis and correction of gradient nonlinearity bias in ADC measurements

PubMed Central

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

2013-01-01

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

A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

PubMed Central

Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

2012-01-01

An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849

Ultrafast Microscopy of Energy and Charge Transport

NASA Astrophysics Data System (ADS)

Huang, Libai

The frontier in solar energy research now lies in learning how to integrate functional entities across multiple length scales to create optimal devices. Advancing the field requires transformative experimental tools that probe energy transfer processes from the nano to the meso lengthscales. To address this challenge, we aim to understand multi-scale energy transport across both multiple length and time scales, coupling simultaneous high spatial, structural, and temporal resolution. In my talk, I will focus on our recent progress on visualization of exciton and charge transport in solar energy harvesting materials from the nano to mesoscale employing ultrafast optical nanoscopy. With approaches that combine spatial and temporal resolutions, we have recently revealed a new singlet-mediated triplet transport mechanism in certain singlet fission materials. This work demonstrates a new triplet exciton transport mechanism leading to favorable long-range triplet exciton diffusion on the picosecond and nanosecond timescales for solar cell applications. We have also performed a direct measurement of carrier transport in space and in time by mapping carrier density with simultaneous ultrafast time resolution and 50 nm spatial precision in perovskite thin films using transient absorption microscopy. These results directly visualize long-range carrier transport of 220nm in 2 ns for solution-processed polycrystalline CH3NH3PbI3 thin films. The spatially and temporally resolved measurements reported here underscore the importance of the local morphology and establish an important first step towards discerning the underlying transport properties of perovskite materials.

The History of the M31 Disk from Resolved Stellar Populations as Seen by PHAT

NASA Astrophysics Data System (ADS)

Lewis, A. R.; Dalcanton, J. J.; Dolphin, A. E.; Weisz, D. R.; Williams, B. F.; PHAT Collaboration

2014-03-01

The Panchromatic Hubble Andromeda Treasury (PHAT) is an HST multi-cycle treasury program that is mapping the resolved stellar populations of ˜1/3 of M31 from the UV through the near-IR. These data provide color and luminosity information for more than 150 million stars in the M31 disk. We use stellar evolution models to fit the luminous main sequence to derive spatially-resolved recent star formation histories (SFHs) over large areas of M31 with 50-100 pc resolution. These include individual star-forming regions as well as quiescent portions of the disk. We use the gridded SFHs to create movies of star formation activity to study the evolution of individual star-forming events across the disk. Outside of the star-forming regions, we use our resolved stellar photometry to derive the full SFHs of larger regions. These allow us to probe spatial and temporal trends in age and metallicity across a large radial baseline, providing constraints on the global formation and evolution of the disk over a Hubble time. M31 is the only large disk galaxy that is close enough to obtain the photometry necessary for this type of spatially-resolved SFH mapping.

Time-resolved diffusion tomographic imaging in highly scattering turbid media

NASA Technical Reports Server (NTRS)

Alfano, Robert R. (Inventor); Cai, Wei (Inventor); Liu, Feng (Inventor); Lax, Melvin (Inventor); Das, Bidyut B. (Inventor)

1998-01-01

A method for imaging objects in highly scattering turbid media. According to one embodiment of the invention, the method involves using a plurality of intersecting source/detectors sets and time-resolving equipment to generate a plurality of time-resolved intensity curves for the diffusive component of light emergent from the medium. For each of the curves, the intensities at a plurality of times are then inputted into the following inverse reconstruction algorithm to form an image of the medium: X.sup.(k+1).spsp.T =?Y.sup.T W+X.sup.(k).spsp.T .LAMBDA.!?W.sup.T W+.LAMBDA.!.sup.-1 wherein W is a matrix relating output at detector position r.sub.d, at time t, to source at position r.sub.s, .LAMBDA. is a regularization matrix, chosen for convenience to be diagonal, but selected in a way related to the ratio of the noise, to fluctuations in the absorption (or diffusion) X.sub.j that we are trying to determine: .LAMBDA..sub.ij =.lambda..sub.j .delta..sub.ij with .lambda..sub.j =/<.DELTA.Xj.DELTA.Xj> Here Y is the data collected at the detectors, and X.sup.k is the kth iterate toward the desired absoption information.

Spatiotemporal study of elderly suicide in Korea by age cohort.

PubMed

Joo, Y

2017-01-01

This study analyzed the spatiotemporal pattern and spatial diffusion of elderly suicide by age cohort, in Korea. The research investigated the elderly suicide rates of the 232 municipal units in South Korea between 2001 and 2011. The Gi* score, which is a spatially weighted indicator of area attributes, was used to identify hot spots and the spatiotemporal pattern of elderly suicide in the nation during the last 10 years. The spatial Markov matrix and spatial dynamic panel data model were employed to identify and estimate the diffusion effect. The suicide rate among elderly individuals 75 years and older was substantially higher than the rate for those between 65 and 74 years of age; however, the spatial patterns of the suicide clusters were similar between the two groups. From 2001 to 2011, the spatial distribution of elderly suicide hot spots differed each year. For both age cohorts, elderly suicide hot spots developed around the north area of South Korea in 2001 and moved to the mid-east area and the mid-western coastal area over 10 years. The spatial Markov matrix indicates that the change in the suicide rate of one area was affected by the suicide rates of neighbouring areas from the previous year, which suggests that suicide increase in one area inflates a neighbouring area's suicide rate over time. Using a spatial dynamic panel data model, elderly suicide diffusion effects were found to be statistically significant for both age cohorts even after economic and demographic indicators and a time variable are included. For individuals 75 years and older, the diffusion effect appeared to be larger. This study demonstrates that elderly suicide can spread spatially over time in both age cohorts. Thus, it is necessary to design a place-based and age-differentiated intervention policy that precisely considers the spatial diffusion of elderly suicide. Copyright © 2016 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

MHD simulation of transition process from the magneto-rotational instability to magnetic turbulence by using a high-order MHD simulation scheme

NASA Astrophysics Data System (ADS)

Hirai, K.; Katoh, Y.; Terada, N.; Kawai, S.

2016-12-01

In accretion disks, magneto-rotational instability (MRI; Balbus & Hawley, 1991) makes the disk gas in the magnetic turbulent state and drives efficient mass accretion into a central star. MRI drives turbulence through the evolution of the parasitic instability (PI; Goodman & Xu, 1994), which is related to both Kelvin-Helmholtz (K-H) instability and magnetic reconnection. The wave number vector of PI is strongly affected by both magnetic diffusivity and fluid viscosity (Pessah, 2010). This fact makes MHD simulation of MRI difficult, because we need to employ the numerical diffusivity for treating discontinuities in compressible MHD simulation schemes. Therefore, it is necessary to use an MHD scheme that has both high-order accuracy so as to resolve MRI driven turbulence and small numerical diffusivity enough to treat discontinuities. We have originally developed an MHD code by employing the scheme proposed by Kawai (2013). This scheme focuses on resolving turbulence accurately by using a high-order compact difference scheme (Lele, 1992), and meanwhile, the scheme treats discontinuities by using the localized artificial diffusivity method (Kawai, 2013). Our code also employs the pipeline algorithm (Matsuura & Kato, 2007) for MPI parallelization without diminishing the accuracy of the compact difference scheme. We carry out a 3-dimensional ideal MHD simulation with a net vertical magnetic field in the local shearing box disk model. We use 256x256x128 grids. Simulation results show that the spatially averaged turbulent stress induced by MRI linearly grows until around 2.8 orbital periods, and decreases after the saturation. We confirm the strong enhancement of the K-H mode PI at a timing just before the saturation, identified by the enhancement of its anisotropic wavenumber spectra in the 2-dimensional wavenumber space. The wave number of the maximum growth of PI reproduced in the simulation result is larger than the linear analysis. This discrepancy is explained by the simulation result that a shear flow created by MRI locally becomes thinner and faster due to interactions between antiparallel vortices induced by K-H mode PI, and this structure induces small scale waves which break the shear flow itself. We report the results of the simulation, and discuss how the saturation amplitude of MRI is determined.

Spatially: resolved heterogeneous dynamics in a strong colloidal gel

NASA Astrophysics Data System (ADS)

Buzzaccaro, Stefano; Alaimo, Matteo David; Secchi, Eleonora; Piazza, Roberto

2015-05-01

We re-examine the classical problem of irreversible colloid aggregation, showing that the application of Digital Fourier Imaging (DFI), a class of optical correlation methods that combine the power of light scattering and imaging, allows one to pick out novel useful evidence concerning the restructuring processes taking place in a strong colloidal gel. In particular, the spatially-resolved displacement fields provided by DFI strongly suggest that the temporally-intermittent local rearrangements taking place in the course of gel ageing are characterized by very long-ranged spatial correlations.

Model of bidirectional reflectance distribution function for metallic materials

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Beyond Conceptual Knowledge: The Impact of Children’s Theory-of-Mind on Dyadic Spatial Tasks

PubMed Central

Viana, Karine M. P.; Zambrana, Imac M.; Karevold, Evalill B.; Pons, Francisco

2016-01-01

Recent studies show that Theory of Mind (ToM) has implications for children’s social competences and psychological well-being. Nevertheless, although it is well documented that children overall take advantage when they have to resolve cognitive problems together with a partner, whether individual difference in ToM is one of the mechanisms that could explain cognitive performances produced in social interaction has received little attention. This study examines to what extent ToM explains children’s spatial performances in a dyadic situation. The sample includes 66 boys and girls between the ages of 5–9 years, who were tested for their ToM and for their competence to resolve a Spatial task involving mental rotation and spatial perspective taking, first individually and then in a dyadic condition. Results showed, in accordance with previous research, that children performed better on the Spatial task when they resolved it with a partner. Specifically, children’s ToM was a better predictor of their spatial performances in the dyadic condition than their age, gender, and spatial performances in the individual setting. The findings are discussed in terms of the relation between having a conceptual understanding of the mind and the practical implications of this knowledge for cognitive performances in social interaction regarding mental rotation and spatial perspective taking. PMID:27812344

Sensitivity Analysis and Requirements for Temporally and Spatially Resolved Thermometry Using Neutron Resonance Spectroscopy

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

Fernandez, Juan Carlos; Barnes, Cris William; Mocko, Michael Jeffrey

This report is intended to examine the use of neutron resonance spectroscopy (NRS) to make time- dependent and spatially-resolved temperature measurements of materials in extreme conditions. Specifically, the sensitivities of the temperature estimate on neutron-beam and diagnostic parameters is examined. Based on that examination, requirements are set on a pulsed neutron-source and diagnostics to make a meaningful measurement.

Nanoscale Characterization of Carrier Dynamic and Surface Passivation in InGaN/GaN Multiple Quantum Wells on GaN Nanorods.

PubMed

Chen, Weijian; Wen, Xiaoming; Latzel, Michael; Heilmann, Martin; Yang, Jianfeng; Dai, Xi; Huang, Shujuan; Shrestha, Santosh; Patterson, Robert; Christiansen, Silke; Conibeer, Gavin

2016-11-23

Using advanced two-photon excitation confocal microscopy, associated with time-resolved spectroscopy, we characterize InGaN/GaN multiple quantum wells on nanorod heterostructures and demonstrate the passivation effect of a KOH treatment. High-quality InGaN/GaN nanorods were fabricated using nanosphere lithography as a candidate material for light-emitting diode devices. The depth- and time-resolved characterization at the nanoscale provides detailed carrier dynamic analysis helpful for understanding the optical properties. The nanoscale spatially resolved images of InGaN quantum well and defects were acquired simultaneously. We demonstrate that nanorod etching improves light extraction efficiency, and a proper KOH treatment has been found to reduce the surface defects efficiently and enhance the luminescence. The optical characterization techniques provide depth-resolved and time-resolved carrier dynamics with nanoscale spatially resolved mapping, which is crucial for a comprehensive and thorough understanding of nanostructured materials and provides novel insight into the improvement of materials fabrication and applications.

Resolving runaway electron distributions in space, time, and energy

NASA Astrophysics Data System (ADS)

Paz-Soldan, C.; Cooper, C. M.; Aleynikov, P.; Eidietis, N. W.; Lvovskiy, A.; Pace, D. C.; Brennan, D. P.; Hollmann, E. M.; Liu, C.; Moyer, R. A.; Shiraki, D.

2018-05-01

Areas of agreement and disagreement with present-day models of runaway electron (RE) evolution are revealed by measuring MeV-level bremsstrahlung radiation from runaway electrons (REs) with a pinhole camera. Spatially resolved measurements localize the RE beam, reveal energy-dependent RE transport, and can be used to perform full two-dimensional (energy and pitch-angle) inversions of the RE phase-space distribution. Energy-resolved measurements find qualitative agreement with modeling on the role of collisional and synchrotron damping in modifying the RE distribution shape. Measurements are consistent with predictions of phase-space attractors that accumulate REs, with non-monotonic features observed in the distribution. Temporally resolved measurements find qualitative agreement with modeling on the impact of collisional and synchrotron damping in varying the RE growth and decay rate. Anomalous RE loss is observed and found to be largest at low energy. Possible roles for kinetic instability or spatial transport to resolve these anomalies are discussed.

Spatially resolved NMR spectra for the Swiss cheese model in heavy fermion PuCoGa5 superconductor

NASA Astrophysics Data System (ADS)

Das, Tanmoy; Zhu, Jian-Xin; Balatsky, A. V.; Graf, M. J.

2011-03-01

Spatially resolved NMR experiments, which probe the local electronic excitations, play a vital role for studying the pairing symmetry of unconventional superconductors. Here we calculate the spatial modulation of the NMR spin-lattice relaxation rate (1/T1) for the Swiss cheese model as a function of impurity concentration in PuCoGa5 superconductor. The local suppression of the superconducting order parameter due to impurities is related to the number of holes in the Swiss cheese model. Our results indicate that Friedel-like oscillations,as seen in the local-density of states near an impurity, are also present in the behavior of 1/T1 as one moves away from the impurity site. We demonstrate that the gap nodes, which are filled by disorder, can be probed by NMR through the local information encoded in the spectra. The advantage of spatially resolved NMR compared to STM measurements is that the former probe is not sensitive to surface states. Work is supported by US DOE.

Characterization of spatially resolved high resolution x-ray spectrometers for HEDP and light-source experiments

NASA Astrophysics Data System (ADS)

Hill, K. W.; Bitter, M.; Delgado-Aparicio, L.; Efthimion, P.; Pablant, N.; Lu, J.; Beiersdorfer, P.; Chen, H.; Magee, E.

2014-10-01

A high resolution 1D imaging x-ray spectrometer concept comprising a spherically bent crystal and a 2D pixelated detector is being optimized for diagnostics of small sources such as high energy density physics (HEDP) and synchrotron radiation or x-ray free electron laser experiments. This instrument is used on tokamak experiments for measurement of spatial profiles of Doppler ion temperature and plasma flow velocity, as well as electron temperature. Laboratory measurements demonstrate a resolving power, E/ ΔE of 10,000 and spatial resolution better than 10 μm. Good performance is obtained for Bragg angles ranging from 23 to 63 degrees. Initial tests of the instrument on HEDP plasmas are being performed with a goal of developing spatially resolved ion and electron temperature diagnostics. This work was performed under the auspices of the US DOE by PPPL under Contract DE-AC02-09CH11466 and by LLNL under Contract DE-AC52-07NA27344.

Development of the Vista Methane Emissions Inventory for Southern California: A GIS-Based Approach for Mapping Methane Emissions

NASA Astrophysics Data System (ADS)

Carranza, V.; Frausto-Vicencio, I.; Rafiq, T.; Verhulst, K. R.; Hopkins, F. M.; Rao, P.; Duren, R. M.; Miller, C. E.

2016-12-01

Atmospheric methane (CH4) is the second most prevalent anthropogenic greenhouse gas. Improved estimates of CH4 emissions from cities is essential for carbon cycle science and climate mitigation efforts. Development of spatially-resolved carbon emissions data sets may offer significant advances in understanding and managing carbon emissions from cities. Urban CH4 emissions in particular require spatially resolved emission maps to help resolve uncertainties in the CH4 budget. This study presents a Geographic Information System (GIS)-based approach to mapping CH4 emissions using locations of infrastructure known to handle and emit methane. We constrain the spatial distribution of sources to the facility level for the major CH4 emitting sources in the South Coast Air Basin. GIS spatial modeling was combined with publicly available datasets to determine the distribution of potential CH4 sources. The datasets were processed and validated to ensure accuracy in the location of individual sources. This information was then used to develop the Vista emissions prior, which is a one-year long, spatially-resolved CH4 emissions estimate. Methane emissions were calculated and spatially allocated to produce 1 km x 1 km gridded CH4 emission map spanning the Los Angeles Basin. In future work, the Vista CH4 emissions prior will be compared with existing, coarser-resolution emissions estimates and will be evaluated in inverse modeling studies using atmospheric observations. The Vista CH4 emissions inventory presents the first detailed spatial maps of CH4 sources and emissions estimates in the Los Angeles Basin and is a critical step towards sectoral attribution of CH4 emissions at local to regional scales.

Global diffusion of cosmic rays in random magnetic fields

NASA Astrophysics Data System (ADS)

Snodin, A. P.; Shukurov, A.; Sarson, G. R.; Bushby, P. J.; Rodrigues, L. F. S.

2016-04-01

The propagation of charged particles, including cosmic rays, in a partially ordered magnetic field is characterized by a diffusion tensor whose components depend on the particle's Larmor radius RL and the degree of order in the magnetic field. Most studies of the particle diffusion presuppose a scale separation between the mean and random magnetic fields (e.g. there being a pronounced minimum in the magnetic power spectrum at intermediate scales). Scale separation is often a good approximation in laboratory plasmas, but not in most astrophysical environments such as the interstellar medium (ISM). Modern simulations of the ISM have numerical resolution of the order of 1 pc, so the Larmor radius of the cosmic rays that dominate in energy density is at least 106 times smaller than the resolved scales. Large-scale simulations of cosmic ray propagation in the ISM thus rely on oversimplified forms of the diffusion tensor. We take the first steps towards a more realistic description of cosmic ray diffusion for such simulations, obtaining direct estimates of the diffusion tensor from test particle simulations in random magnetic fields (with the Larmor radius scale being fully resolved), for a range of particle energies corresponding to 10-2 ≲ RL/lc ≲ 103, where lc is the magnetic correlation length. We obtain explicit expressions for the cosmic ray diffusion tensor for RL/lc ≪ 1, that might be used in a sub-grid model of cosmic ray diffusion. The diffusion coefficients obtained are closely connected with existing transport theories that include the random walk of magnetic lines.

Two-way coupled SPH and particle level set fluid simulation.

PubMed

Losasso, Frank; Talton, Jerry; Kwatra, Nipun; Fedkiw, Ronald

2008-01-01

Grid-based methods have difficulty resolving features on or below the scale of the underlying grid. Although adaptive methods (e.g. RLE, octrees) can alleviate this to some degree, separate techniques are still required for simulating small-scale phenomena such as spray and foam, especially since these more diffuse materials typically behave quite differently than their denser counterparts. In this paper, we propose a two-way coupled simulation framework that uses the particle level set method to efficiently model dense liquid volumes and a smoothed particle hydrodynamics (SPH) method to simulate diffuse regions such as sprays. Our novel SPH method allows us to simulate both dense and diffuse water volumes, fully incorporates the particles that are automatically generated by the particle level set method in under-resolved regions, and allows for two way mixing between dense SPH volumes and grid-based liquid representations.

Modeling the Role of Incisures in Vertebrate Phototransduction

PubMed Central

Caruso, Giovanni; Bisegna, Paolo; Shen, Lixin; Andreucci, Daniele; Hamm, Heidi E.; DiBenedetto, Emmanuele

2006-01-01

Phototransduction is mediated by a G-protein-coupled receptor-mediated cascade, activated by light and localized to rod outer segment (ROS) disk membranes, which, in turn, drives a diffusion process of the second messengers cGMP and Ca2+ in the ROS cytosol. This process is hindered by disks—which, however, bear physical cracks, known as incisures, believed to favor the longitudinal diffusion of cGMP and Ca2+. This article is aimed at highlighting the biophysical functional role and significance of incisures, and their effect on the local and global response of the photocurrent. Previous work on this topic regarded the ROS as well stirred in the radial variables, lumped the diffusion mechanism on the longitudinal axis of the ROS, and replaced the cytosolic diffusion coefficients by effective ones, accounting for incisures through their total patent area only. The fully spatially resolved model recently published by our group is a natural tool to take into account other significant details of incisures, including their geometry and distribution. Using mathematical theories of homogenization and concentrated capacity, it is shown here that the complex diffusion process undergone by the second messengers cGMP and Ca2+ in the ROS bearing incisures can be modeled by a family of two-dimensional diffusion processes on the ROS cross sections, glued together by other two-dimensional diffusion processes, accounting for diffusion in the ROS outer shell and in the bladelike regions comprised by the stack of incisures. Based on this mathematical model, a code has been written, capable of incorporating an arbitrary number of incisures and activation sites, with any given arbitrary distribution within the ROS. The code is aimed at being an operational tool to perform numerical experiments of phototransduction, in rods with incisures of different geometry and structure, under a wide spectrum of operating conditions. The simulation results show that incisures have a dual biophysical function. On the one hand, since incisures line up from disk to disk, they create vertical cytoplasmic channels crossing the disks, thus facilitating diffusion of second messengers; on the other hand, at least in those species bearing multiple incisures, they divide the disks into lobes like the petals of a flower, thus confining the diffusion of activated phosphodiesterase and localizing the photon response. Accordingly, not only the total area of incisures, but their geometrical shape and distribution as well, significantly influence the global photoresponse. PMID:16714347

Experimental measurement of spatially resolved electron density in a filament of a pulsed positive streamer discharge in water

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

Wen, Xiao Qiong; Niu, Zhi Wen; Ren, Chun-Sheng

2015-06-29

By combining a high-speed frame camera with a monochromator, the spatially resolved optical emission spectrum of hydrogen α line in a single filament of a pulsed positive streamer discharge in water has been experimentally measured. The spatially resolved electron densities in a single filament of a pulsed positive streamer discharge in water with a conductivity of 200 μS/cm were investigated. During the experiment, the average energy per pulse of discharge was 90.6 ± 13.6 mJ. The results show that the electron density in the streamer filament is 10{sup 17–18}/cm{sup 3}, and present a decreasing tendency along the axial direction of the streamer filamentmore » with increasing distance from the tip of the anode.« less

Fluorescence correlation spectroscopy of diffusion probed with a Gaussian Lorentzian spatial distribution

NASA Astrophysics Data System (ADS)

Marrocco, Michele

2007-11-01

Fluorescence correlation spectroscopy is fundamental in many physical, chemical and biological studies of molecular diffusion. However, the concept of fluorescence correlation is founded on the assumption that the analytical description of the correlation decay of diffusion can be achieved if the spatial profile of the detected volume obeys a three-dimensional Gaussian distribution. In the present Letter, the analytical result is instead proven for the fundamental Gaussian-Lorentzian profile.

Boundary-induced pattern formation from uniform temporal oscillation

NASA Astrophysics Data System (ADS)

Kohsokabe, Takahiro; Kaneko, Kunihiko

2018-04-01

Pattern dynamics triggered by fixing a boundary is investigated. By considering a reaction-diffusion equation that has a unique spatially uniform and limit cycle attractor under a periodic or Neumann boundary condition, and then by choosing a fixed boundary condition, we found three novel phases depending on the ratio of diffusion constants of activator to inhibitor: transformation of temporally periodic oscillation into a spatially periodic fixed pattern, travelling wave emitted from the boundary, and aperiodic spatiotemporal dynamics. The transformation into a fixed, periodic pattern is analyzed by crossing of local nullclines at each spatial point, shifted by diffusion terms, as is analyzed by using recursive equations, to obtain the spatial pattern as an attractor. The generality of the boundary-induced pattern formation as well as its relevance to biological morphogenesis is discussed.

Alfvén Waves in the Solar Corona

NASA Astrophysics Data System (ADS)

Tomczyk, S.; McIntosh, S. W.; Keil, S. L.; Judge, P. G.; Schad, T.; Seeley, D. H.; Edmondson, J.

2007-08-01

Alfvén waves, transverse incompressible magnetic oscillations, have been proposed as a possible mechanism to heat the Sun’s corona to millions of degrees by transporting convective energy from the photosphere into the diffuse corona. We report the detection of Alfvén waves in intensity, line-of-sight velocity, and linear polarization images of the solar corona taken using the FeXIII 1074.7-nanometer coronal emission line with the Coronal Multi-Channel Polarimeter (CoMP) instrument at the National Solar Observatory, New Mexico. Ubiquitous upward propagating waves were seen, with phase speeds of 1 to 4 megameters per second and trajectories consistent with the direction of the magnetic field inferred from the linear polarization measurements. An estimate of the energy carried by the waves that we spatially resolved indicates that they are too weak to heat the solar corona; however, unresolved Alfvén waves may carry sufficient energy.

The XMM-Newton View of Wolf-Rayet Bubbles

NASA Astrophysics Data System (ADS)

Guerrero, M.; Toala, J.

2017-10-01

The powerful stellar winds of Wolf-Rayet (WR) stars blow large bubble into the circumstellar material ejected in previous phases of stellar evolution. The shock of those stellar winds produces X-ray-emitting hot plasmas which tells us about the diffusion of processed material onto the interstellar medium, about processes of heat conduction and turbulent mixing at the interface, about the late stages of stellar evolution, and about the shaping of the circumstellar environment, just before supernova explosions. The unique sensitivity of XMM-Newton has been key for the detection, mapping and spectral analysis of the X-ray emission from the hot bubbles around WR stars. These observations underscore the importance of the structure of the interstellar medium around massive stars, but they have also unveiled unknown phenomena, such as blowouts of hot gas into the interstellar medium or spatially-resolved spectral properties of the hot gas, which disclose inhomogeneous chemical abundances and physical properties across these bubbles.

Optical asymmetric cryptography based on elliptical polarized light linear truncation and a numerical reconstruction technique.

PubMed

Lin, Chao; Shen, Xueju; Wang, Zhisong; Zhao, Cheng

2014-06-20

We demonstrate a novel optical asymmetric cryptosystem based on the principle of elliptical polarized light linear truncation and a numerical reconstruction technique. The device of an array of linear polarizers is introduced to achieve linear truncation on the spatially resolved elliptical polarization distribution during image encryption. This encoding process can be characterized as confusion-based optical cryptography that involves no Fourier lens and diffusion operation. Based on the Jones matrix formalism, the intensity transmittance for this truncation is deduced to perform elliptical polarized light reconstruction based on two intensity measurements. Use of a quick response code makes the proposed cryptosystem practical, with versatile key sensitivity and fault tolerance. Both simulation and preliminary experimental results that support theoretical analysis are presented. An analysis of the resistance of the proposed method on a known public key attack is also provided.

Prospect of space-based interferometry at EUV and soft X-ray wavelengths

NASA Technical Reports Server (NTRS)

Welsh, Barry Y.; Chakrabarti, Supriya

1992-01-01

We review the current capabilities of high-resolution, spectroscopic, space-borne instrumentation available for both solar and stellar observations in the EUV and soft X-ray wavelength regimes, and describe the basic design of a compact, all-reflection interferometer based on the spatial heterodyne technique; this is capable of producing a resolving power (lambda/Delta-lambda) of about 20,000 in the 100-200 A region using presently available multilayer optical components. Such an instrument can be readily constructed with existing technology. Due to its small size and lack of moving parts, it is ideally suited to spaceborne applications. Based on best estimates of the efficiency of this instrument at soft X-ray wavelengths, we review the possible use of this high-resolution interferometer in obtaining high-resolution full-disk spectroscopy of the sun. We also discuss its possible use for observations of diffuse sources such as the EUV interstellar background radiation.

Figuring Out Gas in Galaxies In Enzo (FOGGIE): Resolving the Inner Circumgalactic Medium

NASA Astrophysics Data System (ADS)

Corlies, Lauren; Peeples, Molly; Tumlinson, Jason; O'Shea, Brian; Smith, Britton

2018-01-01

Cosmological hydrodynamical simulations using every common numerical method have struggled to reproduce the multiphase nature of the circumgalactic medium (CGM) revealed by recent observations. However, to date, resolution in these simulations has been aimed at dense regions — the galactic disk and in-falling satellites — while the diffuse CGM never reaches comparable levels of refinement. Taking advantage of the flexible grid structure of the adaptive mesh refinement code Enzo, we force refinement in a region of the CGM of a Milky Way-like galaxy to the same spatial resolution as that of the disk. In this talk, I will present how the physical and structural distributions of the circumgalactic gas change dramatically as a function of the resolution alone. I will also show the implications these changes have for the observational properties of the gas in the context of the observations.

Diagnosing the Internal Architecture of Zeolite Ferrierite

PubMed Central

Schmidt, Joel E.; Hendriks, Frank C.; Lutz, Martin; Post, L. Christiaan; Fu, Donglong

2017-01-01

Abstract Large crystals of zeolite ferrierite (FER) are important model systems for spatially resolved catalysis and diffusion studies, though there is considerable variation in crystal habit depending on the chemical composition and employed synthesis conditions. A synergistic combination of techniques has been applied, including single crystal X‐ray diffraction, high‐temperature in situ confocal fluorescence microscopy, fluorescent probe molecules, wide‐field microscopy and atomic force microscopy to unravel the internal architecture of three distinct FER zeolites. Pyrolyzed template species can be used as markers for the 8‐membered ring direction as they are trapped in the terraced roof of the FER crystals. This happens as the materials grow in a layer‐by‐layer, defect‐free manner normal to the large crystal surface, and leads to a facile method to diagnose the pore system orientation, which avoids tedious single crystal X‐ray diffraction experiments. PMID:28809081

Laser Blow-Off Impurity Injection Experiments at the HSX Stellarator

NASA Astrophysics Data System (ADS)

Castillo, J. F.; Bader, A.; Likin, K. M.; Anderson, D. T.; Anderson, F. S. B.; Kumar, S. T. A.; Talmadge, J. N.

2017-10-01

Results from the HSX laser blow-off experiment are presented and compared to a synthetic diagnostic implemented in the STRAHL impurity transport modeling code in order to measure the impurity transport diffusivity and convective velocity. A laser blow-off impurity injection system is used to rapidly deposit a small, controlled quantity of aluminum into the confinement volume. Five AXUV photodiode arrays are used to take time-resolved measurements of the impurity radiation. The spatially one-dimensional impurity transport code STRAHL is used to calculate a time-dependent plasma emissivity profile. Modeled intensity signals calculated from a synthetic diagnostic code provide direct comparison between plasma simulation and experimental results. An optimization algorithm with impurity transport coefficients acting as free parameters is used to fit the model to experimental data. This work is supported by US DOE Grant DE-FG02-93ER54222.

Detection of localized inclusions of gold nanoparticles in Intralipid-1% by point-radiance spectroscopy

NASA Astrophysics Data System (ADS)

Grabtchak, Serge; Palmer, Tyler J.; Whelan, William M.

2011-07-01

Interstitial fiber-optic-based approaches used in both diagnostic and therapeutic applications rely on localized light-tissue interactions. We present an optical technique to identify spectrally and spatially specific exogenous chromophores in highly scattering turbid media. Point radiance spectroscopy is based on directional light collection at a single point with a side-firing fiber that can be rotated up to 360 deg. A side firing fiber accepts light within a well-defined, solid angle, thus potentially providing an improved spatial resolution. Measurements were performed using an 800-μm diameter isotropic spherical diffuser coupled to a halogen light source and a 600 μm, ~43 deg cleaved fiber (i.e., radiance detector). The background liquid-based scattering phantom was fabricated using 1% Intralipid. Light was collected with 1 deg increments through 360 deg-segment. Gold nanoparticles , placed into a 3.5-mm diameter capillary tube were used as localized scatterers and absorbers introduced into the liquid phantom both on- and off-axis between source and detector. The localized optical inhomogeneity was detectable as an angular-resolved variation in the radiance polar plots. This technique is being investigated as a potential noninvasive optical modality for prostate cancer monitoring.

Multipoint entanglement in disordered systems

NASA Astrophysics Data System (ADS)

Magán, Javier M.; Paganelli, Simone; Oganesyan, Vadim

2017-02-01

We develop an approach to characterize excited states of disordered many-body systems using spatially resolved structures of entanglement. We show that the behavior of the mutual information (MI) between two parties of a many-body system can signal a qualitative difference between thermal and localized phases - MI is finite in insulators while it approaches zero in the thermodynamic limit in the ergodic phase. Related quantities, such as the recently introduced Codification Volume (CV), are shown to be suitable to quantify the correlation length of the system. These ideas are illustrated using prototypical non-interacting wavefunctions of localized and extended particles and then applied to characterize states of strongly excited interacting spin chains. We especially focus on evolution of spatial structure of quantum information between high temperature diffusive and many-body localized (MBL) phases believed to exist in these models. We study MI as a function of disorder strength both averaged over the eigenstates and in time-evolved product states drawn from continuously deformed family of initial states realizable experimentally. As expected, spectral and time-evolved averages coincide inside the ergodic phase and differ significantly outside. We also highlight dispersion among the initial states within the localized phase - some of these show considerable generation and delocalization of quantum information.

Visible hyperspectral imaging evaluating the cutaneous response to ultraviolet radiation

NASA Astrophysics Data System (ADS)

Ilias, Michail A.; Häggblad, Erik; Anderson, Chris; Salerud, E. Göran

2007-02-01

In vivo diagnostics of skin diseases as well as understanding of the skin biology constitute a field demanding characterization of physiological and anatomical parameters. Biomedical optics has been successfully used, to qualitatively and quantitatively estimate the microcirculatory conditions of superficial skin. Capillaroscopy, laser Doppler techniques and spectroscopy, all elucidate different aspects of microcirculation, e.g. capillary anatomy and distribution, tissue perfusion and hemoglobin oxygenation. We demonstrate the use of a diffuse reflectance hyperspectral imaging system for spatial and temporal characterization of tissue oxygenation, important to skin viability. The system comprises: light source, liquid crystal tunable filter, camera objective, CCD camera, and the decomposition of the spectral signature into relative amounts of oxy- and deoxygenized hemoglobin as well as melanin in every pixel resulting in tissue chromophore images. To validate the system, we used a phototesting model, creating a graded inflammatory response of a known geometry, in order to evaluate the ability to register spatially resolved reflectance spectra. The obtained results demonstrate the possibility to describe the UV inflammatory response by calculating the change in tissue oxygen level, intimately connected to a tissue's metabolism. Preliminary results on the estimation of melanin content are also presented.

Detection of localized inclusions of gold nanoparticles in Intralipid-1% by point-radiance spectroscopy.

PubMed

Grabtchak, Serge; Palmer, Tyler J; Whelan, William M

2011-07-01

Interstitial fiber-optic-based approaches used in both diagnostic and therapeutic applications rely on localized light-tissue interactions. We present an optical technique to identify spectrally and spatially specific exogenous chromophores in highly scattering turbid media. Point radiance spectroscopy is based on directional light collection at a single point with a side-firing fiber that can be rotated up to 360 deg. A side firing fiber accepts light within a well-defined, solid angle, thus potentially providing an improved spatial resolution. Measurements were performed using an 800-μm diameter isotropic spherical diffuser coupled to a halogen light source and a 600 μm, ∼43 deg cleaved fiber (i.e., radiance detector). The background liquid-based scattering phantom was fabricated using 1% Intralipid. Light was collected with 1 deg increments through 360 deg-segment. Gold nanoparticles , placed into a 3.5-mm diameter capillary tube were used as localized scatterers and absorbers introduced into the liquid phantom both on- and off-axis between source and detector. The localized optical inhomogeneity was detectable as an angular-resolved variation in the radiance polar plots. This technique is being investigated as a potential noninvasive optical modality for prostate cancer monitoring.

Hopf Bifurcation Analysis of a Gene Regulatory Network Mediated by Small Noncoding RNA with Time Delays and Diffusion

NASA Astrophysics Data System (ADS)

Li, Chengxian; Liu, Haihong; Zhang, Tonghua; Yan, Fang

2017-12-01

In this paper, a gene regulatory network mediated by small noncoding RNA involving two time delays and diffusion under the Neumann boundary conditions is studied. Choosing the sum of delays as the bifurcation parameter, the stability of the positive equilibrium and the existence of spatially homogeneous and spatially inhomogeneous periodic solutions are investigated by analyzing the corresponding characteristic equation. It is shown that the sum of delays can induce Hopf bifurcation and the diffusion incorporated into the system can effect the amplitude of periodic solutions. Furthermore, the spatially homogeneous periodic solution always exists and the spatially inhomogeneous periodic solution will arise when the diffusion coefficients of protein and mRNA are suitably small. Particularly, the small RNA diffusion coefficient is more robust and its effect on model is much less than protein and mRNA. Finally, the explicit formulae for determining the direction of Hopf bifurcation and the stability of the bifurcating periodic solutions are derived by employing the normal form theory and center manifold theorem for partial functional differential equations. Finally, numerical simulations are carried out to illustrate our theoretical analysis.

NMR 1D-imaging of water infiltration into mesoporous matrices.

PubMed

Le Feunteun, Steven; Diat, Olivier; Guillermo, Armel; Poulesquen, Arnaud; Podor, Renaud

2011-04-01

It is shown that coupling nuclear magnetic resonance (NMR) 1D-imaging with the measure of NMR relaxation times and self-diffusion coefficients can be a very powerful approach to investigate fluid infiltration into porous media. Such an experimental design was used to study the very slow seeping of pure water into hydrophobic materials. We consider here three model samples of nuclear waste conditioning matrices which consist in a dispersion of NaNO(3) (highly soluble) and/or BaSO(4) (poorly soluble) salt grains embedded in a bitumen matrix. Beyond studying the moisture progression according to the sample depth, we analyze the water NMR relaxation times and self-diffusion coefficients along its 1D-concentration profile to obtain spatially resolved information on the solution properties and on the porous structure at different scales. It is also shown that, when the relaxation or self-diffusion properties are multimodal, the 1D-profile of each water population is recovered. Three main levels of information were disclosed along the depth-profiles. They concern (i) the water uptake kinetics, (ii) the salinity and the molecular dynamics of the infiltrated solutions and (iii) the microstructure of the water-filled porosities: open networks coexisting with closed pores. All these findings were fully validated and enriched by NMR cryoporometry experiments and by performing environmental scanning electronic microscopy observations. Surprisingly, results clearly show that insoluble salts enhance the water progression and thereby increase the capability of the material to uptake water. Copyright © 2011 Elsevier Inc. All rights reserved.

Time-resolved mapping of water diffusion coefficients in a working soft actuator device.

PubMed

Naji, Leila; Chudek, John A; Baker, Richard T

2008-08-14

Diffusion-weighted imaging was employed to spatially map the distribution of the diffusion coefficient of water, D, in bare, water-soaked, Li(+)-exchanged, cast Nafion and in an ionic polymer-metal composite (IPMC) soft actuator element, prepared from this bare Nafion by impregnation with Pt electrodes. D was evaluated in two orthogonal directions: along one of the long dimensions of the sample (Dx) and through its thickness (Dz). D-maps of the IPMC element were obtained both in the absence of an applied potential and in situ during the application of a 3 V dc potential across the thickness of the sample. In the bare Nafion, D-maps showed uniform values of both Dx and Dz of about 6 x 10 (-10) m(2) s(-1). In the IPMC two effects were observed: (i) D at the electroded surfaces of the IPMC was higher than at the center of the sample; (ii) this difference was much greater in Dz than in Dx . Both effects were explained by the influence of the impregnated Pt electrodes on polymer structure. The D-maps in the electrochemical measurements showed high values of D (up to 8 x 10(-10) m(2) s(-1)) at the cathode and low values (from 1 x 10(-10) m(2) s(-1)) at the anode. This was explained in terms of the effect on the Nafion nanostructure of the forced electro-migration of Li(H2O)x(+) species toward the cathode.

Depth-resolved monitoring of analytes diffusion in ocular tissues

NASA Astrophysics Data System (ADS)

Larin, Kirill V.; Ghosn, Mohamad G.; Tuchin, Valery V.

2007-02-01

Optical coherence tomography (OCT) is a noninvasive imaging technique with high in-depth resolution. We employed OCT technique for monitoring and quantification of analyte and drug diffusion in cornea and sclera of rabbit eyes in vitro. Different analytes and drugs such as metronidazole, dexamethasone, ciprofloxacin, mannitol, and glucose solution were studied and whose permeability coefficients were calculated. Drug diffusion monitoring was performed as a function of time and as a function of depth. Obtained results suggest that OCT technique might be used for analyte diffusion studies in connective and epithelial tissues.

Particle Trapping Mechanisms Are Different in Spatially Ordered and Disordered Interacting Gels.

PubMed

Hansing, Johann; Netz, Roland R

2018-06-05

Using stochastic simulations, we study the influence of spatial disorder on the diffusion of a single particle through a gel that consists of rigid, straight fibers. The interaction between the particle and the gel fibers consists of an invariant short-range repulsion, the steric part, and an interaction part that can be attractive or repulsive and of varying range. The effect that spatial disorder of the gel structure has on the particle diffusivity depends crucially on the presence of nonsteric interactions. For attractive interactions, disorder slows down diffusion, because in disordered gels, the particle becomes strongly trapped in regions of locally increased fiber density. For repulsive interactions, the diffusivity is minimal for intermediate disorder strength, because highly disordered lattices exhibit abundant passageways of locally low fiber density. The comparison with experimental data on protein and fluorophore diffusion through various hydrogels is favorable. Our findings shed light on particle-diffusion mechanisms in biogels and thus on biological barrier properties, which can be helpful for the optimal design of synthetic diffusors as well as synthetic mucus constructs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Accounting for spatial effects in land use regression for urban air pollution modeling.

PubMed

Bertazzon, Stefania; Johnson, Markey; Eccles, Kristin; Kaplan, Gilaad G

2015-01-01

In order to accurately assess air pollution risks, health studies require spatially resolved pollution concentrations. Land-use regression (LUR) models estimate ambient concentrations at a fine spatial scale. However, spatial effects such as spatial non-stationarity and spatial autocorrelation can reduce the accuracy of LUR estimates by increasing regression errors and uncertainty; and statistical methods for resolving these effects--e.g., spatially autoregressive (SAR) and geographically weighted regression (GWR) models--may be difficult to apply simultaneously. We used an alternate approach to address spatial non-stationarity and spatial autocorrelation in LUR models for nitrogen dioxide. Traditional models were re-specified to include a variable capturing wind speed and direction, and re-fit as GWR models. Mean R(2) values for the resulting GWR-wind models (summer: 0.86, winter: 0.73) showed a 10-20% improvement over traditional LUR models. GWR-wind models effectively addressed both spatial effects and produced meaningful predictive models. These results suggest a useful method for improving spatially explicit models. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Fabrication of microscale materials with programmable composition gradients.

PubMed

Laval, Cédric; Bouchaudy, Anne; Salmon, Jean-Baptiste

2016-04-07

We present an original microfluidic technique coupling pervaporation and the use of Quake valves to fabricate microscale materials (∼10 × 100 μm(2) × 1 cm) with composition gradients along their longest dimension. Our device exploits pervaporation of water through a thin poly(dimethylsiloxane) (PDMS) membrane to continuously pump solutions (or dispersions) contained in different reservoirs connected to a microfluidic channel. This pervaporation-induced flow concentrates solutes (or particles) at the tip of the channel up to the formation of a dense material. The latter invades the channel as it is constantly enriched by an incoming flux of solutes/particles. Upstream Quake valves are used to select which reservoir is connected to the pervaporation channel and thus which solution (or dispersion) enriches the material during its growth. The microfluidic configuration of the pervaporation process is used to impose controlled growth along the channel thus enabling one to program spatial composition gradients using appropriate actuations of the valves. We demonstrate the possibilities offered by our technique through the fabrication of dense assemblies of nanoparticles and polymer composites with programmed gradients of fluorescent dyes. We also address the key issue of the spatial resolution of our gradients and we show that well-defined spatial modulations down to ≈50 μm can be obtained within colloidal materials, whereas gradients within polymer materials are resolved on length scales down to ≈1 mm due to molecular diffusion.

Time-Resolved Diffuse Optical Spectroscopy and Imaging Using Solid-State Detectors: Characteristics, Present Status, and Research Challenges.

PubMed

Alayed, Mrwan; Deen, M Jamal

2017-09-14

Diffuse optical spectroscopy (DOS) and diffuse optical imaging (DOI) are emerging non-invasive imaging modalities that have wide spread potential applications in many fields, particularly for structural and functional imaging in medicine. In this article, we review time-resolved diffuse optical imaging (TR-DOI) systems using solid-state detectors with a special focus on Single-Photon Avalanche Diodes (SPADs) and Silicon Photomultipliers (SiPMs). These TR-DOI systems can be categorized into two types based on the operation mode of the detector (free-running or time-gated). For the TR-DOI prototypes, the physical concepts, main components, figures-of-merit of detectors, and evaluation parameters are described. The performance of TR-DOI prototypes is evaluated according to the parameters used in common protocols to test DOI systems particularly basic instrumental performance (BIP). In addition, the potential features of SPADs and SiPMs to improve TR-DOI systems and expand their applications in the foreseeable future are discussed. Lastly, research challenges and future developments for TR-DOI are discussed for each component in the prototype separately and also for the entire system.

Excitation-dependent carrier lifetime and diffusion length in bulk CdTe determined by time-resolved optical pump-probe techniques

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

Ščajev, Patrik; Miasojedovas, Saulius; Mekys, Algirdas

We applied time-resolved pump-probe spectroscopy based on free carrier absorption and light diffraction on a transient grating for direct measurements of the carrier lifetime and diffusion coefficient D in high-resistivity single crystal CdTe (codoped with In and Er). The bulk carrier lifetime t decreased from 670 +/-50 ns to 60 +/- 10 ns with increase of excess carrier density N from 10 16 to 5 x 10 18cm -3 due to the excitation-dependent radiative recombination rate. In this N range, the carrier diffusion length dropped from 14 um to 6 um due to lifetime decrease. Modeling of in-depth (axial) andmore » in-plane (lateral) carrier diffusion provided the value of surface recombination velocity S = 6 x 10 5 cm/s for the untreated surface. At even higher excitations, in the 10 19-3 x 10 20 cm -3 density range, D increase from 5 to 20 cm^2/s due to carrier degeneracy was observed.« less

Excitation-dependent carrier lifetime and diffusion length in bulk CdTe determined by time-resolved optical pump-probe techniques

DOE PAGES

Ščajev, Patrik; Miasojedovas, Saulius; Mekys, Algirdas; ...

2018-01-14

We applied time-resolved pump-probe spectroscopy based on free carrier absorption and light diffraction on a transient grating for direct measurements of the carrier lifetime and diffusion coefficient D in high-resistivity single crystal CdTe (codoped with In and Er). The bulk carrier lifetime t decreased from 670 +/-50 ns to 60 +/- 10 ns with increase of excess carrier density N from 10 16 to 5 x 10 18cm -3 due to the excitation-dependent radiative recombination rate. In this N range, the carrier diffusion length dropped from 14 um to 6 um due to lifetime decrease. Modeling of in-depth (axial) andmore » in-plane (lateral) carrier diffusion provided the value of surface recombination velocity S = 6 x 10 5 cm/s for the untreated surface. At even higher excitations, in the 10 19-3 x 10 20 cm -3 density range, D increase from 5 to 20 cm^2/s due to carrier degeneracy was observed.« less

Retrospective analysis of the utility of multiparametric MRI for differentiating between benign and malignant breast lesions in women in China

PubMed Central

Fan, Wei Xiong; Chen, Xiao Feng; Cheng, Feng Yan; Cheng, Ya Bao; Xu, Tai; Zhu, Wen Biao; Zhu, Xiao Lei; Li, Gui Jin; Li, Shuai

2018-01-01

Abstract We explored the utility of time-resolved angiography with interleaved stochastic trajectories dynamic contrast-enhanced magnetic resonance imaging (TWIST DCE-MRI), readout segmentation of long variable echo-trains diffusion-weighted magnetic resonance imaging- diffusion-weighted magnetic resonance imaging (RESOLVE-DWI), and echo-planar imaging- diffusion-weighted magnetic resonance imaging (EPI-DWI) for distinguishing between malignant and benign breast lesions. This retrospective analysis included female patients with breast lesions seen at a single center in China between January 2016 and April 2016. Patients were allocated to a benign or malignant group based on pathologic diagnosis. All patients received routine MRI, RESOLVE-DWI, EPI-DWI, and TWIST DCE-T1WI. Variables measured included quantitative parameters (Ktrans, Kep, and Ve), semiquantitative parameters (rate of contrast enhancement for contrast agent inflow [W-in], rate of contrast decay for contrast agent outflow [W-out], and time-to-peak enhancement after contrast agent injection [TTP]) and apparent diffusion coefficient (ADC) values for RESOLVE-DWI (ADCr) and EPI-DWI (ADCe). Receiver-operating characteristic (ROC) curve analysis was used to evaluate the diagnostic utility of each parameter for differentiating malignant from benign breast lesions. A total of 87 patients were included (benign, n = 20; malignant, n = 67). Compared with the benign group, the malignant group had significantly higher Ktrans, Kep and W-in and significantly lower W-out, TTP, ADCe, and ADCr (all P < .05); Ve was not significantly different between groups. RESOLVE-DWI was superior to conventional EPI-DWI at illustrating lesion boundary and morphology, while ADCr was significantly lower than ADCe in all patients. Kep, W-out, ADCr, and ADCe showed the highest diagnostic efficiency (based on AUC value) for differentiating between benign and malignant lesions. Combining 3 parameters (Kep, W-out, and ADCr) had a higher diagnostic efficiency (AUC, 0.965) than any individual parameter and distinguished between benign and malignant lesions with high sensitivity (91.0%), specificity (95.0%), and accuracy (91.9%). An index combining Kep, W-out, and ADCr could potentially be used for the differential diagnosis of breast lesions. PMID:29369183

Retrospective analysis of the utility of multiparametric MRI for differentiating between benign and malignant breast lesions in women in China.

PubMed

Fan, Wei Xiong; Chen, Xiao Feng; Cheng, Feng Yan; Cheng, Ya Bao; Xu, Tai; Zhu, Wen Biao; Zhu, Xiao Lei; Li, Gui Jin; Li, Shuai

2018-01-01

We explored the utility of time-resolved angiography with interleaved stochastic trajectories dynamic contrast-enhanced magnetic resonance imaging (TWIST DCE-MRI), readout segmentation of long variable echo-trains diffusion-weighted magnetic resonance imaging- diffusion-weighted magnetic resonance imaging (RESOLVE-DWI), and echo-planar imaging- diffusion-weighted magnetic resonance imaging (EPI-DWI) for distinguishing between malignant and benign breast lesions.This retrospective analysis included female patients with breast lesions seen at a single center in China between January 2016 and April 2016. Patients were allocated to a benign or malignant group based on pathologic diagnosis. All patients received routine MRI, RESOLVE-DWI, EPI-DWI, and TWIST DCE-T1WI. Variables measured included quantitative parameters (K, Kep, and Ve), semiquantitative parameters (rate of contrast enhancement for contrast agent inflow [W-in], rate of contrast decay for contrast agent outflow [W-out], and time-to-peak enhancement after contrast agent injection [TTP]) and apparent diffusion coefficient (ADC) values for RESOLVE-DWI (ADCr) and EPI-DWI (ADCe). Receiver-operating characteristic (ROC) curve analysis was used to evaluate the diagnostic utility of each parameter for differentiating malignant from benign breast lesions.A total of 87 patients were included (benign, n = 20; malignant, n = 67). Compared with the benign group, the malignant group had significantly higher K, Kep and W-in and significantly lower W-out, TTP, ADCe, and ADCr (all P < .05); Ve was not significantly different between groups. RESOLVE-DWI was superior to conventional EPI-DWI at illustrating lesion boundary and morphology, while ADCr was significantly lower than ADCe in all patients. Kep, W-out, ADCr, and ADCe showed the highest diagnostic efficiency (based on AUC value) for differentiating between benign and malignant lesions. Combining 3 parameters (Kep, W-out, and ADCr) had a higher diagnostic efficiency (AUC, 0.965) than any individual parameter and distinguished between benign and malignant lesions with high sensitivity (91.0%), specificity (95.0%), and accuracy (91.9%).An index combining Kep, W-out, and ADCr could potentially be used for the differential diagnosis of breast lesions.

Measurement of nanoscale three-dimensional diffusion in the interior of living cells by STED-FCS.

PubMed

Lanzanò, Luca; Scipioni, Lorenzo; Di Bona, Melody; Bianchini, Paolo; Bizzarri, Ranieri; Cardarelli, Francesco; Diaspro, Alberto; Vicidomini, Giuseppe

2017-07-06

The observation of molecular diffusion at different spatial scales, and in particular below the optical diffraction limit (<200 nm), can reveal details of the subcellular topology and its functional organization. Stimulated-emission depletion microscopy (STED) has been previously combined with fluorescence correlation spectroscopy (FCS) to investigate nanoscale diffusion (STED-FCS). However, stimulated-emission depletion fluorescence correlation spectroscopy has only been used successfully to reveal functional organization in two-dimensional space, such as the plasma membrane, while, an efficient implementation for measurements in three-dimensional space, such as the cellular interior, is still lacking. Here we integrate the STED-FCS method with two analytical approaches, the recent separation of photons by lifetime tuning and the fluorescence lifetime correlation spectroscopy, to simultaneously probe diffusion in three dimensions at different sub-diffraction scales. We demonstrate that this method efficiently provides measurement of the diffusion of EGFP at spatial scales tunable from the diffraction size down to ∼80 nm in the cytoplasm of living cells.The measurement of molecular diffusion at sub-diffraction scales has been achieved in 2D space using STED-FCS, but an implementation for 3D diffusion is lacking. Here the authors present an analytical approach to probe diffusion in 3D space using STED-FCS and measure the diffusion of EGFP at different spatial scales.

Non-diffusive ignition of a gaseous reactive mixture following time-resolved, spatially distributed energy deposition

NASA Astrophysics Data System (ADS)

Kassoy, D. R.

2014-01-01

Systematic asymptotic methods are applied to the compressible conservation and state equations for a reactive gas, including transport terms, to develop a rational thermomechanical formulation for the ignition of a chemical reaction following time-resolved, spatially distributed thermal energy addition from an external source into a finite volume of gas. A multi-parameter asymptotic analysis is developed for a wide range of energy deposition levels relative to the initial internal energy in the volume when the heating timescale is short compared to the characteristic acoustic timescale of the volume. Below a quantitatively defined threshold for energy addition, a nearly constant volume heating process occurs, with a small but finite internal gas expansion Mach number. Very little added thermal energy is converted to kinetic energy. The gas expelled from the boundary of the hot, high-pressure spot is the source of mechanical disturbances (acoustic and shock waves) that propagate away into the neighbouring unheated gas. When the energy addition reaches the threshold value, the heating process is fully compressible with a substantial internal gas expansion Mach number, the source of blast waves propagating into the unheated environmental gas. This case corresponds to an extremely large non-dimensional hot-spot temperature and pressure. If the former is sufficiently large, a high activation energy chemical reaction is initiated on the short heating timescale. This phenomenon is in contrast to that for more modest levels of energy addition, where a thermal explosion occurs only after the familiar extended ignition delay period for a classical high activation reaction. Transport effects, modulated by an asymptotically small Knudsen number, are shown to be negligible unless a local gradient in temperature, concentration or velocity is exceptionally large.

Considerations in high resolution skeletal muscle DTI using single-shot EPI with stimulated echo preparation and SENSE

PubMed Central

Karampinos, Dimitrios C.; Banerjee, Suchandrima; King, Kevin F.; Link, Thomas M.; Majumdar, Sharmila

2011-01-01

Previous studies have shown that skeletal muscle diffusion tensor imaging (DTI) can non-invasively probe changes in the muscle fiber architecture and microstructure in diseased and damaged muscles. However, DTI fiber reconstruction in small muscles and in muscle regions close to aponeuroses and tendons remains challenging because of partial volume effects. Increasing the spatial resolution of skeletal muscle single-shot diffusion weighted (DW)-EPI can be hindered by the inherently low SNR of muscle DW-EPI due to the short muscle T2 and the high sensitivity of single-shot EPI to off-resonance effects and T2* blurring. In the present work, eddy-current compensated diffusion-weighted stimulated echo preparation is combined with sensitivity encoding (SENSE) to maintain good SNR properties and reduce the sensitivity to distortions and T2* blurring in high resolution skeletal muscle single-shot DW-EPI. An analytical framework is developed for optimizing the reduction factor and diffusion weighting time to achieve maximum SNR. Arguments for the selection of the experimental parameters are then presented considering the compromise between SNR, B0-induced distortions, T2* blurring effects and tissue incoherent motion effects. Based on the selected parameters in a high resolution skeletal muscle single-shot DW-EPI protocol, imaging protocols at lower acquisition matrix sizes are defined with matched bandwidth in the phase-encoding direction and SNR. In vivo results show that high resolution skeletal muscle DTI with minimized sensitivity to geometric distortions and T2* blurring is feasible using the proposed methodology. In particular, a significant benefit is demonstrated from reducing partial volume effects on resolving multi-pennate muscles and muscles with small cross sections in calf muscle DTI. PMID:22081519

Biofilm Shows Spatially Stratified Metabolic Responses to Contaminant Exposure

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

Cao, Bin; Majors, Paul D.; Ahmed, B.

2012-11-01

The objective of this study was to elucidate the spatiotemporal responses of live S. oneidensis MR-1 biofilms to U(VI) (uranyl, UO22+) and Cr(VI) (chromate, CrO42-), important environmental contaminants at DOE contaminated sites. Toward this goal, we applied noninvasive nuclear magnetic resonance (NMR) imaging, diffusion, relaxation and spectroscopy techniques to monitor in situ spatiotemporal responses of S. oneidensis biofilms to U(VI) and Cr(VI) exposure in terms of changes in biofilm structures, diffusion properties, and cellular metabolism. Exposure to U(VI) or Cr(VI) did not appear to change the overall biomass distribution but caused changes in the physicochemical microenvironments inside the biofilm asmore » indicated by diffusion measurements. Changes in the diffusion properties of the biofilms in response to U(VI) and Cr(VI) exposure imply a novel function of the extracellular polymeric substances (EPS) affecting the biotransformation and transport of contaminants in the environment. In the presence of U(VI) or Cr(VI), the anaerobic metabolism of lactate was inhibited significantly, although the biofilms were still capable of reducing U(VI) and Cr(VI). Local concentrations of Cr(III)aq in the biofilm suggested relatively high Cr(VI) reduction activities at the top of the biofilm, near the medium-biofilm interface. The depth-resolved metabolic activities of the biofilm suggested higher diversion effects of gluconeogenesis and C1 metabolism pathways at the bottom of the biofilm and in the presence of U(VI). This study provides a noninvasive means to investigate spatiotemporal responses of biofilms, including surface-associated microbial communities in engineering, natural and medical settings, to various environmental perturbations including exposure to environmental contaminants and antimicrobials.« less

Estimation of white matter fiber parameters from compressed multiresolution diffusion MRI using sparse Bayesian learning.

PubMed

Pisharady, Pramod Kumar; Sotiropoulos, Stamatios N; Duarte-Carvajalino, Julio M; Sapiro, Guillermo; Lenglet, Christophe

2018-02-15

We present a sparse Bayesian unmixing algorithm BusineX: Bayesian Unmixing for Sparse Inference-based Estimation of Fiber Crossings (X), for estimation of white matter fiber parameters from compressed (under-sampled) diffusion MRI (dMRI) data. BusineX combines compressive sensing with linear unmixing and introduces sparsity to the previously proposed multiresolution data fusion algorithm RubiX, resulting in a method for improved reconstruction, especially from data with lower number of diffusion gradients. We formulate the estimation of fiber parameters as a sparse signal recovery problem and propose a linear unmixing framework with sparse Bayesian learning for the recovery of sparse signals, the fiber orientations and volume fractions. The data is modeled using a parametric spherical deconvolution approach and represented using a dictionary created with the exponential decay components along different possible diffusion directions. Volume fractions of fibers along these directions define the dictionary weights. The proposed sparse inference, which is based on the dictionary representation, considers the sparsity of fiber populations and exploits the spatial redundancy in data representation, thereby facilitating inference from under-sampled q-space. The algorithm improves parameter estimation from dMRI through data-dependent local learning of hyperparameters, at each voxel and for each possible fiber orientation, that moderate the strength of priors governing the parameter variances. Experimental results on synthetic and in-vivo data show improved accuracy with a lower uncertainty in fiber parameter estimates. BusineX resolves a higher number of second and third fiber crossings. For under-sampled data, the algorithm is also shown to produce more reliable estimates. Copyright © 2017 Elsevier Inc. All rights reserved.

Exploring time-resolved photoluminescence for nanowires using a three-dimensional computational transient model.

PubMed

Ren, Dingkun; Scofield, Adam C; Farrell, Alan C; Rong, Zixuan; Haddad, Michael A; Laghumavarapu, Ramesh B; Liang, Baolai; Huffaker, Diana L

2018-04-26

Time-resolved photoluminescence (TRPL) has been implemented experimentally to measure the carrier lifetime of semiconductors for decades. For the characterization of nanowires, the rich information embedded in TRPL curves has not been fully interpreted and meaningfully mapped to the respective material properties. This is because their three-dimensional (3-D) geometries result in more complicated mechanisms of carrier recombination than those in thin films and analytical solutions cannot be found for those nanostructures. In this work, we extend the intrinsic power of TRPL by developing a full 3-D transient model, which accounts for different material properties and drift-diffusion, to simulate TRPL curves for nanowires. To show the capability of the model, we perform TRPL measurements on a set of GaAs nanowire arrays grown on silicon substrates and then fit the measured data by tuning various material properties, including carrier mobility, Shockley-Read-Hall recombination lifetime, and surface recombination velocity at the GaAs-Si heterointerface. From the resultant TRPL simulations, we numerically identify the lifetime characteristics of those material properties. In addition, we computationally map the spatial and temporal electron distributions in nanowire segments and reveal the underlying carrier dynamics. We believe this study provides a theoretical foundation for interpretation of TRPL measurements to unveil the complex carrier recombination mechanisms in 3-D nanostructured materials.

A safe, low-cost, and portable instrumentation for bedside time-resolved picosecond near infrared spectroscopy

NASA Astrophysics Data System (ADS)

Amouroux, Marine; Uhring, Wilfried; Pebayle, Thierry; Poulet, Patrick; Marlier, Luc

2009-07-01

Continuous wave Near InfraRed Spectroscopy (NIRS) has been used successfully in clinical environments for several years to detect cerebral activation thanks to oxymetry (i.e. absorption of photons by oxy- and deoxy- hemoglobin) measurement. The goal of our group is to build a clinically-adapted time-resolved NIRS setup i.e. a setup that is compact and robust enough to allow bedside measurements and that matches safety requirements with human patients applications. Indeed our group has already shown that time resolution allows spatial resolution and improves sensitivity of cerebral activation detection. The setup is built with four laser diodes (excitation wavelengths: 685, 780, 830 and 870 nm) whose emitted light is injected into four optical fibers; detection of reflected photons is made through an avalanche photodiode and a high resolution timing module used to record Temporal Point Spread Functions (TPSF). Validation of the device was made using cylindrically-chaped phantoms with absorbing and/or scattering inclusions. Results show that recorded TPSF are typical both of scattering and absorbing materials thus demonstrating that our apparatus would detect variation of optical properties (absorption and scattering) deep within a diffusive media just like a cerebral activation represents a rise of absorption in the cortex underneath head surface.

Kramers turnover: From energy diffusion to spatial diffusion using metadynamics

PubMed Central

Tiwary, Pratyush; Berne, B. J.

2016-01-01

We consider the rate of transition for a particle between two metastable states coupled to a thermal environment for various magnitudes of the coupling strength using the recently proposed infrequent metadynamics approach [P. Tiwary and M. Parrinello, Phys. Rev. Lett. 111, 230602 (2013)]. We are interested in understanding how this approach for obtaining rate constants performs as the dynamics regime changes from energy diffusion to spatial diffusion. Reassuringly, we find that the approach works remarkably well for various coupling strengths in the strong coupling regime, and to some extent even in the weak coupling regime. PMID:27059558

What aspects of vision facilitate haptic processing?

PubMed

Millar, Susanna; Al-Attar, Zainab

2005-12-01

We investigate how vision affects haptic performance when task-relevant visual cues are reduced or excluded. The task was to remember the spatial location of six landmarks that were explored by touch in a tactile map. Here, we use specially designed spectacles that simulate residual peripheral vision, tunnel vision, diffuse light perception, and total blindness. Results for target locations differed, suggesting additional effects from adjacent touch cues. These are discussed. Touch with full vision was most accurate, as expected. Peripheral and tunnel vision, which reduce visuo-spatial cues, differed in error pattern. Both were less accurate than full vision, and significantly more accurate than touch with diffuse light perception, and touch alone. The important finding was that touch with diffuse light perception, which excludes spatial cues, did not differ from touch without vision in performance accuracy, nor in location error pattern. The contrast between spatially relevant versus spatially irrelevant vision provides new, rather decisive, evidence against the hypothesis that vision affects haptic processing even if it does not add task-relevant information. The results support optimal integration theories, and suggest that spatial and non-spatial aspects of vision need explicit distinction in bimodal studies and theories of spatial integration.

Spatial Resolution, Grayscale, and Error Diffusion Trade-offs: Impact on Display System Design

NASA Technical Reports Server (NTRS)

Gille, Jennifer L. (Principal Investigator)

1996-01-01

We examine technology trade-offs related to grayscale resolution, spatial resolution, and error diffusion for tessellated display systems. We present new empirical results from our psychophysical study of these trade-offs and compare them to the predictions of a model of human vision.

Probing GFP-actin diffusion in living cells using fluorescence correlation spectroscopy.

PubMed

Engelke, Hanna; Heinrich, Doris; Rädler, Joachim O

2010-12-22

The cytoskeleton of eukaryotic cells is continuously remodeled by polymerization and depolymerization of actin. Consequently, the relative content of polymerized filamentous actin (F-actin) and monomeric globular actin (G-actin) is subject to temporal and spatial fluctuations. Since fluorescence correlation spectroscopy (FCS) can measure the diffusion of fluorescently labeled actin it seems likely that FCS allows us to determine the dynamics and hence indirectly the structural properties of the cytoskeleton components with high spatial resolution. To this end we investigate the FCS signal of GFP-actin in living Dictyostelium discoideum cells and explore the inherent spatial and temporal signatures of the actin cytoskeleton. Using the free green fluorescent protein (GFP) as a reference, we find that actin diffusion inside cells is dominated by G-actin and slower than diffusion in diluted cell extract. The FCS signal in the dense cortical F-actin network near the cell membrane is probed using the cytoskeleton protein LIM and is found to be slower than cytosolic G-actin diffusion. Furthermore, we show that polymerization of the cytoskeleton induced by Jasplakinolide leads to a substantial decrease of G-actin diffusion. Pronounced fluctuations in the distribution of the FCS correlation curves can be induced by latrunculin, which is known to induce actin waves. Our work suggests that the FCS signal of GFP-actin in combination with scanning or spatial correlation techniques yield valuable information about the local dynamics and concomitant cytoskeletal properties.

Chemistry with spatial control using particles and streams†

PubMed Central

Kalinin, Yevgeniy V.; Murali, Adithya

2012-01-01

Spatial control of chemical reactions, with micro- and nanometer scale resolution, has important consequences for one pot synthesis, engineering complex reactions, developmental biology, cellular biochemistry and emergent behavior. We review synthetic methods to engineer this spatial control using chemical diffusion from spherical particles, shells and polyhedra. We discuss systems that enable both isotropic and anisotropic chemical release from isolated and arrayed particles to create inhomogeneous and spatially patterned chemical fields. In addition to such finite chemical sources, we also discuss spatial control enabled with laminar flow in 2D and 3D microfluidic networks. Throughout the paper, we highlight applications of spatially controlled chemistry in chemical kinetics, reaction-diffusion systems, chemotaxis and morphogenesis. PMID:23145348

Non-Destructive Study of Bulk Crystallinity and Elemental Composition of Natural Gold Single Crystal Samples by Energy-Resolved Neutron Imaging

PubMed Central

Tremsin, Anton S.; Rakovan, John; Shinohara, Takenao; Kockelmann, Winfried; Losko, Adrian S.; Vogel, Sven C.

2017-01-01

Energy-resolved neutron imaging enables non-destructive analyses of bulk structure and elemental composition, which can be resolved with high spatial resolution at bright pulsed spallation neutron sources due to recent developments and improvements of neutron counting detectors. This technique, suitable for many applications, is demonstrated here with a specific study of ~5–10 mm thick natural gold samples. Through the analysis of neutron absorption resonances the spatial distribution of palladium (with average elemental concentration of ~0.4 atom% and ~5 atom%) is mapped within the gold samples. At the same time, the analysis of coherent neutron scattering in the thermal and cold energy regimes reveals which samples have a single-crystalline bulk structure through the entire sample volume. A spatially resolved analysis is possible because neutron transmission spectra are measured simultaneously on each detector pixel in the epithermal, thermal and cold energy ranges. With a pixel size of 55 μm and a detector-area of 512 by 512 pixels, a total of 262,144 neutron transmission spectra are measured concurrently. The results of our experiments indicate that high resolution energy-resolved neutron imaging is a very attractive analytical technique in cases where other conventional non-destructive methods are ineffective due to sample opacity. PMID:28102285

Determination of carrier lifetime and diffusion length in Al-doped 4H-SiC epilayers by time-resolved optical techniques

NASA Astrophysics Data System (ADS)

Liaugaudas, Gediminas; Dargis, Donatas; Kwasnicki, Pawel; Arvinte, Roxana; Zielinski, Marcin; Jarašiūnas, Kęstutis

2015-01-01

A series of p-type 4H-SiC epilayers with aluminium concentration ranging from 2  ×  1016 to 8  ×  1019 cm-3 were investigated by time-resolved optical techniques in order to determine the effect of aluminium doping on high-injection carrier lifetime at room temperature and the diffusion coefficient at different injections (from ≈3  ×  1018 to ≈5  ×  1019 cm-3) and temperatures (from 78 to 730 K). We find that the defect limited carrier lifetime τSRH decreases from 20 ns in the low-doped samples down to ≈0.6 ns in the heavily doped epilayers. Accordingly, the ambipolar diffusion coefficient decreases from Da = 3.5 cm2 s-1 down to ≈0.6 cm2 s-1, corresponding to the hole mobility of µh = 70 cm2 Vs-1 and 12 cm2 Vs-1, respectively. In the highly doped epilayers, the injection-induced decrease of the diffusion coefficient, due to the transition from the minority carrier diffusion to the ambipolar diffusion, provided the electron diffusion coefficient of De ≈ 3 cm2 s-1. The Al-doping resulted in the gradual decrease of the ambipolar diffusion length, from LD = 2.7 µm down to LD = 0.25 µm in the epilayers with the lowest and highest aluminium concentrations.

High Performance Nuclear Magnetic Resonance Imaging Using Magnetic Resonance Force Microscopy

DTIC Science & Technology

2013-12-12

Micron- Size Ferromagnet . Physical Review Letters, 92(3) 037205 (2004) [22] A. Z. Genack and A. G. Redeld. Theory of nuclear spin diusion in a...perform spatially resolved scanned probe studies of spin dynamics in nanoscale ensembles of few electron spins of varying size . Our research culminated...perform spatially resolved scanned probe studies of spin dynamics in nanoscale ensembles of few electron spins of varying size . Our research culminated

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

PubMed Central

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

2017-01-01

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

Spatial diffusion of raccoon rabies in Pennsylvania, USA.

PubMed

Moore, D A

1999-05-14

Identification of the geographic pattern of diffusion of a wildlife disease could lead to information regarding its control. The objective of this study was to model raccoon-rabies diffusion in Pennsylvania to identify geographic constraints on the diffusion pattern for potential use in bait-vaccination strategies. A trend-surface analysis (TSA) was used as a spatial filter for month to first report by county location. A cubic polynomial model was fitted (R2 = 0.80). Velocity vectors were calculated from the partial derivatives of the model and mapped to demonstrate the instantaneous speed of diffusion at each location. A main corridor of diffusion through the ridge and valley section of the state was evident early in the outbreak. Once the disease reached the northern counties, the disease moved west toward Ohio. I believe that TSA was useful in identifying the pattern of raccoon-rabies diffusion across the stage from the inherent noise of disease-reporting data.

Mapping the spatial distribution of star formation in cluster galaxies at z ~0.5 with the Grism Lens-Amplified Survey from Space (GLASS)

NASA Astrophysics Data System (ADS)

Vulcani, Benedetta

2015-08-01

What physical processes regulate star formation in dense environments? Understanding why galaxy evolution is environment dependent is one of the key questions of current astrophysics. I will present the first characterization of the spatial distribution of star formation in cluster galaxies at z~0.5, in order to quantify the role of different physical processes that are believed to be responsible for shutting down star formation. The analysis makes use of data from the Grism Lens-Amplified Survey from Space (GLASS), a large HST cycle-21 program targeting 10 massive galaxy clusters with extensive HST imaging from CLASH and the Frontier Field Initiative. The program consists of 140 primary and 140 parallel orbits of near-infrared WCF3 and optical ACS slitless grism observations, which result in 3D spectroscopy of hundreds of galaxies. The grism data are used to produce spatially resolved maps of the star formation density, while the stellar mass density and optical surface brightness are obtained from multiband imaging. I will describe quantitative measures of the spatial location and extend of the star formation rate, showing that about half of the cluster members with significant Halpha detection have diffused star formation, larger than the optical counterpart. This suggests that star formation occurs out to larger radii than the rest frame continuum. For some systems, nuclear star forming regions are found. I will also present a comparison between the Halpha distribution observed in cluster and field galaxies. The characterization of the spatial distribution of Halpha provides a new window, yet poorly exploited, on the mechanisms that regulate star formation and morphological transformation in dense environments.

Spatial and Social Diffusion of Information and Influence: Models and Algorithms

ERIC Educational Resources Information Center

Doo, Myungcheol

2012-01-01

In this dissertation research, we argue that spatial alarms and activity-based social networks are two fundamentally new types of information and influence diffusion channels. Such new channels have the potential of enriching our professional experiences and our personal life quality in many unprecedented ways. First, we develop an activity driven…

Stochastic Analysis of Reaction–Diffusion Processes

PubMed Central

Hu, Jifeng; Kang, Hye-Won

2013-01-01

Reaction and diffusion processes are used to model chemical and biological processes over a wide range of spatial and temporal scales. Several routes to the diffusion process at various levels of description in time and space are discussed and the master equation for spatially discretized systems involving reaction and diffusion is developed. We discuss an estimator for the appropriate compartment size for simulating reaction–diffusion systems and introduce a measure of fluctuations in a discretized system. We then describe a new computational algorithm for implementing a modified Gillespie method for compartmental systems in which reactions are aggregated into equivalence classes and computational cells are searched via an optimized tree structure. Finally, we discuss several examples that illustrate the issues that have to be addressed in general systems. PMID:23719732

Atmospheric-pressure diffuse dielectric barrier discharges in Ar/O2 gas mixture using 200 kHz/13.56 MHz dual frequency excitation

NASA Astrophysics Data System (ADS)

Liu, Y.; Starostin, S. A.; Peeters, F. J. J.; van de Sanden, M. C. M.; de Vries, H. W.

2018-03-01

Atmospheric-pressure diffuse dielectric barrier discharges (DBDs) were obtained in Ar/O2 gas mixture using dual-frequency (DF) excitation at 200 kHz low frequency (LF) and 13.56 MHz radio frequency (RF). The excitation dynamics and the plasma generation mechanism were studied by means of electrical characterization and phase resolved optical emission spectroscopy (PROES). The DF excitation results in a time-varying electric field which is determined by the total LF and RF gas voltage and the spatial ion distribution which only responds to the LF component. By tuning the amplitude ratio of the superimposed LF and RF signals, the effect of each frequency component on the DF discharge mechanism was analysed. The LF excitation results in a transient plasma with the formation of an electrode sheath and therefore a pronounced excitation near the substrate. The RF oscillation allows the electron trapping in the gas gap and helps to improve the plasma uniformity by contributing to the pre-ionization and by controlling the discharge development. The possibility of temporally modifying the electric field and thus the plasma generation mechanism in the DF discharge exhibits potential applications in plasma-assisted surface processing and plasma-assisted gas phase chemical conversion.

PIV study of flow through porous structure using refractive index matching

NASA Astrophysics Data System (ADS)

Häfeli, Richard; Altheimer, Marco; Butscher, Denis; Rudolf von Rohr, Philipp

2014-05-01

An aqueous solution of sodium iodide and zinc iodide is proposed as a fluid that matches the refractive index of a solid manufactured by rapid prototyping. This enabled optical measurements in single-phase flow through porous structures. Experiments were also done with an organic index-matching fluid (anisole) in porous structures of different dimensions. To compare experiments with different viscosities and dimensions, we employed Reynolds similarity to deduce the scaling laws. One of the target quantities of our investigation was the dissipation rate of turbulent kinetic energy. Different models for the dissipation rate estimation were evaluated by comparing isotropy ratios. As in many other studies also, our experiments were not capable of resolving the velocity field down to the Kolmogorov length scale, and therefore, the dissipation rate has to be considered as underestimated. This is visible in experiments of different relative resolutions. However, being near the Kolmogorov scale allows estimating a reproducible, yet underestimated spatial distribution of dissipation rate inside the porous structure. Based on these results, the model was used to estimate the turbulent diffusivity. Comparing it to the dispersion coefficient obtained in the same porous structure, we conclude that even at the turbulent diffusivity makes up only a small part of mass transfer in axial direction. The main part is therefore attributed to Taylor dispersion.

Quantitative characterization of steady and time-varying, sooting, laminar diffusion flames using optical techniques

NASA Astrophysics Data System (ADS)

Connelly, Blair C.

In order to reduce the emission of pollutants such as soot and NO x from combustion systems, a detailed understanding of pollutant formation is required. In addition to environmental concerns, this is important for a fundamental understanding of flame behavior as significant quantities of soot lower local flame temperatures, increase overall flame length and affect the formation of such temperature-dependent species as NOx. This problem is investigated by carrying out coupled computational and experimental studies of steady and time-varying sooting, coflow diffusion flames. Optical diagnostic techniques are a powerful tool for characterizing combustion systems, as they provide a noninvasive method of probing the environment. Laser diagnostic techniques have added advantages, as systems can be probed with high spectral, temporal and spatial resolution, and with species selectivity. Experimental soot volume fractions were determined by using two-dimensional laser-induced incandescence (LII), calibrated with an on-line extinction measurement, and soot pyrometry. Measurements of soot particle size distributions are made using time-resolved LII (TR-LII). Laser-induced fluorescence measurements are made of NO and formaldehyde. These experimental measurements, and others, are compared with computational results in an effort to understand and model soot formation and to examine the coupled relationship of soot and NO x formation.

Can a one-layer optical skin model including melanin and inhomogeneously distributed blood explain spatially resolved diffuse reflectance spectra?

NASA Astrophysics Data System (ADS)

Karlsson, Hanna; Pettersson, Anders; Larsson, Marcus; Strömberg, Tomas

2011-02-01

Model based analysis of calibrated diffuse reflectance spectroscopy can be used for determining oxygenation and concentration of skin chromophores. This study aimed at assessing the effect of including melanin in addition to hemoglobin (Hb) as chromophores and compensating for inhomogeneously distributed blood (vessel packaging), in a single-layer skin model. Spectra from four humans were collected during different provocations using a twochannel fiber optic probe with source-detector separations 0.4 and 1.2 mm. Absolute calibrated spectra using data from either a single distance or both distances were analyzed using inverse Monte Carlo for light transport and Levenberg-Marquardt for non-linear fitting. The model fitting was excellent using a single distance. However, the estimated model failed to explain spectra from the other distance. The two-distance model did not fit the data well at either distance. Model fitting was significantly improved including melanin and vessel packaging. The most prominent effect when fitting data from the larger separation compared to the smaller separation was a different light scattering decay with wavelength, while the tissue fraction of Hb and saturation were similar. For modeling spectra at both distances, we propose using either a multi-layer skin model or a more advanced model for the scattering phase function.

Determination of spatially dependent diffusion parameters in bovine bone using Kalman filter.

PubMed

Shokry, Abdallah; Ståhle, Per; Svensson, Ingrid

2015-11-07

Although many studies have been made for homogenous constant diffusion, bone is an inhomogeneous material. It has been suggested that bone porosity decreases from the inner boundaries to the outer boundaries of the long bones. The diffusivity of substances in the bone matrix is believed to increase as the bone porosity increases. In this study, an experimental set up is used where bovine bone samples, saturated with potassium chloride (KCl), were put into distilled water and the conductivity of the water was followed. Chloride ions in the bone samples escaped out in the water through diffusion and the increase of the conductivity was measured. A one-dimensional, spatially dependent mathematical model describing the diffusion process is used. The diffusion parameters in the model are determined using a Kalman filter technique. The parameters for spatially dependent at endosteal and periosteal surfaces are found to be (12.8 ± 4.7) × 10(-11) and (5 ± 3.5) × 10(-11)m(2)/s respectively. The mathematical model function using the obtained diffusion parameters fits very well with the experimental data with mean square error varies from 0.06 × 10(-6) to 0.183 × 10(-6) (μS/m)(2). Copyright © 2015 Elsevier Ltd. All rights reserved.

Time-Optimized High-Resolution Readout-Segmented Diffusion Tensor Imaging

PubMed Central

Reishofer, Gernot; Koschutnig, Karl; Langkammer, Christian; Porter, David; Jehna, Margit; Enzinger, Christian; Keeling, Stephen; Ebner, Franz

2013-01-01

Readout-segmented echo planar imaging with 2D navigator-based reacquisition is an uprising technique enabling the sampling of high-resolution diffusion images with reduced susceptibility artifacts. However, low signal from the small voxels and long scan times hamper the clinical applicability. Therefore, we introduce a regularization algorithm based on total variation that is applied directly on the entire diffusion tensor. The spatially varying regularization parameter is determined automatically dependent on spatial variations in signal-to-noise ratio thus, avoiding over- or under-regularization. Information about the noise distribution in the diffusion tensor is extracted from the diffusion weighted images by means of complex independent component analysis. Moreover, the combination of those features enables processing of the diffusion data absolutely user independent. Tractography from in vivo data and from a software phantom demonstrate the advantage of the spatially varying regularization compared to un-regularized data with respect to parameters relevant for fiber-tracking such as Mean Fiber Length, Track Count, Volume and Voxel Count. Specifically, for in vivo data findings suggest that tractography results from the regularized diffusion tensor based on one measurement (16 min) generates results comparable to the un-regularized data with three averages (48 min). This significant reduction in scan time renders high resolution (1×1×2.5 mm3) diffusion tensor imaging of the entire brain applicable in a clinical context. PMID:24019951

Resolving runaway electron distributions in space, time, and energy

DOE PAGES

Paz-Soldan, Carlos; Cooper, C. M.; Aleynikov, P.; ...

2018-05-01

Areas of agreement and disagreement with present-day models of RE evolution are revealed by measuring MeV-level bremsstrahlung radiation from runaway electrons (REs) with a pinhole camera. Spatially-resolved measurements localize the RE beam, reveal energy-dependent RE transport, and can be used to perform full two-dimensional (energy and pitch-angle) inversions of the RE phase space distribution. Energy-resolved measurements find qualitative agreement with modeling on the role of collisional and synchrotron damping in modifying the RE distribution shape. Measurements are consistent with predictions of phase-space attractors that accumulate REs, with non-monotonic features observed in the distribution. Temporally-resolved measurements find qualitative agreement with modelingmore » on the impact of collisional and synchrotron damping in varying the RE growth and decay rate. Anomalous RE loss is observed and found to be largest at low energy. As a result, possible roles for kinetic instability or spatial transport to resolve these anomalies are discussed.« less

Resolving runaway electron distributions in space, time, and energy

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

Paz-Soldan, Carlos; Cooper, C. M.; Aleynikov, P.

Areas of agreement and disagreement with present-day models of RE evolution are revealed by measuring MeV-level bremsstrahlung radiation from runaway electrons (REs) with a pinhole camera. Spatially-resolved measurements localize the RE beam, reveal energy-dependent RE transport, and can be used to perform full two-dimensional (energy and pitch-angle) inversions of the RE phase space distribution. Energy-resolved measurements find qualitative agreement with modeling on the role of collisional and synchrotron damping in modifying the RE distribution shape. Measurements are consistent with predictions of phase-space attractors that accumulate REs, with non-monotonic features observed in the distribution. Temporally-resolved measurements find qualitative agreement with modelingmore » on the impact of collisional and synchrotron damping in varying the RE growth and decay rate. Anomalous RE loss is observed and found to be largest at low energy. As a result, possible roles for kinetic instability or spatial transport to resolve these anomalies are discussed.« less

Considerations in high-resolution skeletal muscle diffusion tensor imaging using single-shot echo planar imaging with stimulated-echo preparation and sensitivity encoding.

PubMed

Karampinos, Dimitrios C; Banerjee, Suchandrima; King, Kevin F; Link, Thomas M; Majumdar, Sharmila

2012-05-01

Previous studies have shown that skeletal muscle diffusion tensor imaging (DTI) can noninvasively probe changes in the muscle fiber architecture and microstructure in diseased and damaged muscles. However, DTI fiber reconstruction in small muscles and in muscle regions close to aponeuroses and tendons remains challenging because of partial volume effects. Increasing the spatial resolution of skeletal muscle single-shot diffusion-weighted echo planar imaging (DW-EPI) can be hindered by the inherently low signal-to-noise ratio (SNR) of muscle DW-EPI because of the short muscle T(2) and the high sensitivity of single-shot EPI to off-resonance effects and T(2)* blurring. In this article, eddy current-compensated diffusion-weighted stimulated-echo preparation is combined with sensitivity encoding (SENSE) to maintain good SNR properties and to reduce the sensitivity to distortions and T(2)* blurring in high-resolution skeletal muscle single-shot DW-EPI. An analytical framework is developed to optimize the reduction factor and diffusion weighting time to achieve maximum SNR. Arguments for the selection of the experimental parameters are then presented considering the compromise between SNR, B(0)-induced distortions, T(2)* blurring effects and tissue incoherent motion effects. On the basis of the selected parameters in a high-resolution skeletal muscle single-shot DW-EPI protocol, imaging protocols at lower acquisition matrix sizes are defined with matched bandwidth in the phase-encoding direction and SNR. In  vivo results show that high-resolution skeletal muscle DTI with minimized sensitivity to geometric distortions and T(2)* blurring is feasible using the proposed methodology. In particular, a significant benefit is demonstrated from a reduction in partial volume effects for resolving multi-pennate muscles and muscles with small cross-sections in calf muscle DTI. Copyright © 2011 John Wiley & Sons, Ltd.

Discontinuous Galerkin method for multicomponent chemically reacting flows and combustion

NASA Astrophysics Data System (ADS)

Lv, Yu; Ihme, Matthias

2014-08-01

This paper presents the development of a discontinuous Galerkin (DG) method for application to chemically reacting flows in subsonic and supersonic regimes under the consideration of variable thermo-viscous-diffusive transport properties, detailed and stiff reaction chemistry, and shock capturing. A hybrid-flux formulation is developed for treatment of the convective fluxes, combining a conservative Riemann-solver and an extended double-flux scheme. A computationally efficient splitting scheme is proposed, in which advection and diffusion operators are solved in the weak form, and the chemically stiff substep is advanced in the strong form using a time-implicit scheme. The discretization of the viscous-diffusive transport terms follows the second form of Bassi and Rebay, and the WENO-based limiter due to Zhong and Shu is extended to multicomponent systems. Boundary conditions are developed for subsonic and supersonic flow conditions, and the algorithm is coupled to thermochemical libraries to account for detailed reaction chemistry and complex transport. The resulting DG method is applied to a series of test cases of increasing physico-chemical complexity. Beginning with one- and two-dimensional multispecies advection and shock-fluid interaction problems, computational efficiency, convergence, and conservation properties are demonstrated. This study is followed by considering a series of detonation and supersonic combustion problems to investigate the convergence-rate and the shock-capturing capability in the presence of one- and multistep reaction chemistry. The DG algorithm is then applied to diffusion-controlled deflagration problems. By examining convergence properties for polynomial order and spatial resolution, and comparing these with second-order finite-volume solutions, it is shown that optimal convergence is achieved and that polynomial refinement provides advantages in better resolving the localized flame structure and complex flow-field features associated with multidimensional and hydrodynamic/thermo-diffusive instabilities in deflagration and detonation systems. Comparisons with standard third- and fifth-order WENO schemes are presented to illustrate the benefit of the DG scheme for application to detonation and multispecies flow/shock-interaction problems.

Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures

PubMed Central

Zavodszky, Maria I.

2017-01-01

Background Tumor heterogeneity can manifest itself by sub-populations of cells having distinct phenotypic profiles expressed as diverse molecular, morphological and spatial distributions. This inherent heterogeneity poses challenges in terms of diagnosis, prognosis and efficient treatment. Consequently, tools and techniques are being developed to properly characterize and quantify tumor heterogeneity. Multiplexed immunofluorescence (MxIF) is one such technology that offers molecular insight into both inter-individual and intratumor heterogeneity. It enables the quantification of both the concentration and spatial distribution of 60+ proteins across a tissue section. Upon bioimage processing, protein expression data can be generated for each cell from a tissue field of view. Results The Multi-Omics Heterogeneity Analysis (MOHA) tool was developed to compute tissue heterogeneity metrics from MxIF spatially resolved tissue imaging data. This technique computes the molecular state of each cell in a sample based on a pathway or gene set. Spatial states are then computed based on the spatial arrangements of the cells as distinguished by their respective molecular states. MOHA computes tissue heterogeneity metrics from the distributions of these molecular and spatially defined states. A colorectal cancer cohort of approximately 700 subjects with MxIF data is presented to demonstrate the MOHA methodology. Within this dataset, statistically significant correlations were found between the intratumor AKT pathway state diversity and cancer stage and histological tumor grade. Furthermore, intratumor spatial diversity metrics were found to correlate with cancer recurrence. Conclusions MOHA provides a simple and robust approach to characterize molecular and spatial heterogeneity of tissues. Research projects that generate spatially resolved tissue imaging data can take full advantage of this useful technique. The MOHA algorithm is implemented as a freely available R script (see supplementary information). PMID:29190747

Spatial-mode storage in a gradient-echo memory

NASA Astrophysics Data System (ADS)

Higginbottom, D. B.; Sparkes, B. M.; Rancic, M.; Pinel, O.; Hosseini, M.; Lam, P. K.; Buchler, B. C.

2012-08-01

Three-level atomic gradient echo memory (Λ-GEM) is a proposed candidate for efficient quantum storage and for linear optical quantum computation with time-bin multiplexing [Hosseini , Nature (London)NATUAS0028-083610.1038/nature08325 461, 241 (2009)]. In this paper we investigate the spatial multimode properties of a Λ-GEM system. Using a high-speed triggered CCD, we demonstrate the storage of complex spatial modes and images. We also present an in-principle demonstration of spatial multiplexing by showing selective recall of spatial elements of a stored spin wave. Using our measurements, we consider the effect of diffusion within the atomic vapor and investigate its role in spatial decoherence. Our measurements allow us to quantify the spatial distortion due to both diffusion and inhomogeneous control field scattering and compare these to theoretical models.

A CTRW-based model of time-resolved fluorescence lifetime imaging in a turbid medium

NASA Astrophysics Data System (ADS)

Chernomordik, Victor; Gandjbakhche, Amir H.; Hassan, Moinuddin; Pajevic, Sinisa; Weiss, George H.

2010-12-01

We develop an analytic model of time-resolved fluorescent imaging of photons migrating through a semi-infinite turbid medium bounded by an infinite plane in the presence of a single stationary point fluorophore embedded in the medium. In contrast to earlier models of fluorescent imaging in which photon motion is assumed to be some form of continuous diffusion process, the present analysis is based on a continuous-time random walk (CTRW) on a simple cubic lattice, the objective being to estimate the position and lifetime of the fluorophore. This can provide information related to local variations in pH and temperature with potential medical significance. Aspects of the theory were tested using time-resolved measurements of the fluorescence from small inclusions inside tissue-like phantoms. The experimental results were found to be in good agreement with theoretical predictions provided that the fluorophore was not located too close to the planar boundary, a common problem in many diffusive systems.

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.

Passive Standoff Super Resolution Imaging using Spatial-Spectral Multiplexing

DTIC Science & Technology

2017-08-14

94 5.0 Four -Dimensional Object-Space Data Reconstruction Using Spatial...103 5.3 Four -dimensional scene reconstruction using SSM...transitioning to systems based on spectrally resolved longitudinal spatial coherence interferometry. This document also includes research related to four

Spatially and time resolved kinetics of indirect magnetoexcitons

NASA Astrophysics Data System (ADS)

Hasling, Matthew; Dorow, Chelsey; Calman, Erica; Butov, Leonid; Wilkes, Joe; Campman, Kenneth; Gossard, Arthur

The small exciton mass and binding energy give the opportunity to realize the high magnetic field regime for excitons in magnetic fields of few Tesla achievable in lab Long lifetimes of indirect exciton give the opportunity to study kinetics of magnetoexciton transport by time-resolved optical imaging of exciton emission. We present spatially and time resolved measurements showing the effect of increased magnetic field on transport of magnetoexcitons. We observe that increased magnetic field leads to slowing down of magnetoexciton transport. Supported by NSF Grant No. 1407277. J.W. was supported by the EPSRC (Grant EP/L022990/1). C.J.D. was supported by the NSF Graduate Research Fellowship Program under Grant No. DGE-1144086.

Spatial variation in soil properties and diffuse losses between and within grassland fields with similar short-term management.

PubMed

Peukert, S; Griffith, B A; Murray, P J; Macleod, C J A; Brazier, R E

2016-07-01

One of the major challenges for agriculture is to understand the effects of agricultural practices on soil properties and diffuse pollution, to support practical farm-scale land management. Three conventionally managed grassland fields with similar short-term management, but different ploughing histories, were studied on a long-term research platform: the North Wyke Farm Platform. The aims were to (i) quantify the between-field and within-field spatial variation in soil properties by geostatistical analysis, (ii) understand the effects of soil condition (in terms of nitrogen, phosphorus and carbon contents) on the quality of discharge water and (iii) establish robust baseline data before the implementation of various grassland management scenarios. Although the fields sampled had experienced the same land use and similar management for at least 6 years, there were differences in their mean soil properties. They showed different patterns of soil spatial variation and different rates of diffuse nutrient losses to water. The oldest permanent pasture field had the largest soil macronutrient concentrations and the greatest diffuse nutrient losses. We show that management histories affect soil properties and diffuse losses. Potential gains in herbage yield or benefits in water quality might be achieved by characterizing every field or by area-specific management within fields (a form of precision agriculture for grasslands). Permanent pasture per se cannot be considered a mitigation measure for diffuse pollution. The between- and within-field soil spatial variation emphasizes the importance of baseline characterization and will enable the reliable identification of any effects of future management change on the Farm Platform. Quantification of soil and water quality in grassland fields with contrasting management histories.Considerable spatial variation in soil properties and diffuse losses between and within fields.Contrasting management histories within and between fields strongly affected soil and water quality.Careful pasture management needed: the oldest pasture transferred the most nutrients from soil to water.

Comparison of multi-fiber reproducibility of PAS-MRI and Q-ball with empirical multiple b-value HARDI

NASA Astrophysics Data System (ADS)

Nath, Vishwesh; Schilling, Kurt G.; Blaber, Justin A.; Ding, Zhaohua; Anderson, Adam W.; Landman, Bennett A.

2017-02-01

Crossing fibers are prevalent in human brains and a subject of intense interest for neuroscience. Diffusion tensor imaging (DTI) can resolve tissue orientation but is blind to crossing fibers. Many advanced diffusion-weighted magnetic resolution imaging (MRI) approaches have been presented to extract crossing-fibers from high angular resolution diffusion imaging (HARDI), but the relative sensitivity and specificity of approaches remains unclear. Here, we examine two leading approaches (PAS and q-ball) in the context of a large-scale, single subject reproducibility study. A single healthy individual was scanned 11 times with 96 diffusion weighted directions and 10 reference volumes for each of five b-values (1000, 1500, 2000, 2500, 3000 s/mm2) for a total of 5830 volumes (over the course of three sessions). We examined the reproducibility of the number of fibers per voxel, volume fraction, and crossing-fiber angles. For each method, we determined the minimum resolvable angle for each acquisition. Reproducibility of fiber counts per voxel was generally high ( 80% consensus for PAS and 70% for q-ball), but there was substantial bias between individual repetitions and model estimated with all data ( 10% lower consensus for PAS and 15% lower for q-ball). Both PAS and q-ball predominantly discovered fibers crossing at near 90 degrees, but reproducibility was higher for PAS across most measures. Within voxels with low anisotropy, q-ball finds more intra-voxel structure; meanwhile, PAS resolves multiple fibers at greater than 75 degrees for more voxels. These results can inform researchers when deciding between HARDI approaches or interpreting findings across studies.

Spatially resolved rest-UV spectroscopy of a prototypical quasar driven superwind at low-z

NASA Astrophysics Data System (ADS)

Johnson, Sean

2017-08-01

Powerful galaxy-wide winds launched by quasars are thought to be a common evolutionary phase of massive galaxies, but observations of this phenomena are scarce. We have conducted a multi-wavelength observational campaign for J1356+1026, a poster-child obscured quasar driving a superwind at z=0.123. J1356+1026 is driving a nuclear molecular outflow and an extended ionized outflow observed as an [OIII] emitting bubble at 10 kpc that is spatially coincident with soft X-ray emission. Quasar-driven winds carry material at a wide range of densities and temperatures making it difficult to measure their energetics and the dominant phases are unknown. Here we propose spatially resolved rest-UV spectroscopy by acquiring circum-nuclear absorption spectra of J1356+1026 and emission spectra of its off-nucleus bubble using COS+G140L. The circum-nuclear spectrum will provide measurements of the outflow velocity through blueshifted absorption while the off-nuclear spectrum of the bubble will measure the ionization state and mechanisms of the outflow through powerful UV diagnostic lines. Together, these spectra will enable a more complete mass, energy and momentum accounting of a spatially resolved quasar driven superwind for the first time. Furthermore, detection of shocked gas through OVI emission will enable us to infer properties of the enigmatic volume-filling, low density component of the wind. To our knowledge, this will be the first spatially resolved rest UV spectroscopy of a quasar wind and the proposed observations will serve as a pilot to guide future HST proposals.

Effects of calcium leaching on diffusion properties of hardened and altered cement pastes

NASA Astrophysics Data System (ADS)

Kurumisawa, Kiyofumi; Haga, Kazuko; Hayashi, Daisuke; Owada, Hitoshi

2017-06-01

It is very important to predict alterations in the concrete used for fabricating disposal containers for radioactive waste. Therefore, it is necessary to understand the alteration of cementitious materials caused by calcium leaching when they are in contact with ground water in the long term. To evaluate the long-term transport characteristics of cementitious materials, the microstructural behavior of these materials should be considered. However, many predictive models of transport characteristics focus on the pore structure, while only few such models consider both, the spatial distribution of calcium silicate hydrate (C-S-H), portlandite, and the pore spaces. This study focused on the spatial distribution of these cement phases. The auto-correlation function of each phase of cementitious materials was calculated from two-dimensional backscattered electron imaging, and the three-dimensional spatial image of the cementitious material was produced using these auto-correlation functions. An attempt was made to estimate the diffusion coefficient of chloride from the three-dimensional spatial image. The estimated diffusion coefficient of the altered sample from the three-dimensional spatial image was found to be comparable to the measured value. This demonstrated that it is possible to predict the diffusion coefficient of the altered cement paste by using the proposed model.

Optimizing information flow in small genetic networks. IV. Spatial coupling

NASA Astrophysics Data System (ADS)

Sokolowski, Thomas R.; Tkačik, Gašper

2015-06-01

We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the input) by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively different regulatory strategy emerges where individual cells respond to the input in a nearly steplike fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.

Spatio-temporal diffusion pattern and hotspot detection of dengue in Chachoengsao province, Thailand.

PubMed

Jeefoo, Phaisarn; Tripathi, Nitin Kumar; Souris, Marc

2011-01-01

In recent years, dengue has become a major international public health concern. In Thailand it is also an important concern as several dengue outbreaks were reported in last decade. This paper presents a GIS approach to analyze the spatial and temporal dynamics of dengue epidemics. The major objective of this study was to examine spatial diffusion patterns and hotspot identification for reported dengue cases. Geospatial diffusion pattern of the 2007 dengue outbreak was investigated. Map of daily cases was generated for the 153 days of the outbreak. Epidemiological data from Chachoengsao province, Thailand (reported dengue cases for the years 1999-2007) was used for this study. To analyze the dynamic space-time pattern of dengue outbreaks, all cases were positioned in space at a village level. After a general statistical analysis (by gender and age group), data was subsequently analyzed for temporal patterns and correlation with climatic data (especially rainfall), spatial patterns and cluster analysis, and spatio-temporal patterns of hotspots during epidemics. The results revealed spatial diffusion patterns during the years 1999-2007 representing spatially clustered patterns with significant differences by village. Villages on the urban fringe reported higher incidences. The space and time of the cases showed outbreak movement and spread patterns that could be related to entomologic and epidemiologic factors. The hotspots showed the spatial trend of dengue diffusion. This study presents useful information related to the dengue outbreak patterns in space and time and may help public health departments to plan strategies to control the spread of disease. The methodology is general for space-time analysis and can be applied for other infectious diseases as well.

Effect of upstream ULF waves on the energetic ion diffusion at the earth's foreshock: Theory, Simulation, and Observations

NASA Astrophysics Data System (ADS)

Otsuka, F.; Matsukiyo, S.; Kis, A.; Hada, T.

2017-12-01

Spatial diffusion of energetic particles is an important problem not only from a fundamental physics point of view but also for its application to particle acceleration processes at astrophysical shocks. Quasi-linear theory can provide the spatial diffusion coefficient as a function of the wave turbulence spectrum. By assuming a simple power-law spectrum for the turbulence, the theory has been successfully applied to diffusion and acceleration of cosmic rays in the interplanetary and interstellar medium. Near the earth's foreshock, however, the wave spectrum often has an intense peak, presumably corresponding to the upstream ULF waves generated by the field-aligned beam (FAB). In this presentation, we numerically and theoretically discuss how the intense ULF peak in the wave spectrum modifies the spatial parallel diffusion of energetic ions. The turbulence is given as a superposition of non-propagating transverse MHD waves in the solar wind rest frame, and its spectrum is composed of a piecewise power-law spectrum with different power-law indices. The diffusion coefficients are then estimated by using the quasi-linear theory and test particle simulations. We find that the presence of the ULF peak produces a concave shape of the diffusion coefficient when it is plotted versus the ion energy. The results above are used to discuss the Cluster observations of the diffuse ions at the Earth's foreshock. Using the density gradients of the energetic ions detected by the Cluster spacecraft, we determine the e-folding distances, equivalently, the spatial diffusion coefficients, of ions with their energies from 10 to 32 keV. The observed e-folding distances are significantly smaller than those estimated in the past statistical studies. This suggests that the particle acceleration at the foreshock can be more efficient than considered before. Our test particle simulation explains well the small estimate of the e-folding distances, by using the observed wave turbulence spectrum near the shock.

Time-resolved measurements in diffuse reflectance: effects of the instrument response function of different detection systems on the depth sensitivity

NASA Astrophysics Data System (ADS)

Puszka, Agathe; Planat-Chrétien, Anne; Berger, Michel; Hervé, Lionel; Dinten, Jean-Marc

2014-02-01

We demonstrate the loss of depth sensitivity induced by the instrument response function on reflectance time-resolved diffuse optical tomography through the comparison of 3 detection systems: on one hand a photomultiplier tube (PMT) and a hybrid PMT coupled with a time-correlated single-photon counting card and on the other hand a high rate intensified camera. We experimentally evaluate the depth sensitivity achieved for each detection module with an absorbing inclusion embedded in a turbid medium. The different interfiber distances of 5, 10 and 15 mm are considered. Finally, we determine a maximal depth reached for each detection system by using 3D tomographic reconstructions based on the Mellin-Laplace transform.

Duration of bubble rearrangements in a coarsening foam probed by time-resolved diffusing-wave spectroscopy: Impact of interfacial rigidity

NASA Astrophysics Data System (ADS)

Le Merrer, Marie; Cohen-Addad, Sylvie; Höhler, Reinhard

2013-08-01

In aqueous foams, the diffusive gas transfer among neighboring bubbles drives a coarsening process which is accompanied by intermittent rearrangements of the structure. Using time-resolved diffusing-wave spectroscopy, we probe the dynamics of these events as a function of the rigidity of the gas-liquid interfaces, liquid viscosity, bubble size, and confinement pressure. We present in detail two independent techniques for analyzing the light scattering data, from which we extract the rearrangement duration. Our results show that interfacial rheology has a major impact on this duration. In the case of low interfacial rigidity, the rearrangements strongly slow down as the pressure is decreased close to the value zero where the bubble packing unjams. In contrast, if the interfaces are rigid, rearrangement durations are independent of the confinement pressure in the same investigated range. Using scaling arguments, we discuss dissipation mechanisms that may explain the observed dependency of the rearrangement dynamics on foam structure, pressure, and physicochemical solution properties.

Spatially Resolving Ocean Color and Sediment Dispersion in River Plumes, Coastal Systems, and Continental Shelf Waters

NASA Technical Reports Server (NTRS)

Aurin, Dirk Alexander; Mannino, Antonio; Franz, Bryan

2013-01-01

Satellite remote sensing of ocean color in dynamic coastal, inland, and nearshorewaters is impeded by high variability in optical constituents, demands specialized atmospheric correction, and is limited by instrument sensitivity. To accurately detect dispersion of bio-optical properties, remote sensors require ample signal-to-noise ratio (SNR) to sense small variations in ocean color without saturating over bright pixels, an atmospheric correction that can accommodate significantwater-leaving radiance in the near infrared (NIR), and spatial and temporal resolution that coincides with the scales of variability in the environment. Several current and historic space-borne sensors have met these requirements with success in the open ocean, but are not optimized for highly red-reflective and heterogeneous waters such as those found near river outflows or in the presence of sediment resuspension. Here we apply analytical approaches for determining optimal spatial resolution, dominant spatial scales of variability ("patches"), and proportions of patch variability that can be resolved from four river plumes around the world between 2008 and 2011. An offshore region in the Sargasso Sea is analyzed for comparison. A method is presented for processing Moderate Resolution Imaging Spectroradiometer (MODIS) Aqua and Terra imagery including cloud detection, stray lightmasking, faulty detector avoidance, and dynamic aerosol correction using short-wave- and near-infrared wavebands in extremely turbid regions which pose distinct optical and technical challenges. Results showthat a pixel size of approx. 520 mor smaller is generally required to resolve spatial heterogeneity in ocean color and total suspended materials in river plumes. Optimal pixel size increases with distance from shore to approx. 630 m in nearshore regions, approx 750 m on the continental shelf, and approx. 1350 m in the open ocean. Greater than 90% of the optical variability within plume regions is resolvable with 500 m resolution, and small, but significant, differences were found between peak and nadir river flow periods in terms of optimal resolution and resolvable proportion of variability.

REMOVING BIASES IN RESOLVED STELLAR MASS MAPS OF GALAXY DISKS THROUGH SUCCESSIVE BAYESIAN MARGINALIZATION

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

Martínez-García, Eric E.; González-Lópezlira, Rosa A.; Bruzual A, Gustavo

2017-01-20

Stellar masses of galaxies are frequently obtained by fitting stellar population synthesis models to galaxy photometry or spectra. The state of the art method resolves spatial structures within a galaxy to assess the total stellar mass content. In comparison to unresolved studies, resolved methods yield, on average, higher fractions of stellar mass for galaxies. In this work we improve the current method in order to mitigate a bias related to the resolved spatial distribution derived for the mass. The bias consists in an apparent filamentary mass distribution and a spatial coincidence between mass structures and dust lanes near spiral arms.more » The improved method is based on iterative Bayesian marginalization, through a new algorithm we have named Bayesian Successive Priors (BSP). We have applied BSP to M51 and to a pilot sample of 90 spiral galaxies from the Ohio State University Bright Spiral Galaxy Survey. By quantitatively comparing both methods, we find that the average fraction of stellar mass missed by unresolved studies is only half what previously thought. In contrast with the previous method, the output BSP mass maps bear a better resemblance to near-infrared images.« less

Time-resolved Sensing of Meso-scale Shock Compression with Multilayer Photonic Crystal Structures

NASA Astrophysics Data System (ADS)

Scripka, David; Lee, Gyuhyon; Summers, Christopher J.; Thadhani, Naresh

2017-06-01

Multilayer Photonic Crystal structures can provide spatially and temporally resolved data needed to validate theoretical and computational models relevant for understanding shock compression in heterogeneous materials. Two classes of 1-D photonic crystal multilayer structures were studied: optical microcavities (OMC) and distributed Bragg reflectors (DBR). These 0.5 to 5 micron thick structures were composed of SiO2, Al2O3, Ag, and PMMA layers fabricated primarily via e-beam evaporation. The multilayers have unique spectral signatures inherently linked to their time-resolved physical states. By observing shock-induced changes in these signatures, an optically-based pressure sensor was developed. Results to date indicate that both OMCs and DBRs exhibit nanosecond-resolved spectral shifts of several to 10s of nanometers under laser-driven shock compression loads of 0-10 GPa, with the magnitude of the shift strongly correlating to the shock load magnitude. Additionally, spatially and temporally resolved spectral shifts under heterogeneous laser-driven shock compression created by partial beam blocking have been successfully demonstrated. These results illustrate the potential for multilayer structures to serve as meso-scale sensors, capturing temporal and spatial pressure profile evolutions in shock-compressed heterogeneous materials, and revealing meso-scale pressure distributions across a shocked surface. Supported by DTRA Grant HDTRA1-12-1-005 and DoD, AFOSR, National Defense Science and Eng. Graduate Fellowship, 32 CFR 168a.

Time-Resolved Diffuse Optical Spectroscopy and Imaging Using Solid-State Detectors: Characteristics, Present Status, and Research Challenges

PubMed Central

Alayed, Mrwan

2017-01-01

Diffuse optical spectroscopy (DOS) and diffuse optical imaging (DOI) are emerging non-invasive imaging modalities that have wide spread potential applications in many fields, particularly for structural and functional imaging in medicine. In this article, we review time-resolved diffuse optical imaging (TR-DOI) systems using solid-state detectors with a special focus on Single-Photon Avalanche Diodes (SPADs) and Silicon Photomultipliers (SiPMs). These TR-DOI systems can be categorized into two types based on the operation mode of the detector (free-running or time-gated). For the TR-DOI prototypes, the physical concepts, main components, figures-of-merit of detectors, and evaluation parameters are described. The performance of TR-DOI prototypes is evaluated according to the parameters used in common protocols to test DOI systems particularly basic instrumental performance (BIP). In addition, the potential features of SPADs and SiPMs to improve TR-DOI systems and expand their applications in the foreseeable future are discussed. Lastly, research challenges and future developments for TR-DOI are discussed for each component in the prototype separately and also for the entire system. PMID:28906462

Recent Advances in 3D Time-Resolved Contrast-Enhanced MR Angiography

PubMed Central

Riederer, Stephen J.; Haider, Clifton R.; Borisch, Eric A.; Weavers, Paul T.; Young, Phillip M.

2015-01-01

Contrast-enhanced MR angiography (CE-MRA) was first introduced for clinical studies approximately 20 years ago. Early work provided 3 to 4 mm spatial resolution with acquisition times in the 30 sec range. Since that time there has been continuing effort to provide improved spatial resolution with reduced acquisition time, allowing high resolution three-dimensional (3D) time-resolved studies. The purpose of this work is to describe how this has been accomplished. Specific technical enablers have been: improved gradients allowing reduced repetition times, improved k-space sampling and reconstruction methods, parallel acquisition particularly in two directions, and improved and higher count receiver coil arrays. These have collectively made high resolution time-resolved studies readily available for many anatomic regions. Depending on the application, approximate 1 mm isotropic resolution is now possible with frame times of several seconds. Clinical applications of time-resolved CE-MRA are briefly reviewed. PMID:26032598

A Modeling Framework for Inference of Surface Emissions Using Mobile Observations

NASA Astrophysics Data System (ADS)

Fasoli, B.; Mitchell, L.; Crosman, E.; Mendoza, D. L.; Lin, J. C.

2016-12-01

Our ability to quantify surface emissions depends on the precision of observations and the spatial density of measurement networks. Mobile measurement techniques offer a cost effective strategy for quantifying atmospheric conditions over space without requiring a dense network of in-situ sites. However, interpretation of these data and inversion of dispersed measurements to estimate surface emissions can be difficult. We introduce a framework using the Stochastic Time-Inverted Lagrangian Transport (STILT) model that assimilates both spatially resolved observations and an emissions inventory to better estimate surface fluxes. Salt Lake City is a unique laboratory for the study of urban carbon emissions. It is the only U.S. city that utilizes light-rail trains to continuously measure high frequency carbon dioxide (CO2) and methane (CH4); it is home to one of the longest and most spatially resolved high precision CO2 measurement networks (air.utah.edu); and it is one of four cities in the world for which the Hestia anthropogenic emissions inventory has been produced which characterizes CO2 emissions at the scale of individual buildings and roadways. Using these data and modeling resources, we evaluate spatially resolved CO2 measurements and transported CO2 emissions on hourly timescales at a dense spatial resolution across Salt Lake City.

A spatially resolving x-ray crystal spectrometer for measurement of ion-temperature and rotation-velocity profiles on the Alcator C-Mod tokamak.

PubMed

Hill, K W; Bitter, M L; Scott, S D; Ince-Cushman, A; Reinke, M; Rice, J E; Beiersdorfer, P; Gu, M-F; Lee, S G; Broennimann, Ch; Eikenberry, E F

2008-10-01

A new spatially resolving x-ray crystal spectrometer capable of measuring continuous spatial profiles of high resolution spectra (lambda/d lambda>6000) of He-like and H-like Ar K alpha lines with good spatial (approximately 1 cm) and temporal (approximately 10 ms) resolutions has been installed on the Alcator C-Mod tokamak. Two spherically bent crystals image the spectra onto four two-dimensional Pilatus II pixel detectors. Tomographic inversion enables inference of local line emissivity, ion temperature (T(i)), and toroidal plasma rotation velocity (upsilon(phi)) from the line Doppler widths and shifts. The data analysis techniques, T(i) and upsilon(phi) profiles, analysis of fusion-neutron background, and predictions of performance on other tokamaks, including ITER, will be presented.

Computing eddy-driven effective diffusivity using Lagrangian particles

DOE PAGES

Wolfram, Phillip J.; Ringler, Todd D.

2017-08-14

A novel method to derive effective diffusivity from Lagrangian particle trajectory data sets is developed and then analyzed relative to particle-derived meridional diffusivity for eddy-driven mixing in an idealized circumpolar current. Quantitative standard dispersion- and transport-based mixing diagnostics are defined, compared and contrasted to motivate the computation and use of effective diffusivity derived from Lagrangian particles. We compute the effective diffusivity by first performing scalar transport on Lagrangian control areas using stored trajectories computed from online Lagrangian In-situ Global High-performance particle Tracking (LIGHT) using the Model for Prediction Across Scales Ocean (MPAS-O). Furthermore, the Lagrangian scalar transport scheme is comparedmore » against an Eulerian scalar transport scheme. Spatially-variable effective diffusivities are computed from resulting time-varying cumulative concentrations that vary as a function of cumulative area. The transport-based Eulerian and Lagrangian effective diffusivity diagnostics are found to be qualitatively consistent with the dispersion-based diffusivity. All diffusivity estimates show a region of increased subsurface diffusivity within the core of an idealized circumpolar current and results are within a factor of two of each other. The Eulerian and Lagrangian effective diffusivities are most similar; smaller and more spatially diffused values are obtained with the dispersion-based diffusivity computed with particle clusters.« less

Computing eddy-driven effective diffusivity using Lagrangian particles

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

Wolfram, Phillip J.; Ringler, Todd D.

A novel method to derive effective diffusivity from Lagrangian particle trajectory data sets is developed and then analyzed relative to particle-derived meridional diffusivity for eddy-driven mixing in an idealized circumpolar current. Quantitative standard dispersion- and transport-based mixing diagnostics are defined, compared and contrasted to motivate the computation and use of effective diffusivity derived from Lagrangian particles. We compute the effective diffusivity by first performing scalar transport on Lagrangian control areas using stored trajectories computed from online Lagrangian In-situ Global High-performance particle Tracking (LIGHT) using the Model for Prediction Across Scales Ocean (MPAS-O). Furthermore, the Lagrangian scalar transport scheme is comparedmore » against an Eulerian scalar transport scheme. Spatially-variable effective diffusivities are computed from resulting time-varying cumulative concentrations that vary as a function of cumulative area. The transport-based Eulerian and Lagrangian effective diffusivity diagnostics are found to be qualitatively consistent with the dispersion-based diffusivity. All diffusivity estimates show a region of increased subsurface diffusivity within the core of an idealized circumpolar current and results are within a factor of two of each other. The Eulerian and Lagrangian effective diffusivities are most similar; smaller and more spatially diffused values are obtained with the dispersion-based diffusivity computed with particle clusters.« less

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

David, M.-L.; Pailloux, F.; Mauchamp, V.

The understanding of the mechanisms of helium bubble formation and evolution in materials requires the quantitative determination of several key quantities such as the helium density in the bubbles. Helium nanobubbles of about 16 nm in diameter were created in silicon by helium implantation at high fluence and subsequent annealing. Individual nanobubbles were analyzed by spatially resolved Electron Energy-loss Spectroscopy (EELS). We report on the in situ probing of helium desorption from the nanobubbles under electron irradiation. This opens new perspectives for a more accurate determination of the helium density through spatially resolved EELS.

The Orbiting Carbon Observatory Mission: Watching the Earth Breathe Mapping CO2 from Space

NASA Technical Reports Server (NTRS)

Boain, Ron

2007-01-01

Approach: Collect spatially resolved, high resolution spectroscopic observations of CO2 and O2 absorption in reflected sunlight. Use these data to resolve spatial and temporal variations in the column averaged CO2 dry air mole fraction, X(sub CO2) over the sunlit hemisphere. Employ independent calibration and validation approaches to produce X(sub CO2) estimates with random errors and biases no larger than 1-2 ppm (0.3-0.5%) on regional scales at monthly intervals.

Control of experimental uncertainties in filtered Rayleigh scattering measurements

NASA Technical Reports Server (NTRS)

Forkey, Joseph N.; Finkelstein, N. D.; Lempert, Walter R.; Miles, Richard B.

1995-01-01

Filtered Rayleigh Scattering is a technique which allows for measurement of velocity, temperature, and pressure in unseeded flows, spatially resolved in 2-dimensions. We present an overview of the major components of a Filtered Rayleigh Scattering system. In particular, we develop and discuss a detailed theoretical model along with associated model parameters and related uncertainties. Based on this model, we then present experimental results for ambient room air and for a Mach 2 free jet, including spatially resolved measurements of velocity, temperature, and pressure.

Assessment of craniospinal arteriovenous malformations at 3T with highly temporally and highly spatially resolved contrast-enhanced MR angiography.

PubMed

Saleh, R S; Lohan, D G; Villablanca, J P; Duckwiler, G; Kee, S T; Finn, J P

2008-05-01

Patients with arteriovenous malformation (AVM) are known to have an elevated risk of complications with conventional catheter angiography (CCA) but nonetheless require monitoring of hemodynamics. Thus, we aimed to evaluate both anatomy and hemodynamics in patients with AVM noninvasively by using contrast-enhanced MR angiography (CE-MRA) at 3T and to compare the results with CCA. Institutional review board approval and informed consent were obtained for this Health Insurance Portability and Accountability Act-compliant study. Twenty control subjects without vascular malformation (6 men, 18-70 years of age) and 10 patients with AVMs (6 men, 20-74 years of age) underwent supra-aortic time-resolved and high-spatial-resolution CE-MRA at 3T. Large-field-of-view coronal acquisitions extending from the root of the aorta to the cranial vertex were obtained for both MRA techniques. Image quality was assessed by 2 specialized radiologists by using a 4-point scale. AVM characteristics and nidus size were evaluated by using both CE-MRA and CCA in all patients. In patients, 96.6% (319/330) of arterial segments on high-spatial-resolution MRA and 87.7% (272/310) of arterial segments on time-resolved MRA were graded excellent/good. MRA showed 100% specificity for detecting feeding arteries and venous drainage (n = 8) and complete obliteration of the AVM in 2 cases (concordance with CCA). Nidus diameters measured by both MRA and CCA resulted in a very strong correlation (r = 0.99) with a mild overestimation by MRA (0.10 cm by using the Bland-Altman plot). By combining highly temporally resolved and highly spatially resolved MRA at 3T as complementary studies, one can assess vascular anatomy and hemodynamics noninvasively in patients with AVM.

ISM DUST GRAINS AND N-BAND SPECTRAL VARIABILITY IN THE SPATIALLY RESOLVED SUBARCSECOND BINARY UY Aur

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

Skemer, Andrew J.; Close, Laird M.; Hinz, Philip M.

2010-03-10

The 10 {mu}m silicate feature is an essential diagnostic of dust-grain growth and planet formation in young circumstellar disks. The Spitzer Space Telescope has revolutionized the study of this feature, but due to its small (85 cm) aperture, it cannot spatially resolve small/medium-separation binaries ({approx}<3''; {approx}< 420 AU) at the distances of the nearest star-forming regions ({approx}140 pc). Large, 6-10 m ground-based telescopes with mid-infrared instruments can resolve these systems. In this paper, we spatially resolve the 0.''88 binary, UY Aur, with MMTAO/BLINC-MIRAC4 mid-infrared spectroscopy. We then compare our spectra to Spitzer/IRS (unresolved) spectroscopy, and resolved images from IRTF/MIRAC2, Keck/OSCIR,more » and Gemini/Michelle, which were taken over the past decade. We find that UY Aur A has extremely pristine, interstellar medium (ISM)-like grains and that UY Aur B has an unusually shaped silicate feature, which is probably the result of blended emission and absorption from foreground extinction in its disk. We also find evidence for variability in both UY Aur A and UY Aur B by comparing synthetic photometry from our spectra with resolved imaging from previous epochs. The photometric variability of UY Aur A could be an indication that the silicate emission itself is variable, as was recently found in EX Lupi. Otherwise, the thermal continuum is variable, and either the ISM-like dust has never evolved, or it is being replenished, perhaps by UY Aur's circumbinary disk.« less

A hybrid algorithm for coupling partial differential equation and compartment-based dynamics.

PubMed

Harrison, Jonathan U; Yates, Christian A

2016-09-01

Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing particle numbers. An alternative description of many of these systems can be derived in the diffusive limit as a deterministic, continuum system of partial differential equations (PDEs). Although the numerical solution of such PDEs is, in general, much more efficient than the full stochastic simulation, the deterministic continuum description is generally not valid when copy numbers are low and stochastic effects dominate. Therefore, to take advantage of the benefits of both of these types of models, each of which may be appropriate in different parts of a spatial domain, we have developed an algorithm that can be used to couple these two types of model together. This hybrid coupling algorithm uses an overlap region between the two modelling regimes. By coupling fluxes at one end of the interface and using a concentration-matching condition at the other end, we ensure that mass is appropriately transferred between PDE- and compartment-based regimes. Our methodology gives notable reductions in simulation time in comparison with using a fully stochastic model, while maintaining the important stochastic features of the system and providing detail in appropriate areas of the domain. We test our hybrid methodology robustly by applying it to several biologically motivated problems including diffusion and morphogen gradient formation. Our analysis shows that the resulting error is small, unbiased and does not grow over time. © 2016 The Authors.

A hybrid algorithm for coupling partial differential equation and compartment-based dynamics

PubMed Central

Yates, Christian A.

2016-01-01

Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction–diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing particle numbers. An alternative description of many of these systems can be derived in the diffusive limit as a deterministic, continuum system of partial differential equations (PDEs). Although the numerical solution of such PDEs is, in general, much more efficient than the full stochastic simulation, the deterministic continuum description is generally not valid when copy numbers are low and stochastic effects dominate. Therefore, to take advantage of the benefits of both of these types of models, each of which may be appropriate in different parts of a spatial domain, we have developed an algorithm that can be used to couple these two types of model together. This hybrid coupling algorithm uses an overlap region between the two modelling regimes. By coupling fluxes at one end of the interface and using a concentration-matching condition at the other end, we ensure that mass is appropriately transferred between PDE- and compartment-based regimes. Our methodology gives notable reductions in simulation time in comparison with using a fully stochastic model, while maintaining the important stochastic features of the system and providing detail in appropriate areas of the domain. We test our hybrid methodology robustly by applying it to several biologically motivated problems including diffusion and morphogen gradient formation. Our analysis shows that the resulting error is small, unbiased and does not grow over time. PMID:27628171

Extremely faint, diffuse satellite systems in the M31 halo: exceptional star clusters or tiny dwarf galaxies?

NASA Astrophysics Data System (ADS)

Mackey, Dougal

2013-10-01

Recent years have seen the discovery of a variety of low surface brightness, diffuse stellar systems in the Local Group. Of particular prominence are the ultra-faint dwarf satellites of the Milky Way and the extended globular clusters seen in M31, M33, and NGC 6822. As part of the major Pan-Andromeda Archaeological Survey {PAndAS} we have discovered several very faint and diffuse stellar satellites in the M31 halo. In Cycle 19 we obtained ACS/WFC imaging for one of these, PAndAS-48, which has revealed it to be a puzzling and unusual object. On the size-luminosity plane it falls between the extended clusters and ultra-faint dwarfs; however, its characteristics do not allow us to unambiguously class it as either type of system. If PAndAS-48 is an extended cluster then it is the most elliptical, isolated, metal-poor, and lowest-luminosity example yet uncovered. Conversely, while its properties are generally consistent with those observed for the faint dwarf satellites of the Milky Way, it would be a factor 2-3 smaller in spatial extent than its Galactic counterparts at comparable luminosity. Here we propose deep resolved imaging of the remaining five similar objects in our sample, with the aim of probing this hitherto poorly-explored region of parameter space in greater detail. If we are able to confirm any of these objects as faint dwarfs, they will provide the first insight into the behaviour of this class of object in a galaxy other than the Milky Way.

Testing high resolution numerical models for analysis of contaminant storage and release from low permeability zones

NASA Astrophysics Data System (ADS)

Chapman, Steven W.; Parker, Beth L.; Sale, Tom C.; Doner, Lee Ann

2012-08-01

It is now widely recognized that contaminant release from low permeability zones can sustain plumes long after primary sources are depleted, particularly for chlorinated solvents where regulatory limits are orders of magnitude below source concentrations. This has led to efforts to appropriately characterize sites and apply models for prediction incorporating these effects. A primary challenge is that diffusion processes are controlled by small-scale concentration gradients and capturing mass distribution in low permeability zones requires much higher resolution than commonly practiced. This paper explores validity of using numerical models (HydroGeoSphere, FEFLOW, MODFLOW/MT3DMS) in high resolution mode to simulate scenarios involving diffusion into and out of low permeability zones: 1) a laboratory tank study involving a continuous sand body with suspended clay layers which was 'loaded' with bromide and fluorescein (for visualization) tracers followed by clean water flushing, and 2) the two-layer analytical solution of Sale et al. (2008) involving a relatively simple scenario with an aquifer and underlying low permeability layer. All three models are shown to provide close agreement when adequate spatial and temporal discretization are applied to represent problem geometry, resolve flow fields and capture advective transport in the sands and diffusive transfer with low permeability layers and minimize numerical dispersion. The challenge for application at field sites then becomes appropriate site characterization to inform the models, capturing the style of the low permeability zone geometry and incorporating reasonable hydrogeologic parameters and estimates of source history, for scenario testing and more accurate prediction of plume response, leading to better site decision making.

The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems

PubMed Central

Wu, Sheng; Li, Hong; Petzold, Linda R.

2015-01-01

The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy. PMID:26609185

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

PubMed Central

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

2015-01-01

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

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

Spatial averaging for small molecule diffusion in condensed phase environments

NASA Astrophysics Data System (ADS)

Plattner, Nuria; Doll, J. D.; Meuwly, Markus

2010-07-01

Spatial averaging is a new approach for sampling rare-event problems. The approach modifies the importance function which improves the sampling efficiency while keeping a defined relation to the original statistical distribution. In this work, spatial averaging is applied to multidimensional systems for typical problems arising in physical chemistry. They include (I) a CO molecule diffusing on an amorphous ice surface, (II) a hydrogen molecule probing favorable positions in amorphous ice, and (III) CO migration in myoglobin. The systems encompass a wide range of energy barriers and for all of them spatial averaging is found to outperform conventional Metropolis Monte Carlo. It is also found that optimal simulation parameters are surprisingly similar for the different systems studied, in particular, the radius of the point cloud over which the potential energy function is averaged. For H2 diffusing in amorphous ice it is found that facile migration is possible which is in agreement with previous suggestions from experiment. The free energy barriers involved are typically lower than 1 kcal/mol. Spatial averaging simulations for CO in myoglobin are able to locate all currently characterized metastable states. Overall, it is found that spatial averaging considerably improves the sampling of configurational space.

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.

Improved spatial regression analysis of diffusion tensor imaging for lesion detection during longitudinal progression of multiple sclerosis in individual subjects

NASA Astrophysics Data System (ADS)

Liu, Bilan; Qiu, Xing; Zhu, Tong; Tian, Wei; Hu, Rui; Ekholm, Sven; Schifitto, Giovanni; Zhong, Jianhui

2016-03-01

Subject-specific longitudinal DTI study is vital for investigation of pathological changes of lesions and disease evolution. Spatial Regression Analysis of Diffusion tensor imaging (SPREAD) is a non-parametric permutation-based statistical framework that combines spatial regression and resampling techniques to achieve effective detection of localized longitudinal diffusion changes within the whole brain at individual level without a priori hypotheses. However, boundary blurring and dislocation limit its sensitivity, especially towards detecting lesions of irregular shapes. In the present study, we propose an improved SPREAD (dubbed improved SPREAD, or iSPREAD) method by incorporating a three-dimensional (3D) nonlinear anisotropic diffusion filtering method, which provides edge-preserving image smoothing through a nonlinear scale space approach. The statistical inference based on iSPREAD was evaluated and compared with the original SPREAD method using both simulated and in vivo human brain data. Results demonstrated that the sensitivity and accuracy of the SPREAD method has been improved substantially by adapting nonlinear anisotropic filtering. iSPREAD identifies subject-specific longitudinal changes in the brain with improved sensitivity, accuracy, and enhanced statistical power, especially when the spatial correlation is heterogeneous among neighboring image pixels in DTI.

Time-resolved diffusion tomographic 2D and 3D imaging in highly scattering turbid media

NASA Technical Reports Server (NTRS)

Alfano, Robert R. (Inventor); Cai, Wei (Inventor); Liu, Feng (Inventor); Lax, Melvin (Inventor); Das, Bidyut B. (Inventor)

1999-01-01

A method for imaging objects in highly scattering turbid media. According to one embodiment of the invention, the method involves using a plurality of intersecting source/detectors sets and time-resolving equipment to generate a plurality of time-resolved intensity curves for the diffusive component of light emergent from the medium. For each of the curves, the intensities at a plurality of times are then inputted into the following inverse reconstruction algorithm to form an image of the medium: ##EQU1## wherein W is a matrix relating output at source and detector positions r.sub.s and r.sub.d, at time t, to position r, .LAMBDA. is a regularization matrix, chosen for convenience to be diagonal, but selected in a way related to the ratio of the noise, to fluctuations in the absorption (or diffusion) X.sub.j that we are trying to determine: .LAMBDA..sub.ij =.lambda..sub.j .delta..sub.ij with .lambda..sub.j =/<.DELTA.Xj.DELTA.Xj> Y is the data collected at the detectors, and X.sup.k is the kth iterate toward the desired absoption information. An algorithm, which combines a two dimensional (2D) matrix inversion with a one-dimensional (1D) Fourier transform inversion is used to obtain images of three dimensional hidden objects in turbid scattering media.

Time-resolved diffusion tomographic 2D and 3D imaging in highly scattering turbid media

NASA Technical Reports Server (NTRS)

Alfano, Robert R. (Inventor); Cai, Wei (Inventor); Gayen, Swapan K. (Inventor)

2000-01-01

A method for imaging objects in highly scattering turbid media. According to one embodiment of the invention, the method involves using a plurality of intersecting source/detectors sets and time-resolving equipment to generate a plurality of time-resolved intensity curves for the diffusive component of light emergent from the medium. For each of the curves, the intensities at a plurality of times are then inputted into the following inverse reconstruction algorithm to form an image of the medium: wherein W is a matrix relating output at source and detector positions r.sub.s and r.sub.d, at time t, to position r, .LAMBDA. is a regularization matrix, chosen for convenience to be diagonal, but selected in a way related to the ratio of the noise, to fluctuations in the absorption (or diffusion) X.sub.j that we are trying to determine: .LAMBDA..sub.ij =.lambda..sub.j .delta..sub.ij with .lambda..sub.j =/<.DELTA.Xj.DELTA.Xj> Y is the data collected at the detectors, and X.sup.k is the kth iterate toward the desired absorption information. An algorithm, which combines a two dimensional (2D) matrix inversion with a one-dimensional (1D) Fourier transform inversion is used to obtain images of three dimensional hidden objects in turbid scattering media.

Spatially resolved x-ray fluorescence spectroscopy of beryllium capsule implosions at the NIF

NASA Astrophysics Data System (ADS)

MacDonald, M. J.; Bishel, D. T.; Saunders, A. M.; Scott, H. A.; Kyrala, G.; Kline, J.; MacLaren, S.; Thorn, D. B.; Yi, S. A.; Zylstra, A. B.; Falcone, R. W.; Doeppner, T.

2017-10-01

Beryllium ablators used in indirectly driven inertial confinement fusion implosions are doped with copper to prevent preheat of the cryogenic hydrogen fuel. Here, we present analysis of spatially resolved copper K- α fluorescence spectra from the beryllium ablator layer. It has been shown that K- α fluorescence spectroscopy can be used to measure plasma conditions of partially ionized dopants in high energy density systems. In these experiments, K-shell vacancies in the copper dopant are created by the hotspot emission at stagnation, resulting in K-shell fluorescence at bang time. Spatially resolved copper K- α emission spectra are compared to atomic kinetics and radiation code simulations to infer density and temperature profiles. This work was supported by the US DOE under Grant No. DE-NA0001859, under the auspices of the US DOE by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and by Los Alamos National Laboratory under contract DE-AC52-06NA52396.

Investigation of dissimilar metal welds by energy-resolved neutron imaging

DOE PAGES

Tremsin, Anton S.; Ganguly, Supriyo; Meco, Sonia M.; ...

2016-06-09

A nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participatingmore » alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al–steel weld is clearly resolved and could be used to optimize the welding process. As a result, a highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption.« less

Investigation of dissimilar metal welds by energy-resolved neutron imaging

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

Tremsin, Anton S.; Ganguly, Supriyo; Meco, Sonia M.

A nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participatingmore » alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al–steel weld is clearly resolved and could be used to optimize the welding process. As a result, a highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption.« less

Investigation of dissimilar metal welds by energy-resolved neutron imaging

PubMed Central

Tremsin, Anton S.; Ganguly, Supriyo; Meco, Sonia M.; Pardal, Goncalo R.; Shinohara, Takenao; Feller, W. Bruce

2016-01-01

A nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participating alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al–steel weld is clearly resolved and could be used to optimize the welding process. A highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption. PMID:27504075

Presence of lacunar infarctions is associated with the spatial navigation impairment in patients with mild cognitive impairment: a DTI study

PubMed Central

Liu, Qing-Ping; He, Wen-Wen; Ding, Hong; Nedelska, Zuzana; Hort, Jakub; Zhang, Bing; Xu, Yun

2016-01-01

Lacunar cerebral infarction (LI) is one of risk factors of vascular dementia and correlates with progression of cognitive impairment including the executive functions. However, little is known on spatial navigation impairment and its underlying microstructural alteration of white matter in patients with LI and with or without mild cognitive impairment (MCI). Our aim was to investigate whether the spatial navigation impairment correlated with the white matter integrity in LI patients with MCI (LI-MCI). Thirty patients with LI were included in the study and were divided into LI-MCI (n=17) and non MCI (LI-Non MCI) groups (n=13) according neuropsychological tests.The microstructural integrity of white matter was assessed by calculating a fractional anisotropy (FA) and mean diffusivity (MD) from diffusion tensor imaging (DTI) scans. The spatial navigation accuracy, separately evaluated as egocentric and allocentric, was assessed by a computerized human analogue of the Morris Water Maze tests Amunet. LI-MCI performed worse than the CN and LI-NonMCI groups on egocentric and delayed spatial navigation subtests. LI-MCI patients have spatial navigation deficits. The microstructural abnormalities in diffuse brain regions, including hippocampus, uncinate fasciculus and other brain regions may contribute to the spatial navigation impairment in LI-MCI patients at follow-up. PMID:27861154

Lateral diffusion contributes to FRET from lanthanide-tagged membrane proteins

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

Lan, Tien-Hung; Wu, Guangyu; Lambert, Nevin A., E-mail: nelambert@gru.edu

2015-08-14

Diffusion can enhance Förster resonance energy transfer (FRET) when donors or acceptors diffuse distances that are similar to the distances separating them during the donor's excited state lifetime. Lanthanide donors remain in the excited state for milliseconds, which makes them useful for time-resolved FRET applications but also allows time for diffusion to enhance energy transfer. Here we show that diffusion dramatically enhances FRET between membrane proteins labeled with lanthanide donors. This phenomenon complicates interpretation of experiments that use long-lived donors to infer association or proximity of mobile membrane proteins, but also offers a method of monitoring diffusion in membrane domainsmore » in real time in living cells. - Highlights: • Diffusion enhances TR-FRET from membrane proteins labeled with lanthanide donors. • Diffusion-dependent FRET can overshadow FRET due to oligomerization or clustering. • FRET studies using lanthanide-tagged membrane proteins should consider diffusion. • FRET from lanthanide donors can be used to monitor membrane protein diffusion.« less

Diffusion of a particle in the spatially correlated exponential random energy landscape: Transition from normal to anomalous diffusion.

PubMed

Novikov, S V

2018-01-14

Diffusive transport of a particle in a spatially correlated random energy landscape having exponential density of states has been considered. We exactly calculate the diffusivity in the nondispersive quasi-equilibrium transport regime for the 1D transport model and found that for slow decaying correlation functions the diffusivity becomes singular at some particular temperature higher than the temperature of the transition to the true non-equilibrium dispersive transport regime. It means that the diffusion becomes anomalous and does not follow the usual ∝ t 1/2 law. In such situation, the fully developed non-equilibrium regime emerges in two stages: first, at some temperature there is the transition from the normal to anomalous diffusion, and then at lower temperature the average velocity for the infinite medium goes to zero, thus indicating the development of the true dispersive regime. Validity of the Einstein relation is discussed for the situation where the diffusivity does exist. We provide also some arguments in favor of conservation of the major features of the new transition scenario in higher dimensions.

Rumor diffusion model with spatio-temporal diffusion and uncertainty of behavior decision in complex social networks

NASA Astrophysics Data System (ADS)

Zhu, Liang; Wang, Youguo

2018-07-01

In this paper, a rumor diffusion model with uncertainty of human behavior under spatio-temporal diffusion framework is established. Take physical significance of spatial diffusion into account, a diffusion threshold is set under which the rumor is not a trend topic and only spreads along determined physical connections. Heterogeneity of degree distribution and distance distribution has also been considered in theoretical model at the same time. The global existence and uniqueness of classical solution are proved with a Lyapunov function and an approximate classical solution in form of infinite series is constructed with a system of eigenfunction. Simulations and numerical solutions both on Watts-Strogatz (WS) network and Barabási-Albert (BA) network display the variation of density of infected connections from spatial and temporal dimensions. Relevant results show that the density of infected connections is dominated by network topology and uncertainty of human behavior at threshold time. With increase of social capability, rumor diffuses to the steady state in a higher speed. And the variation trends of diffusion size with uncertainty are diverse on different artificial networks.

A Framework for Widespread Replication of a Highly Spatially Resolved Childhood Lead Exposure Risk Model

PubMed Central

Kim, Dohyeong; Galeano, M. Alicia Overstreet; Hull, Andrew; Miranda, Marie Lynn

2008-01-01

Background Preventive approaches to childhood lead poisoning are critical for addressing this longstanding environmental health concern. Moreover, increasing evidence of cognitive effects of blood lead levels < 10 μg/dL highlights the need for improved exposure prevention interventions. Objectives Geographic information system–based childhood lead exposure risk models, especially if executed at highly resolved spatial scales, can help identify children most at risk of lead exposure, as well as prioritize and direct housing and health-protective intervention programs. However, developing highly resolved spatial data requires labor-and time-intensive geocoding and analytical processes. In this study we evaluated the benefit of increased effort spent geocoding in terms of improved performance of lead exposure risk models. Methods We constructed three childhood lead exposure risk models based on established methods but using different levels of geocoded data from blood lead surveillance, county tax assessors, and the 2000 U.S. Census for 18 counties in North Carolina. We used the results to predict lead exposure risk levels mapped at the individual tax parcel unit. Results The models performed well enough to identify high-risk areas for targeted intervention, even with a relatively low level of effort on geocoding. Conclusions This study demonstrates the feasibility of widespread replication of highly spatially resolved childhood lead exposure risk models. The models guide resource-constrained local health and housing departments and community-based organizations on how best to expend their efforts in preventing and mitigating lead exposure risk in their communities. PMID:19079729

Combustion Diagnostics and Flow Visualization of Hypergolic Combustion and Gelled Mixing Behavior

DTIC Science & Technology

1997-12-19

difference. Also, Exciplex Flourescence imaging has been implented to visualize diffusion layers which form at the contact interface of mixing...have been implemented and developed as a result of this effort. Among these techniques the most noteworthy involves a unique application of Exciplex ...fluorescence for visualization of diffusion layers formed between mixing liquids. Time resolved images of Exciplex fluorescence have been obtained

CO(J = 3-2) on-the-fly mapping of the nearby spiral galaxies NGC 628 and NGC 7793: Spatially resolved CO(J = 3-2) star-formation law

NASA Astrophysics Data System (ADS)

Muraoka, Kazuyuki; Takeda, Miho; Yanagitani, Kazuki; Kaneko, Hiroyuki; Nakanishi, Kouichiro; Kuno, Nario; Sorai, Kazuo; Tosaki, Tomoka; Kohno, Kotaro

2016-04-01

We present the results of CO(J = 3-2) on-the-fly mappings of two nearby non-barred spiral galaxies, NGC 628 and NGC 7793, with the Atacama Submillimeter Telescope Experiment at an effective angular resolution of 25″. We successfully obtained global distributions of CO(J = 3-2) emission over the entire disks at a sub-kpc resolution for both galaxies. We examined the spatially resolved (sub-kpc) relationship between CO(J = 3-2) luminosities (L^' }_CO(3-2)) and infrared (IR) luminosities (LIR) for NGC 628, NGC 7793, and M 83, and compared it with global luminosities of a JCMT (James Clerk Maxwell Telescope) Nearby Galaxy Legacy Survey sample. We found a striking linear L^' }_CO(3-2)-LIR correlation over the four orders of magnitude, and the correlation is consistent even with that for ultraluminous IR galaxies and submillimeter-selected galaxies. In addition, we examined the spatially resolved relationship between CO(J = 3-2) intensities (ICO(3-2)) and extinction-corrected star formation rates (SFRs) for NGC 628, NGC 7793, and M 83, and compared it with that for Giant Molecular Clouds in M 33 and 14 nearby galaxy centers. We found a linear ICO(3-2)-SFR correlation with ˜1 dex scatter. We conclude that the CO(J = 3-2) star-formation law (i.e., linear L^' }_CO(3-2)-LIR and ICO(3-2)-SFR correlations) is universally applicable to various types and spatial scales of galaxies; from spatially resolved nearby galaxy disks to distant IR-luminous galaxies, within ˜1 dex scatter.

Spatially resolved chemical analysis of cicada wings using laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS).

PubMed

Román, Jessica K; Walsh, Callee M; Oh, Junho; Dana, Catherine E; Hong, Sungmin; Jo, Kyoo D; Alleyne, Marianne; Miljkovic, Nenad; Cropek, Donald M

2018-03-01

Laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS) is an emerging bioanalytical tool for direct imaging and analysis of biological tissues. Performing ionization in an ambient environment, this technique requires little sample preparation and no additional matrix, and can be performed on natural, uneven surfaces. When combined with optical microscopy, the investigation of biological samples by LAESI allows for spatially resolved compositional analysis. We demonstrate here the applicability of LAESI-IMS for the chemical analysis of thin, desiccated biological samples, specifically Neotibicen pruinosus cicada wings. Positive-ion LAESI-IMS accurate ion-map data was acquired from several wing cells and superimposed onto optical images allowing for compositional comparisons across areas of the wing. Various putative chemical identifications were made indicating the presence of hydrocarbons, lipids/esters, amines/amides, and sulfonated/phosphorylated compounds. With the spatial resolution capability, surprising chemical distribution patterns were observed across the cicada wing, which may assist in correlating trends in surface properties with chemical distribution. Observed ions were either (1) equally dispersed across the wing, (2) more concentrated closer to the body of the insect (proximal end), or (3) more concentrated toward the tip of the wing (distal end). These findings demonstrate LAESI-IMS as a tool for the acquisition of spatially resolved chemical information from fragile, dried insect wings. This LAESI-IMS technique has important implications for the study of functional biomaterials, where understanding the correlation between chemical composition, physical structure, and biological function is critical. Graphical abstract Positive-ion laser-ablation electrospray ionization mass spectrometry coupled with optical imaging provides a powerful tool for the spatially resolved chemical analysis of cicada wings.

Assessment of mean-field microkinetic models for CO methanation on stepped metal surfaces using accelerated kinetic Monte Carlo

NASA Astrophysics Data System (ADS)

Andersen, Mie; Plaisance, Craig P.; Reuter, Karsten

2017-10-01

First-principles screening studies aimed at predicting the catalytic activity of transition metal (TM) catalysts have traditionally been based on mean-field (MF) microkinetic models, which neglect the effect of spatial correlations in the adsorbate layer. Here we critically assess the accuracy of such models for the specific case of CO methanation over stepped metals by comparing to spatially resolved kinetic Monte Carlo (kMC) simulations. We find that the typical low diffusion barriers offered by metal surfaces can be significantly increased at step sites, which results in persisting correlations in the adsorbate layer. As a consequence, MF models may overestimate the catalytic activity of TM catalysts by several orders of magnitude. The potential higher accuracy of kMC models comes at a higher computational cost, which can be especially challenging for surface reactions on metals due to a large disparity in the time scales of different processes. In order to overcome this issue, we implement and test a recently developed algorithm for achieving temporal acceleration of kMC simulations. While the algorithm overall performs quite well, we identify some challenging cases which may lead to a breakdown of acceleration algorithms and discuss possible directions for future algorithm development.

Can dispersion modeling of air pollution be improved by land-use regression? An example from Stockholm, Sweden

PubMed Central

Korek, Michal; Johansson, Christer; Svensson, Nina; Lind, Tomas; Beelen, Rob; Hoek, Gerard; Pershagen, Göran; Bellander, Tom

2017-01-01

Both dispersion modeling (DM) and land-use regression modeling (LUR) are often used for assessment of long-term air pollution exposure in epidemiological studies, but seldom in combination. We developed a hybrid DM–LUR model using 93 biweekly observations of NOx at 31 sites in greater Stockholm (Sweden). The DM was based on spatially resolved topographic, physiographic and emission data, and hourly meteorological data from a diagnostic wind model. Other data were from land use, meteorology and routine monitoring of NOx. We built a linear regression model for NOx, using a stepwise forward selection of covariates. The resulting model predicted observed NOx (R2=0.89) better than the DM without covariates (R2=0.68, P-interaction <0.001) and with minimal apparent bias. The model included (in descending order of importance) DM, traffic intensity on the nearest street, population (number of inhabitants) within 100 m radius, global radiation (direct sunlight plus diffuse or scattered light) and urban contribution to NOx levels (routine urban NOx, less routine rural NOx). Our results indicate that there is a potential for improving estimates of air pollutant concentrations based on DM, by incorporating further spatial characteristics of the immediate surroundings, possibly accounting for imperfections in the emission data. PMID:27485990

Can dispersion modeling of air pollution be improved by land-use regression? An example from Stockholm, Sweden.

PubMed

Korek, Michal; Johansson, Christer; Svensson, Nina; Lind, Tomas; Beelen, Rob; Hoek, Gerard; Pershagen, Göran; Bellander, Tom

2017-11-01

Both dispersion modeling (DM) and land-use regression modeling (LUR) are often used for assessment of long-term air pollution exposure in epidemiological studies, but seldom in combination. We developed a hybrid DM-LUR model using 93 biweekly observations of NO x at 31 sites in greater Stockholm (Sweden). The DM was based on spatially resolved topographic, physiographic and emission data, and hourly meteorological data from a diagnostic wind model. Other data were from land use, meteorology and routine monitoring of NO x . We built a linear regression model for NO x , using a stepwise forward selection of covariates. The resulting model predicted observed NO x (R 2 =0.89) better than the DM without covariates (R 2 =0.68, P-interaction <0.001) and with minimal apparent bias. The model included (in descending order of importance) DM, traffic intensity on the nearest street, population (number of inhabitants) within 100 m radius, global radiation (direct sunlight plus diffuse or scattered light) and urban contribution to NO x levels (routine urban NO x , less routine rural NO x ). Our results indicate that there is a potential for improving estimates of air pollutant concentrations based on DM, by incorporating further spatial characteristics of the immediate surroundings, possibly accounting for imperfections in the emission data.

Towards a conceptual multi-agent-based framework to simulate the spatial group decision-making process

NASA Astrophysics Data System (ADS)

Ghavami, Seyed Morsal; Taleai, Mohammad

2017-04-01

Most spatial problems are multi-actor, multi-issue and multi-phase in nature. In addition to their intrinsic complexity, spatial problems usually involve groups of actors from different organizational and cognitive backgrounds, all of whom participate in a social structure to resolve or reduce the complexity of a given problem. Hence, it is important to study and evaluate what different aspects influence the spatial problem resolution process. Recently, multi-agent systems consisting of groups of separate agent entities all interacting with each other have been put forward as appropriate tools to use to study and resolve such problems. In this study, then in order to generate a better level of understanding regarding the spatial problem group decision-making process, a conceptual multi-agent-based framework is used that represents and specifies all the necessary concepts and entities needed to aid group decision making, based on a simulation of the group decision-making process as well as the relationships that exist among the different concepts involved. The study uses five main influencing entities as concepts in the simulation process: spatial influence, individual-level influence, group-level influence, negotiation influence and group performance measures. Further, it explains the relationship among different concepts in a descriptive rather than explanatory manner. To illustrate the proposed framework, the approval process for an urban land use master plan in Zanjan—a provincial capital in Iran—is simulated using MAS, the results highlighting the effectiveness of applying an MAS-based framework when wishing to study the group decision-making process used to resolve spatial problems.

Chandra imaging of the kpc extended outflow in 1H 0419-577

NASA Astrophysics Data System (ADS)

Di Gesu, L.; Costantini, E.; Piconcelli, E.; Kaastra, J. S.; Mehdipour, M.; Paltani, S.

2017-12-01

The Seyfert 1 galaxy 1H 0419-577 hosts a kpc extended outflow that is evident in the [O III] image and that is also detected as a warm absorber in the UV/X-ray spectrum. Here, we analyze a 30 ks Chandra-ACIS X-ray image, with the aim of resolving the diffuse extranuclear X-ray emission and of investigating its relationship with the galactic outflow. Thanks to its sub-arcsecond spatial resolution, Chandra resolves the circumnuclear X-ray emission, which extends up to a projected distance of at least 16 kpc from the center. The morphology of the diffuse X-ray emission is spherically symmetrical. We could not recover a morphological resemblance between the soft X-ray emission and the ionization bicone that is traced by the [O III] outflow. Our spectral analysis indicates that one of the possible explanations for the extended emission is thermal emission from a low-density (nH 10-3 cm-3) hot plasma (Te 0.22 keV). If this is the case, we may be witnessing the cooling of a shock-heated wind bubble. In this scenario, the [O III] emission line and the X-ray/UV absorption lines may trace cooler clumps that are entrained in the hot outflow. Alternatively, the extended emission could be to due to a blend of emission lines from a photoionized gas component having a hydrogen column density of NH 2.1 × 1022 cm-2 and an ionization parameter of log ξ 1.3. Because the source is viewed almost edge-on we argue that the photoionized gas nebula must be distributed mostly along the polar directions, outside our line of sight. In this geometry, the X-ray/UV warm absorber must trace a different gas component, physically disconnected from the emitting gas, and located closer to the equatorial plane.

Effective diffusion coefficient including the Marangoni effect

NASA Astrophysics Data System (ADS)

Kitahata, Hiroyuki; Yoshinaga, Natsuhiko

2018-04-01

Surface-active molecules supplied from a particle fixed at the water surface create a spatial gradient of the molecule concentration, resulting in Marangoni convection. Convective flow transports the molecules far from the particle, enhancing diffusion. We analytically derive the effective diffusion coefficient associated with the Marangoni convection rolls. The resulting estimated effective diffusion coefficient is consistent with our numerical results and the apparent diffusion coefficient measured in experiments.

The Matryoshka Disk: Keck/NIRC2 Discovery of a Solar-system-scale, Radially Segregated Residual Protoplanetary Disk around HD 141569A

NASA Astrophysics Data System (ADS)

Currie, Thayne; Grady, Carol A.; Cloutier, Ryan; Konishi, Mihoko; Stassun, Keivan; Debes, John; van der Marel, Nienke; Muto, Takayuki; Jayawardhana, Ray; Ratzka, Thorsten

2016-03-01

Using Keck/NIRC2 {L}\\prime (3.78 μm) data, we report the direct imaging discovery of a scattered-light-resolved, solar-system-scale residual protoplanetary disk around the young A-type star HD 141569A, interior to and concentric with the two ring-like structures at wider separations. The disk is resolved down to ˜0.″25 and appears as an arc-like rim with attached hook-like features. It is located at an angular separation intermediate between that of warm CO gas identified from spatially resolved mid-infrared spectroscopy and diffuse dust emission recently discovered with the Hubble Space Telescope. The inner disk has a radius of ˜39 au, a position angle consistent with north up, and an inclination of I ˜ 56o and has a center offset from the star. Forward modeling of the disk favors a thick torus-like emission sharply truncated at separations beyond the torus’s photocenter and heavily depleted at smaller separations. In particular, the best-fit density power law for the dust suggests that the inner disk dust and gas (as probed by CO) are radially segregated, a feature consistent with the dust trapping mechanism inferred from observations of “canonical” transitional disks. However, the inner disk component may instead be explained by radiation pressure-induced migration in optically thin conditions, in contrast to the two stellar companion/planet-influenced ring-like structures at wider separations. HD 141569A’s circumstellar environment—with three nested, gapped, concentric dust populations—is an excellent laboratory for understanding the relationship between planet formation and the evolution of both dust grains and disk architecture.

Improvements in brain activation detection using time-resolved diffuse optical means

NASA Astrophysics Data System (ADS)

Montcel, Bruno; Chabrier, Renee; Poulet, Patrick

2005-08-01

An experimental method based on time-resolved absorbance difference is described. The absorbance difference is calculated over each temporal step of the optical signal with the time-resolved Beer-Lambert law. Finite element simulations show that each step corresponds to a different scanned zone and that cerebral contribution increases with the arrival time of photons. Experiments are conducted at 690 and 830 nm with a time-resolved system consisting of picosecond laser diodes, micro-channel plate photo-multiplier tube and photon counting modules. The hemodynamic response to a short finger tapping stimulus is measured over the motor cortex. Time-resolved absorbance difference maps show that variations in the optical signals are not localized in superficial regions of the head, which testify for their cerebral origin. Furthermore improvements in the detection of cerebral activation is achieved through the increase of variations in absorbance by a factor of almost 5 for time-resolved measurements as compared to non-time-resolved measurements.

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.

Cosmic ray propagation in interplanetary space

NASA Technical Reports Server (NTRS)

Voelk, H. J.

1975-01-01

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

Nonlinear Optical Spectroscopy of Two-Dimensional Materials

NASA Astrophysics Data System (ADS)

Cui, Qiannan

Nonlinear optical properties of two-dimensional (2D) materials, such as transition metal dichalcogenides (TMDs), graphene, black phosphorus, and so on, play a key role of understanding nanoscale light-matter interactions, as well as developing nanophotonics applications from solar cells to quantum computation. With ultrafast lasers, we experimentally study nonlinear optical properties of 2D materials. Employing transient absorption microscopy, we study several members of 2D materials, such as WSe2, TiS3 and ReS2. The dynamical saturable absorption process of 2D excitons is spatiotemporally resolved. Intrinsic parameters of these 2D materials, such as exciton lifetime, exciton diffusion coefficient, and exciton mobility, are effectively measured. Especially, in-plane anisotropy of transient absorption and diffusive transport is observed for 2D excitons in monolayer ReS2, demonstrating the in-plane degree of freedom. Furthermore, with quantum interference and control nanoscopy, we all-optically inject, detect and manipulate nanoscale ballistic charge currents in a ReS2 thin film. By tuning the phase difference between one photon absorption and two photon absorption transition paths, sub-picosecond timescale of ballistic currents is coherently controlled for the first time in TMDs. In addition, the spatial resolution is two-order of magnitude smaller than optical diffraction limit. The second-order optical nonlinearity of 2D monolayers is resolved by second harmonic generation (SHG) microscopy. We measure the second-order susceptibility of monolayer MoS 2. The angular dependence of SHG in monolayer MoS2 shows strong symmetry dependence on its crystal lattice structure. Hence, second harmonic generation microscopy can serve as a powerful tool to noninvasively determine the crystalline directions of 2D monolayers. The real and imaginary parts of third-order optical nonlinearity of 2D monolayers are resolved by third harmonic generation (THG) microscopy and two-photon transient absorption microscopy, respectively. With third harmonic generation microscopy, we observe strong and anisotropic THG in monolayer and multilayer ReS2. Comparing with 2D materials with hexagonal lattice, such as MoS2, the third-order susceptibility is higher by one order of magnitude in ReS2 with a distorted 1T structure. The in-plane anisotropy of THG is attributed to the lattice distortion in ReS2 after comparing with a symmetry analysis. With two-photon transient absorption microscopy, we observe a giant two-photon absorption coefficient of monolayer WS2.

Modelling the perennial energy crop market: the role of spatial diffusion

PubMed Central

Alexander, Peter; Moran, Dominic; Rounsevell, Mark D. A.; Smith, Pete

2013-01-01

Biomass produced from energy crops, such as Miscanthus and short rotation coppice is expected to contribute to renewable energy targets, but the slower than anticipated development of the UK market implies the need for greater understanding of the factors that govern adoption. Here, we apply an agent-based model of the UK perennial energy crop market, including the contingent interaction of supply and demand, to understand the spatial and temporal dynamics of energy crop adoption. Results indicate that perennial energy crop supply will be between six and nine times lower than previously published, because of time lags in adoption arising from a spatial diffusion process. The model simulates time lags of at least 20 years, which is supported empirically by the analogue of oilseed rape adoption in the UK from the 1970s. This implies the need to account for time lags arising from spatial diffusion in evaluating land-use change, climate change (mitigation or adaptation) or the adoption of novel technologies. PMID:24026474

Modelling the perennial energy crop market: the role of spatial diffusion.

PubMed

Alexander, Peter; Moran, Dominic; Rounsevell, Mark D A; Smith, Pete

2013-11-06

Biomass produced from energy crops, such as Miscanthus and short rotation coppice is expected to contribute to renewable energy targets, but the slower than anticipated development of the UK market implies the need for greater understanding of the factors that govern adoption. Here, we apply an agent-based model of the UK perennial energy crop market, including the contingent interaction of supply and demand, to understand the spatial and temporal dynamics of energy crop adoption. Results indicate that perennial energy crop supply will be between six and nine times lower than previously published, because of time lags in adoption arising from a spatial diffusion process. The model simulates time lags of at least 20 years, which is supported empirically by the analogue of oilseed rape adoption in the UK from the 1970s. This implies the need to account for time lags arising from spatial diffusion in evaluating land-use change, climate change (mitigation or adaptation) or the adoption of novel technologies.

Diffusion in realistic biophysical systems can lead to aliasing effects in diffusion spectrum imaging.

PubMed

Lacerda, Luis M; Sperl, Jonathan I; Menzel, Marion I; Sprenger, Tim; Barker, Gareth J; Dell'Acqua, Flavio

2016-12-01

Diffusion spectrum imaging (DSI) is an imaging technique that has been successfully applied to resolve white matter crossings in the human brain. However, its accuracy in complex microstructure environments has not been well characterized. Here we have simulated different tissue configurations, sampling schemes, and processing steps to evaluate DSI performances' under realistic biophysical conditions. A novel approach to compute the orientation distribution function (ODF) has also been developed to include biophysical constraints, namely integration ranges compatible with axial fiber diffusivities. Performed simulations identified several DSI configurations that consistently show aliasing artifacts caused by fast diffusion components for both isotropic diffusion and fiber configurations. The proposed method for ODF computation showed some improvement in reducing such artifacts and improving the ability to resolve crossings, while keeping the quantitative nature of the ODF. In this study, we identified an important limitation of current DSI implementations, specifically the presence of aliasing due to fast diffusion components like those from pathological tissues, which are not well characterized, and can lead to artifactual fiber reconstructions. To minimize this issue, a new way of computing the ODF was introduced, which removes most of these artifacts and offers improved angular resolution. Magn Reson Med 76:1837-1847, 2016. © 2015 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2015 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Nonequilibrium transition and pattern formation in a linear reaction-diffusion system with self-regulated kinetics

NASA Astrophysics Data System (ADS)

Paul, Shibashis; Ghosh, Shyamolina; Ray, Deb Shankar

2018-02-01

We consider a reaction-diffusion system with linear, stochastic activator-inhibitor kinetics where the time evolution of concentration of a species at any spatial location depends on the relative average concentration of its neighbors. This self-regulating nature of kinetics brings in spatial correlation between the activator and the inhibitor. An interplay of this correlation in kinetics and disparity of diffusivities of the two species leads to symmetry breaking non-equilibrium transition resulting in stationary pattern formation. The role of initial noise strength and the linear reaction terms has been analyzed for pattern selection.

Stability and Hopf Bifurcation in a Reaction-Diffusion Model with Chemotaxis and Nonlocal Delay Effect

NASA Astrophysics Data System (ADS)

Li, Dong; Guo, Shangjiang

Chemotaxis is an observed phenomenon in which a biological individual moves preferentially toward a relatively high concentration, which is contrary to the process of natural diffusion. In this paper, we study a reaction-diffusion model with chemotaxis and nonlocal delay effect under Dirichlet boundary condition by using Lyapunov-Schmidt reduction and the implicit function theorem. The existence, multiplicity, stability and Hopf bifurcation of spatially nonhomogeneous steady state solutions are investigated. Moreover, our results are illustrated by an application to the model with a logistic source, homogeneous kernel and one-dimensional spatial domain.

Reduction of Poisson noise in measured time-resolved data for time-domain diffuse optical tomography.

PubMed

Okawa, S; Endo, Y; Hoshi, Y; Yamada, Y

2012-01-01

A method to reduce noise for time-domain diffuse optical tomography (DOT) is proposed. Poisson noise which contaminates time-resolved photon counting data is reduced by use of maximum a posteriori estimation. The noise-free data are modeled as a Markov random process, and the measured time-resolved data are assumed as Poisson distributed random variables. The posterior probability of the occurrence of the noise-free data is formulated. By maximizing the probability, the noise-free data are estimated, and the Poisson noise is reduced as a result. The performances of the Poisson noise reduction are demonstrated in some experiments of the image reconstruction of time-domain DOT. In simulations, the proposed method reduces the relative error between the noise-free and noisy data to about one thirtieth, and the reconstructed DOT image was smoothed by the proposed noise reduction. The variance of the reconstructed absorption coefficients decreased by 22% in a phantom experiment. The quality of DOT, which can be applied to breast cancer screening etc., is improved by the proposed noise reduction.

On the eddy-resolving capability of high-order discontinuous Galerkin approaches to implicit LES / under-resolved DNS of Euler turbulence

NASA Astrophysics Data System (ADS)

Moura, R. C.; Mengaldo, G.; Peiró, J.; Sherwin, S. J.

2017-02-01

We present estimates of spectral resolution power for under-resolved turbulent Euler flows obtained with high-order discontinuous Galerkin (DG) methods. The '1% rule' based on linear dispersion-diffusion analysis introduced by Moura et al. (2015) [10] is here adapted for 3D energy spectra and validated through the inviscid Taylor-Green vortex problem. The 1% rule estimates the wavenumber beyond which numerical diffusion induces an artificial dissipation range on measured energy spectra. As the original rule relies on standard upwinding, different Riemann solvers are tested. Very good agreement is found for solvers which treat the different physical waves in a consistent manner. Relatively good agreement is still found for simpler solvers. The latter however displayed spurious features attributed to the inconsistent treatment of different physical waves. It is argued that, in the limit of vanishing viscosity, such features might have a significant impact on robustness and solution quality. The estimates proposed are regarded as useful guidelines for no-model DG-based simulations of free turbulence at very high Reynolds numbers.

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

NASA Astrophysics Data System (ADS)

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

1996-10-01

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

The 7BM beamline at the APS: a facility for time-resolved fluid dynamics measurements

PubMed Central

Kastengren, Alan; Powell, Christopher F.; Arms, Dohn; Dufresne, Eric M.; Gibson, Harold; Wang, Jin

2012-01-01

In recent years, X-ray radiography has been used to probe the internal structure of dense sprays with microsecond time resolution and a spatial resolution of 15 µm even in high-pressure environments. Recently, the 7BM beamline at the Advanced Photon Source (APS) has been commissioned to focus on the needs of X-ray spray radiography measurements. The spatial resolution and X-ray intensity at this beamline represent a significant improvement over previous time-resolved X-ray radiography measurements at the APS. PMID:22713903

ISM Dust Grains and N-band Spectral Variability in the Spatially Resolved Subarcsecond Binary UY Aur

NASA Astrophysics Data System (ADS)

Skemer, Andrew J.; Close, Laird M.; Hinz, Philip M.; Hoffmann, William F.; Greene, Thomas P.; Males, Jared R.; Beck, Tracy L.

2010-03-01

The 10 μm silicate feature is an essential diagnostic of dust-grain growth and planet formation in young circumstellar disks. The Spitzer Space Telescope has revolutionized the study of this feature, but due to its small (85 cm) aperture, it cannot spatially resolve small/medium-separation binaries (lsim3''; <~ 420 AU) at the distances of the nearest star-forming regions (~140 pc). Large, 6-10 m ground-based telescopes with mid-infrared instruments can resolve these systems. In this paper, we spatially resolve the 0farcs88 binary, UY Aur, with MMTAO/BLINC-MIRAC4 mid-infrared spectroscopy. We then compare our spectra to Spitzer/IRS (unresolved) spectroscopy, and resolved images from IRTF/MIRAC2, Keck/OSCIR, and Gemini/Michelle, which were taken over the past decade. We find that UY Aur A has extremely pristine, interstellar medium (ISM)-like grains and that UY Aur B has an unusually shaped silicate feature, which is probably the result of blended emission and absorption from foreground extinction in its disk. We also find evidence for variability in both UY Aur A and UY Aur B by comparing synthetic photometry from our spectra with resolved imaging from previous epochs. The photometric variability of UY Aur A could be an indication that the silicate emission itself is variable, as was recently found in EX Lupi. Otherwise, the thermal continuum is variable, and either the ISM-like dust has never evolved, or it is being replenished, perhaps by UY Aur's circumbinary disk. The observations reported here were partially obtained at the Infrared Telescope Facility, which is operated by the University of Hawaii under Cooperative Agreement no. NCC 5-538 with the National Aeronautics and Space Administration, Science Mission Directorate, Planetary Astronomy Program.

Understanding the mechanisms of amorphous creep through molecular simulation

NASA Astrophysics Data System (ADS)

Cao, Penghui; Short, Michael P.; Yip, Sidney

2017-12-01

Molecular processes of creep in metallic glass thin films are simulated at experimental timescales using a metadynamics-based atomistic method. Space-time evolutions of the atomic strains and nonaffine atom displacements are analyzed to reveal details of the atomic-level deformation and flow processes of amorphous creep in response to stress and thermal activations. From the simulation results, resolved spatially on the nanoscale and temporally over time increments of fractions of a second, we derive a mechanistic explanation of the well-known variation of creep rate with stress. We also construct a deformation map delineating the predominant regimes of diffusional creep at low stress and high temperature and deformational creep at high stress. Our findings validate the relevance of two original models of the mechanisms of amorphous plasticity: one focusing on atomic diffusion via free volume and the other focusing on stress-induced shear deformation. These processes are found to be nonlinearly coupled through dynamically heterogeneous fluctuations that characterize the slow dynamics of systems out of equilibrium.

Dynamical measurements of motion behavior of free fluorescent sphere using the wide field temporal focusing microscopy with astigmatism method (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lien, Chi-Hsiang; Lin, Chun-Yu; Chen, Shean-Jen; Chien, Fan-Ching

2017-02-01

A three-dimensional (3D) single fluorescent particle tracking strategy based on temporal focusing multiphoton excitation microscopy (TFMPEM) combined with astigmatism imaging is proposed for delivering nanoscale-level axial information that reveals 3D trajectories of single fluorospheres in the axially-resolved multiphoton excitation volume without z-axis scanning. It provides the dynamical ability by measuring the diffusion coefficient of fluorospheres in glycerol solutions with a position standard deviation of 14 nm and 21 nm in the lateral and axial direction and a frame rate of 100 Hz. Moreover, the optical trapping force based on the TFMPEM is minimized to avoid the interference in the tracing measurements compared to that in the spatial focusing MPE approaches. Therefore, we presented a three dimensional single particle tracking strategy to overcome the limitation of the time resolution of the multiphoton imaging using fast frame rate of TFMPEM, and provide three dimensional locations of multiple particles using an astigmatism method.

Study of the time-resolved, 3-dimensional current density distribution in solid metallic liners at 1 MA

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

Bott-Suzuki, S. C.; Cordaro, S. W.; Caballero Bendixsen, L. S.

We present a study of the time varying current density distribution in solid metallic liner experiments at the 1MA level. Measurements are taken using an array of magnetic field probes which provide 2D triangulation of the average centroid of the drive current in the load at 3 discrete axial positions. These data are correlated with gated optical self-emission imaging which directly images the breakdown and plasma formation region. Results show that the current density is azimuthally non-uniform, and changes significantly throughout the 100ns experimental timescale. Magnetic field probes show clearly motion of the current density around the liner azimuth overmore » 10ns timescales. If breakdown is initiated at one azimuthal location, the current density remains non-uniform even over large spatial extents throughout the current drive. The evolution timescales are suggestive of a resistive diffusion process or uneven current distributions among simultaneously formed but discrete plasma conduction paths.« less

Two dimensional, transient catalytic combustion of CO-air on platinum

NASA Technical Reports Server (NTRS)

Sinha, N.; Bruno, C.; Bracco, F. V.

1985-01-01

The light off transient of catalytic combustion of lean CO-air mixtures in a platinum coated channel of a honeycomb monolith is studied with a model that resolves transient radial and axial gradients in both the gas and the solid. For the conditions studied it is concluded that: the initial heat release occurs near the entrance at the gas-solid interface and is controlled by heterogeneous reactions; large spatial and temporal temperature gradients occur in the solid near the entrance controlled mostly by the availability of fuel; the temperature of the solid near the entrance achieves almost its steady state value before significant heating of the back; heterogeneous reactions and the gas heated up front and flowing downstream heat the back of the solid; the overall transient time is controlled by the thermal inertia of the solid and by forced convection; radiation significantly influences both transient and steady state particularly near the entrance; the oxidation of CO occurs mostly on the catalyst and becomes diffusion controlled soon into the transient.

Study of the time-resolved, 3-dimensional current density distribution in solid metallic liners at 1 MA

DOE PAGES

Bott-Suzuki, S. C.; Cordaro, S. W.; Caballero Bendixsen, L. S.; ...

2016-09-01

We present a study of the time varying current density distribution in solid metallic liner experiments at the 1MA level. Measurements are taken using an array of magnetic field probes which provide 2D triangulation of the average centroid of the drive current in the load at 3 discrete axial positions. These data are correlated with gated optical self-emission imaging which directly images the breakdown and plasma formation region. Results show that the current density is azimuthally non-uniform, and changes significantly throughout the 100ns experimental timescale. Magnetic field probes show clearly motion of the current density around the liner azimuth overmore » 10ns timescales. If breakdown is initiated at one azimuthal location, the current density remains non-uniform even over large spatial extents throughout the current drive. The evolution timescales are suggestive of a resistive diffusion process or uneven current distributions among simultaneously formed but discrete plasma conduction paths.« less

Visualizing the chemistry and structure dynamics in lithium-ion batteries by in-situ neutron diffraction

PubMed Central

Wang, Xun-Li; An, Ke; Cai, Lu; Feng, Zhili; Nagler, Stephen E.; Daniel, Claus; Rhodes, Kevin J.; Stoica, Alexandru D.; Skorpenske, Harley D.; Liang, Chengdu; Zhang, Wei; Kim, Joon; Qi, Yue; Harris, Stephen J.

2012-01-01

We report an in-situ neutron diffraction study of a large format pouch battery cell. The succession of Li-Graphite intercalation phases was fully captured under an 1C charge-discharge condition (i.e., charge to full capacity in 1 hour). However, the lithiation and dilithiation pathways are distinctively different and, unlike in slowing charging experiments with which the Li-Graphite phase diagram was established, no LiC24 phase was found during charge at 1C rate. Approximately 75 mol. % of the graphite converts to LiC6 at full charge, and a lattice dilation as large as 4% was observed during a charge-discharge cycle. Our work demonstrates the potential of in-situ, time and spatially resolved neutron diffraction study of the dynamic chemical and structural changes in “real-world” batteries under realistic cycling conditions, which should provide microscopic insights on degradation and the important role of diffusion kinetics in energy storage materials. PMID:23087812

Chandra Observations of Extended X-Ray Emission in ARP 220

NASA Technical Reports Server (NTRS)

McDowell, J. C.; Clements, D. L.; Lamb, S. A.; Shaked, S.; Hearn, N. C.; Colina, L.; Mundell, C.; Borne, K.; Baker, A. C.; Arribas, S.

2003-01-01

We resolve the extended X-ray emission from the prototypical ultraluminous infrared galaxy Arp 220. Extended, faint, edge-brightened, soft X-ray lobes outside the optical galaxy are observed to a distance of 1CL 15 kpc on each side of the nuclear region. Bright plumes inside the optical isophotes coincide with the optical line emission and extend 1 1 kpc from end to end across the nucleus. The data for the plumes cannot be fitted by a single-temperature plasma and display a range of temperatures from 0.2 to 1 keV. The plumes emerge from bright, diffuse circumnuclear emission in the inner 3 kpc centered on the Ha peak, which is displaced from the radio nuclei. There is a close morphological correspondence between the Ha and soft X-ray emission on all spatial scales. We interpret the plumes as a starburst-driven superwind and discuss two interpretations of the emission from the lobes in the context of simulations of the merger dynamics of Arp 220.

Particle-based modeling of heterogeneous chemical kinetics including mass transfer.

PubMed

Sengar, A; Kuipers, J A M; van Santen, Rutger A; Padding, J T

2017-08-01

Connecting the macroscopic world of continuous fields to the microscopic world of discrete molecular events is important for understanding several phenomena occurring at physical boundaries of systems. An important example is heterogeneous catalysis, where reactions take place at active surfaces, but the effective reaction rates are determined by transport limitations in the bulk fluid and reaction limitations on the catalyst surface. In this work we study the macro-micro connection in a model heterogeneous catalytic reactor by means of stochastic rotation dynamics. The model is able to resolve the convective and diffusive interplay between participating species, while including adsorption, desorption, and reaction processes on the catalytic surface. Here we apply the simulation methodology to a simple straight microchannel with a catalytic strip. Dimensionless Damkohler numbers are used to comment on the spatial concentration profiles of reactants and products near the catalyst strip and in the bulk. We end the discussion with an outlook on more complicated geometries and increasingly complex reactions.

Particle-based modeling of heterogeneous chemical kinetics including mass transfer

NASA Astrophysics Data System (ADS)

Sengar, A.; Kuipers, J. A. M.; van Santen, Rutger A.; Padding, J. T.

2017-08-01

Connecting the macroscopic world of continuous fields to the microscopic world of discrete molecular events is important for understanding several phenomena occurring at physical boundaries of systems. An important example is heterogeneous catalysis, where reactions take place at active surfaces, but the effective reaction rates are determined by transport limitations in the bulk fluid and reaction limitations on the catalyst surface. In this work we study the macro-micro connection in a model heterogeneous catalytic reactor by means of stochastic rotation dynamics. The model is able to resolve the convective and diffusive interplay between participating species, while including adsorption, desorption, and reaction processes on the catalytic surface. Here we apply the simulation methodology to a simple straight microchannel with a catalytic strip. Dimensionless Damkohler numbers are used to comment on the spatial concentration profiles of reactants and products near the catalyst strip and in the bulk. We end the discussion with an outlook on more complicated geometries and increasingly complex reactions.

SVBRDF-Invariant Shape and Reflectance Estimation from a Light-Field Camera.

PubMed

Wang, Ting-Chun; Chandraker, Manmohan; Efros, Alexei A; Ramamoorthi, Ravi

2018-03-01

Light-field cameras have recently emerged as a powerful tool for one-shot passive 3D shape capture. However, obtaining the shape of glossy objects like metals or plastics remains challenging, since standard Lambertian cues like photo-consistency cannot be easily applied. In this paper, we derive a spatially-varying (SV)BRDF-invariant theory for recovering 3D shape and reflectance from light-field cameras. Our key theoretical insight is a novel analysis of diffuse plus single-lobe SVBRDFs under a light-field setup. We show that, although direct shape recovery is not possible, an equation relating depths and normals can still be derived. Using this equation, we then propose using a polynomial (quadratic) shape prior to resolve the shape ambiguity. Once shape is estimated, we also recover the reflectance. We present extensive synthetic data on the entire MERL BRDF dataset, as well as a number of real examples to validate the theory, where we simultaneously recover shape and BRDFs from a single image taken with a Lytro Illum camera.

An approach to spin-resolved molecular gas microscopy

NASA Astrophysics Data System (ADS)

Covey, Jacob P.; De Marco, Luigi; Acevedo, Óscar L.; Rey, Ana Maria; Ye, Jun

2018-04-01

Ultracold polar molecules are an ideal platform for studying many-body physics with long-range dipolar interactions. Experiments in this field have progressed enormously, and several groups are pursuing advanced apparatus for manipulation of molecules with electric fields as well as single-atom-resolved in situ detection. Such detection has become ubiquitous for atoms in optical lattices and tweezer arrays, but has yet to be demonstrated for ultracold polar molecules. Here we present a proposal for the implementation of site-resolved microscopy for polar molecules, and specifically discuss a technique for spin-resolved molecular detection. We use numerical simulation of spin dynamics of lattice-confined polar molecules to show how such a scheme would be of utility in a spin-diffusion experiment.

Simulation of space-based (GRACE) gravity variations caused by storage changes in large confined and unconfined aquifers

NASA Astrophysics Data System (ADS)

Pool, D. R.; Scanlon, B. R.

2017-12-01

There is uncertainty of how storage change in confined and unconfined aquifers would register from space-based platforms, such as the GRACE (Gravity Recovery and Climate Experiment) satellites. To address this concern, superposition groundwater models (MODFLOW) of equivalent storage change in simplified confined and unconfined aquifers of extent, 500 km2 or approximately 5X5 degrees at mid-latitudes, and uniform transmissivity were constructed. Gravity change resulting from the spatial distribution of aquifer storage change for each aquifer type was calculated at the initial GRACE satellite altitude ( 500 km). To approximate real-world conditions, the confined aquifer includes a small region of unconfined conditions at one margin. A uniform storage coefficient (specific yield) was distributed across the unconfined aquifer. For both cases, storage change was produced by 1 year of groundwater withdrawal from identical aquifer-centered well distributions followed by decades of no withdrawal and redistribution of the initial storage loss toward a new steady-state condition. The transient simulated storage loss includes equivalent volumes for both conceptualizations, but spatial distributions differ because of the contrasting aquifer diffusivity (Transmissivity/Storativity). Much higher diffusivity in the confined aquifer results in more rapid storage redistribution across a much larger area than for the unconfined aquifer. After the 1 year of withdrawals, the two simulated storage loss distributions are primarily limited to small regions within the model extent. Gravity change after 1 year observed at the satellite altitude is similar for both aquifers including maximum gravity reductions that are coincident with the aquifer center. With time, the maximum gravity reduction for the confined aquifer case shifts toward the aquifer margin as much as 200 km because of increased storage loss in the unconfined region. Results of the exercise indicate that GRACE observations are largely insensitive to confined or unconfined conditions for most aquifers. Lateral shifts in storage change with time in confined aquifers could be resolved by space-based gravity missions with durations of decades and improved spatial resolution, 1 degree or less ( 100 km), over the GRACE resolution of 3 degrees ( 300 km).

Characterizing Extragalactic Star Formation with GALEX Legacy Photometric Analysis of UV-Bright Stellar Complexes

NASA Astrophysics Data System (ADS)

Thilker, David

At the close of nearly a decade of observing, GALEX has accumulated an unprecedented archive of ultraviolet (UV) images revealing both the scope and intricacy of star formation (SF) in many thousands of galaxies inhabiting the local universe. If the observed hierarchical SF morphology can be quantified systematically, and physically interpreted with multi-wavelength ancillary data and modeling, then the low redshift GALEX legacy will approach completion. However, the GALEX GR6 pipeline database contains a highly incomplete census of young stellar complexes even for very well-studied galaxies. We propose to apply a dedicated photometry algorithm that has been optimized for measuring the properties of irregularly shaped sources in crowded galaxy images containing spatially variant, diffuse intra-clump emission. Structures will be selected in the UV, but we will compile UV-visible-MIR SEDs for each detection utilizing Pan-STARRS1+SDSS and WISE data. These SEDs will then be fit using population-synthesis models to derive estimated stellar mass, age, and extinction. Processing will be completed for the entire diameter-limited GALEX Large Galaxy Atlas (GLGA) sample of 20,000+ galaxies, at a variety of standardized spatial resolutions. Although the precise categorization of the cataloged substructures will depend on galaxy distance, the outcome of our analysis will be a catalog similar to the stellar association surveys of past decades for very nearby galaxies based on resolved stars (e.g. van den Bergh 1964, Hodge 1986, Efremov et al. 1987), except that our investigation will probe a galaxy sample of dramatically larger size using the integrated UV light from such groupings of young stars. Our algorithm is multi-scale in nature and will thus preserve the hierarchical properties of the stellar distribution, by linking sub-clumps to their larger-scale parent feature(s). The resulting database will be a fundamental resource for follow-up multi-wavelength studies probing SF-driven galaxy evolution using both existing NASA databases and operating instruments, in addition to upcoming space telescopes. While a legacy of our project will be the hierarchical photometric database (disseminated via MAST and NED) which supports extragalactic community science, our own goals from the proposed comprehensive measurements address some vital issues: (i) Currently there is controversy regarding the power-law slope of the empirical star formation law (SFL). Is there constant star formation efficiency above the HI-to-H_2 transition gas surface density (implying ~unity slope, see papers by Bigiel et al. and Leroy et al.), or is the SFL relation a stronger function of gas density with a super-linear form (as observed by Kennicutt et al. 2007)? Liu et al. (2011) have shown that the answer may depend critically on whether or not diffuse emission underlying star-forming substructures is removed. Our analysis will allow firm resolution of this issue, as we will also apply our photometry algorithm to Spitzer imaging for a subset of our sample galaxies, thus providing background-subtracted L(UV) and L(IR) measurements for substructures which can then be compared to existing and forthcoming (ALMA) CO imaging. (ii) We will also verify/calibrate our SED-fit based determination of age, extinction, and mass for UV-bright structures via direct comparison to the ground-truth stemming from resolved stellar populations (e.g. in ANGST galaxies) and also high-resolution HST UV-optical star cluster surveys (further out in the Local Volume). (iii) Finally, we will measure the diffuse UV fraction in a few hundred of the nearest galaxies (accounting for variation tied only to spatial resolution), trying to ascertain the characteristic fraction in galaxies of different Hubble type and dust-to-gas ratio. Systematic local variations in diffuse fraction and color will also be quantified as a function of environment.

Sub-nanosecond time-resolved near-field scanning magneto-optical microscope.

PubMed

Rudge, J; Xu, H; Kolthammer, J; Hong, Y K; Choi, B C

2015-02-01

We report on the development of a new magnetic microscope, time-resolved near-field scanning magneto-optical microscope, which combines a near-field scanning optical microscope and magneto-optical contrast. By taking advantage of the high temporal resolution of time-resolved Kerr microscope and the sub-wavelength spatial resolution of a near-field microscope, we achieved a temporal resolution of ∼50 ps and a spatial resolution of <100 nm. In order to demonstrate the spatiotemporal magnetic imaging capability of this microscope, the magnetic field pulse induced gyrotropic vortex dynamics occurring in 1 μm diameter, 20 nm thick CoFeB circular disks has been investigated. The microscope provides sub-wavelength resolution magnetic images of the gyrotropic motion of the vortex core at a resonance frequency of ∼240 MHz.

Selective spatial enhancement: Attentional spotlight size impacts spatial but not temporal perception.

PubMed

Goodhew, Stephanie C; Shen, Elizabeth; Edwards, Mark

2016-08-01

An important but often neglected aspect of attention is how changes in the attentional spotlight size impact perception. The zoom-lens model predicts that a small ("focal") attentional spotlight enhances all aspects of perception relative to a larger ("diffuse" spotlight). However, based on the physiological properties of the two major classes of visual cells (magnocellular and parvocellular neurons) we predicted trade-offs in spatial and temporal acuity as a function of spotlight size. Contrary to both of these accounts, however, across two experiments we found that attentional spotlight size affected spatial acuity, such that spatial acuity was enhanced for a focal relative to a diffuse spotlight, whereas the same modulations in spotlight size had no impact on temporal acuity. This likely reflects the function of attention: to induce the high spatial resolution of the fovea in periphery, where spatial resolution is poor but temporal resolution is good. It is adaptive, therefore, for the attentional spotlight to enhance spatial acuity, whereas enhancing temporal acuity does not confer the same benefit.

Spatial dilemmas of diffusible public goods

PubMed Central

Allen, Benjamin; Gore, Jeff; Nowak, Martin A

2013-01-01

The emergence of cooperation is a central question in evolutionary biology. Microorganisms often cooperate by producing a chemical resource (a public good) that benefits other cells. The sharing of public goods depends on their diffusion through space. Previous theory suggests that spatial structure can promote evolution of cooperation, but the diffusion of public goods introduces new phenomena that must be modeled explicitly. We develop an approach where colony geometry and public good diffusion are described by graphs. We find that the success of cooperation depends on a simple relation between the benefits and costs of the public good, the amount retained by a producer, and the average amount retained by each of the producer’s neighbors. These quantities are derived as analytic functions of the graph topology and diffusion rate. In general, cooperation is favored for small diffusion rates, low colony dimensionality, and small rates of decay of the public good. DOI: http://dx.doi.org/10.7554/eLife.01169.001 PMID:24347543

Super-diffusion of excited carriers in semiconductors

PubMed Central

Najafi, Ebrahim; Ivanov, Vsevolod; Zewail, Ahmed; Bernardi, Marco

2017-01-01

The ultrafast spatial and temporal dynamics of excited carriers are important to understanding the response of materials to laser pulses. Here we use scanning ultrafast electron microscopy to image the dynamics of electrons and holes in silicon after excitation with a short laser pulse. We find that the carriers exhibit a diffusive dynamics at times shorter than 200 ps, with a transient diffusivity up to 1,000 times higher than the room temperature value, D0≈30 cm2s−1. The diffusivity then decreases rapidly, reaching a value of D0 roughly 500 ps after the excitation pulse. We attribute the transient super-diffusive behaviour to the rapid expansion of the excited carrier gas, which equilibrates with the environment in 100−150 ps. Numerical solution of the diffusion equation, as well as ab initio calculations, support our interpretation. Our findings provide new insight into the ultrafast spatial dynamics of excited carriers in materials. PMID:28492283

A Diffuse Interface Model with Immiscibility Preservation

PubMed Central

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

2013-01-01

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

Spatially explicit control of invasive species using a reaction-diffusion model

USGS Publications Warehouse

Bonneau, Mathieu; Johnson, Fred A.; Romagosa, Christina M.

2016-01-01

Invasive species, which can be responsible for severe economic and environmental damages, must often be managed over a wide area with limited resources, and the optimal allocation of effort in space and time can be challenging. If the spatial range of the invasive species is large, control actions might be applied only on some parcels of land, for example because of property type, accessibility, or limited human resources. Selecting the locations for control is critical and can significantly impact management efficiency. To help make decisions concerning the spatial allocation of control actions, we propose a simulation based approach, where the spatial distribution of the invader is approximated by a reaction–diffusion model. We extend the classic Fisher equation to incorporate the effect of control both in the diffusion and local growth of the invader. The modified reaction–diffusion model that we propose accounts for the effect of control, not only on the controlled locations, but on neighboring locations, which are based on the theoretical speed of the invasion front. Based on simulated examples, we show the superiority of our model compared to the state-of-the-art approach. We illustrate the use of this model for the management of Burmese pythons in the Everglades (Florida, USA). Thanks to the generality of the modified reaction–diffusion model, this framework is potentially suitable for a wide class of management problems and provides a tool for managers to predict the effects of different management strategies.

Spatial variation in carrier dynamics along a single CdSSe nanowire

NASA Astrophysics Data System (ADS)

Blake, Jolie C.; Eldridge, Peter S.; Gundlach, Lars

2014-10-01

Ultrafast charge carrier dynamics along individual CdSxSe1-x nanowires has been measured. The use of an improved ultrafast Kerr-gated microscope allows for spatially resolved luminescence measurements along a single nanowire. Amplified spontaneous emission (ASE) was observed at high excitation fluences. Position dependent variations of ultrafast ASE dynamics were observed. SEM and colorimetric measurements showed that the difference in dynamics can be attributed to variations in non-radiative recombination rates along the wire. The dominant Shockley-Read recombination rate can be extracted from ASE dynamics and can be directly related to charge carrier mobility and defect density. Employing ASE as a probe for defect densities provides a new sub-micron spatially resolved, contactless method for measurements of charge carrier mobility.

Bioluminescent signals spatially amplified by wavelength-specific diffusion through the shell of a marine snail.

PubMed

Deheyn, Dimitri D; Wilson, Nerida G

2011-07-22

Some living organisms produce visible light (bioluminescence) for intra- or interspecific visual communication. Here, we describe a remarkable bioluminescent adaptation in the marine snail Hinea brasiliana. This species produces a luminous display in response to mechanical stimulation caused by encounters with other motile organisms. The light is produced from discrete areas on the snail's body beneath the snail's shell, and must thus overcome this structural barrier to be viewed by an external receiver. The diffusion and transmission efficiency of the shell is greater than a commercial diffuser reference material. Most strikingly, the shell, although opaque and pigmented, selectively diffuses the blue-green wavelength of the species bioluminescence. This diffusion generates a luminous display that is enlarged relative to the original light source. This unusual shell thus allows spatially amplified outward transmission of light communication signals from the snail, while allowing the animal to remain safely inside its hard protective shell.

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

NASA Astrophysics Data System (ADS)

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

2012-03-01

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

Noninvasive observation of skeletal muscle contraction using near-infrared time-resolved reflectance and diffusing-wave spectroscopy

NASA Astrophysics Data System (ADS)

Belau, Markus; Ninck, Markus; Hering, Gernot; Spinelli, Lorenzo; Contini, Davide; Torricelli, Alessandro; Gisler, Thomas

2010-09-01

We introduce a method for noninvasively measuring muscle contraction in vivo, based on near-infrared diffusing-wave spectroscopy (DWS). The method exploits the information about time-dependent shear motions within the contracting muscle that are contained in the temporal autocorrelation function g(1)(τ,t) of the multiply scattered light field measured as a function of lag time, τ, and time after stimulus, t. The analysis of g(1)(τ,t) measured on the human M. biceps brachii during repetitive electrical stimulation, using optical properties measured with time-resolved reflectance spectroscopy, shows that the tissue dynamics giving rise to the speckle fluctuations can be described by a combination of diffusion and shearing. The evolution of the tissue Cauchy strain e(t) shows a strong correlation with the force, indicating that a significant part of the shear observed with DWS is due to muscle contraction. The evolution of the DWS decay time shows quantitative differences between the M. biceps brachii and the M. gastrocnemius, suggesting that DWS allows to discriminate contraction of fast- and slow-twitch muscle fibers.

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.

Selective sweeps in growing microbial colonies

NASA Astrophysics Data System (ADS)

Korolev, Kirill S.; Müller, Melanie J. I.; Karahan, Nilay; Murray, Andrew W.; Hallatschek, Oskar; Nelson, David R.

2012-04-01

Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction-diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction-diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays.

Retinal Oxygen: from animals to humans

PubMed Central

Linsenmeier, Robert A.; Zhang, Hao F.

2017-01-01

This article discusses retinal oxygenation and retinal metabolism by focusing on measurements made with two of the principal methods used to study O2 in the retina: measurements of PO2 with oxygen-sensitive microelectrodes in vivo in animals with a retinal circulation similar to that of humans, and oximetry, which can be used non-invasively in both animals and humans to measure O2 concentration in retinal vessels. Microelectrodes uniquely have high spatial resolution, allowing the mapping of PO2 in detail, and when combined with mathematical models of diffusion and consumption, they provide information about retinal metabolism. Mathematical models, grounded in experiments, can also be used to simulate situations that are not amenable to experimental study. New methods of oximetry, particularly photoacoustic ophthalmoscopy and visible light optical coherence tomography, provide depth-resolved methods that can separate signals from blood vessels and surrounding tissues, and can be combined with blood flow measures to determine metabolic rate. We discuss the effects on retinal oxygenation of illumination, hypoxia and hyperoxia, and describe retinal oxygenation in diabetes, retinal detachment, arterial occlusion, and macular degeneration. We explain how the metabolic measurements obtained from microelectrodes and imaging are different, and how they need to be brought together in the future. Finally, we argue for revisiting the clinical use of hyperoxia in ophthalmology, particularly in retinal arterial occlusions and retinal detachment, based on animal research and diffusion theory. PMID:28109737

The Role of Standardized and Study-specific Human Brain Diffusion Tensor Templates in Inter-subject Spatial Normalization

PubMed Central

Zhang, Shengwei; Arfanakis, Konstantinos

2012-01-01

Purpose To investigate the effect of standardized and study-specific human brain diffusion tensor templates on the accuracy of spatial normalization, without ignoring the important roles of data quality and registration algorithm effectiveness. Materials and Methods Two groups of diffusion tensor imaging (DTI) datasets, with and without visible artifacts, were normalized to two standardized diffusion tensor templates (IIT2, ICBM81) as well as study-specific templates, using three registration approaches. The accuracy of inter-subject spatial normalization was compared across templates, using the most effective registration technique for each template and group of data. Results It was demonstrated that, for DTI data with visible artifacts, the study-specific template resulted in significantly higher spatial normalization accuracy than standardized templates. However, for data without visible artifacts, the study-specific template and the standardized template of higher quality (IIT2) resulted in similar normalization accuracy. Conclusion For DTI data with visible artifacts, a carefully constructed study-specific template may achieve higher normalization accuracy than that of standardized templates. However, as DTI data quality improves, a high-quality standardized template may be more advantageous than a study-specific template, since in addition to high normalization accuracy, it provides a standard reference across studies, as well as automated localization/segmentation when accompanied by anatomical labels. PMID:23034880

Spatially dependent diffusion coefficient as a model for pH sensitive microgel particles in microchannels

PubMed Central

Pieprzyk, S.; Heyes, D. M.; Brańka, A. C.

2016-01-01

Solute transport and intermixing in microfluidic devices is strongly dependent on diffusional processes. Brownian Dynamics simulations of pressure-driven flow of model microgel particles in microchannels have been carried out to explore these processes and the factors that influence them. The effects of a pH-field that induces a spatial dependence of particle size and consequently the self-diffusion coefficient and system thermodynamic state were focused on. Simulations were carried out in 1D to represent some of the cross flow dependencies, and in 2D and 3D to include the effects of flow and particle concentration, with typical stripe-like diffusion coefficient spatial variations. In 1D, the mean square displacement and particle displacement probability distribution function agreed well with an analytically solvable model consisting of infinitely repulsive walls and a discontinuous pH-profile in the middle of the channel. Skew category Brownian motion and non-Gaussian dynamics were observed, which follows from correlations of step lengths in the system, and can be considered to be an example of so-called “diffusing diffusivity.” In Poiseuille flow simulations, the particles accumulated in regions of larger diffusivity and the largest particle concentration throughput was found when this region was in the middle of the channel. The trends in the calculated cross-channel diffusional behavior were found to be very similar in 2D and 3D. PMID:27795750

Cortical fibers orientation mapping using in-vivo whole brain 7 T diffusion MRI.

PubMed

Gulban, Omer F; De Martino, Federico; Vu, An T; Yacoub, Essa; Uğurbil, Kamil; Lenglet, Christophe

2018-05-10

Diffusion MRI of the cortical gray matter is challenging because the micro-environment probed by water molecules is much more complex than within the white matter. High spatial and angular resolutions are therefore necessary to uncover anisotropic diffusion patterns and laminar structures, which provide complementary (e.g. to anatomical and functional MRI) microstructural information about the cortex architectonic. Several ex-vivo and in-vivo MRI studies have recently addressed this question, however predominantly with an emphasis on specific cortical areas. There is currently no whole brain in-vivo data leveraging multi-shell diffusion MRI acquisition at high spatial resolution, and depth dependent analysis, to characterize the complex organization of cortical fibers. Here, we present unique in-vivo human 7T diffusion MRI data, and a dedicated cortical depth dependent analysis pipeline. We leverage the high spatial (1.05 mm isotropic) and angular (198 diffusion gradient directions) resolution of this whole brain dataset to improve cortical fiber orientations mapping, and study neurites (axons and/or dendrites) trajectories across cortical depths. Tangential fibers in superficial cortical depths and crossing fiber configurations in deep cortical depths are identified. Fibers gradually inserting into the gyral walls are visualized, which contributes to mitigating the gyral bias effect. Quantitative radiality maps and histograms in individual subjects and cortex-based aligned datasets further support our results. Copyright © 2018 Elsevier Inc. All rights reserved.

Functional imaging and assessment of the glucose diffusion rate in epithelial tissues in optical coherence tomography

NASA Astrophysics Data System (ADS)

Larin, K. V.; Tuchin, V. V.

2008-06-01

Functional imaging, monitoring and quantitative description of glucose diffusion in epithelial and underlying stromal tissues in vivo and controlling of the optical properties of tissues are extremely important for many biomedical applications including the development of noninvasive or minimally invasive glucose sensors as well as for therapy and diagnostics of various diseases, such as cancer, diabetic retinopathy, and glaucoma. Recent progress in the development of a noninvasive molecular diffusion biosensor based on optical coherence tomography (OCT) is described. The diffusion of glucose was studied in several epithelial tissues both in vitro and in vivo. Because OCT provides depth-resolved imaging of tissues with high in-depth resolution, the glucose diffusion is described not only as a function of time but also as a function of depth.

Effect of Annealing on Exciton Diffusion in a High Performance Small Molecule Organic Photovoltaic Material.

PubMed

Long, Yun; Hedley, Gordon J; Ruseckas, Arvydas; Chowdhury, Mithun; Roland, Thomas; Serrano, Luis A; Cooke, Graeme; Samuel, Ifor D W

2017-05-03

Singlet exciton diffusion was studied in the efficient organic photovoltaic electron donor material DTS(FBTTh 2 ) 2 . Three complementary time-resolved fluorescence measurements were performed: quenching in planar heterojunctions with an electron acceptor, exciton-exciton annihilation, and fluorescence depolarization. The average exciton diffusivity increases upon annealing from 1.6 × 10 -3 to 3.6 × 10 -3 cm 2 s -1 , resulting in an enhancement of the mean two-dimensional exciton diffusion length (L D = (4Dτ) 1/2 ) from 15 to 27 nm. About 30% of the excitons get trapped very quickly in as-cast films. The high exciton diffusion coefficient of the material leads to it being able to harvest excitons efficiently from large donor domains in bulk heterojunctions.

Effect of Annealing on Exciton Diffusion in a High Performance Small Molecule Organic Photovoltaic Material

PubMed Central

2017-01-01

Singlet exciton diffusion was studied in the efficient organic photovoltaic electron donor material DTS(FBTTh2)2. Three complementary time-resolved fluorescence measurements were performed: quenching in planar heterojunctions with an electron acceptor, exciton–exciton annihilation, and fluorescence depolarization. The average exciton diffusivity increases upon annealing from 1.6 × 10–3 to 3.6 × 10–3 cm2 s–1, resulting in an enhancement of the mean two-dimensional exciton diffusion length (LD = (4Dτ)1/2) from 15 to 27 nm. About 30% of the excitons get trapped very quickly in as-cast films. The high exciton diffusion coefficient of the material leads to it being able to harvest excitons efficiently from large donor domains in bulk heterojunctions. PMID:28358189