Morphological and Electrochemical Characterization of Nanostructured Li 4Ti 5O 12 Electrodes Using Multiple Imaging Mode Synchrotron X-ray Computed Tomography

DOE PAGES

Kashkooli, Ali Ghorbani; Foreman, Evan; Farhad, Siamak; ...

2017-09-21

In this study, synchrotron X-ray computed tomography has been utilized using two different imaging modes, absorption and Zernike phase contrast, to reconstruct the real three-dimensional (3D) morphology of nanostructured Li 4Ti 5O 12 (LTO) electrodes. The morphology of the high atomic number active material has been obtained using the absorption contrast mode, whereas the percolated solid network composed of active material and carbon-doped polymer binder domain (CBD) has been obtained using the Zernike phase contrast mode. The 3D absorption contrast image revealed that some LTO nano-particles tend to agglomerate and form secondary micro-sized particles with varying degrees of sphericity. Themore » tortuosity of electrode’s pore and solid phases were found to have directional dependence, different from Bruggeman’s tortuosity commonly used in macro-homogeneous models. The electrode’s heterogeneous structure was investigated by developing a numerical model to simulate galvanostatic discharge process using the Zernike phase contrast mode. The inclusion of CBD in the Zernike phase contrast results in an integrated percolated network of active material and CBD that is highly suited for continuum modeling. As a result, the simulation results highlight the importance of using the real 3D geometry since the spatial distribution of physical and electrochemical properties have a strong non-uniformity due to microstructural heterogeneities.« less

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

Krumeich, F., E-mail: krumeich@inorg.chem.ethz.ch; Mueller, E.; Wepf, R.A.

While HRTEM is the well-established method to characterize the structure of dodecagonal tantalum (vanadium) telluride quasicrystals and their periodic approximants, phase-contrast imaging performed on an aberration-corrected scanning transmission electron microscope (STEM) represents a favorable alternative. The (Ta,V){sub 151}Te{sub 74} clusters, the basic structural unit in all these phases, can be visualized with high resolution. A dependence of the image contrast on defocus and specimen thickness has been observed. In thin areas, the projected crystal potential is basically imaged with either dark or bright contrast at two defocus values close to Scherzer defocus as confirmed by image simulations utilizing the principlemore » of reciprocity. Models for square-triangle tilings describing the arrangement of the basic clusters can be derived from such images. - Graphical abstract: PC-STEM image of a (Ta,V){sub 151}Te{sub 74} cluster. Highlights: Black-Right-Pointing-Pointer C{sub s}-corrected STEM is applied for the characterization of dodecagonal quasicrystals. Black-Right-Pointing-Pointer The projected potential of the structure is mirrored in the images. Black-Right-Pointing-Pointer Phase-contrast STEM imaging depends on defocus and thickness. Black-Right-Pointing-Pointer For simulations of phase-contrast STEM images, the reciprocity theorem is applicable.« less

Quantitative breast tissue characterization using grating-based x-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Willner, M.; Herzen, J.; Grandl, S.; Auweter, S.; Mayr, D.; Hipp, A.; Chabior, M.; Sarapata, A.; Achterhold, K.; Zanette, I.; Weitkamp, T.; Sztrókay, A.; Hellerhoff, K.; Reiser, M.; Pfeiffer, F.

2014-04-01

X-ray phase-contrast imaging has received growing interest in recent years due to its high capability in visualizing soft tissue. Breast imaging became the focus of particular attention as it is considered the most promising candidate for a first clinical application of this contrast modality. In this study, we investigate quantitative breast tissue characterization using grating-based phase-contrast computed tomography (CT) at conventional polychromatic x-ray sources. Different breast specimens have been scanned at a laboratory phase-contrast imaging setup and were correlated to histopathology. Ascertained tumor types include phylloides tumor, fibroadenoma and infiltrating lobular carcinoma. Identified tissue types comprising adipose, fibroglandular and tumor tissue have been analyzed in terms of phase-contrast Hounsfield units and are compared to high-quality, high-resolution data obtained with monochromatic synchrotron radiation, as well as calculated values based on tabulated tissue properties. The results give a good impression of the method’s prospects and limitations for potential tumor detection and the associated demands on such a phase-contrast breast CT system. Furthermore, the evaluated quantitative tissue values serve as a reference for simulations and the design of dedicated phantoms for phase-contrast mammography.

A feasibility study of X-ray phase-contrast mammographic tomography at the Imaging and Medical beamline of the Australian Synchrotron.

PubMed

Nesterets, Yakov I; Gureyev, Timur E; Mayo, Sheridan C; Stevenson, Andrew W; Thompson, Darren; Brown, Jeremy M C; Kitchen, Marcus J; Pavlov, Konstantin M; Lockie, Darren; Brun, Francesco; Tromba, Giuliana

2015-11-01

Results are presented of a recent experiment at the Imaging and Medical beamline of the Australian Synchrotron intended to contribute to the implementation of low-dose high-sensitivity three-dimensional mammographic phase-contrast imaging, initially at synchrotrons and subsequently in hospitals and medical imaging clinics. The effect of such imaging parameters as X-ray energy, source size, detector resolution, sample-to-detector distance, scanning and data processing strategies in the case of propagation-based phase-contrast computed tomography (CT) have been tested, quantified, evaluated and optimized using a plastic phantom simulating relevant breast-tissue characteristics. Analysis of the data collected using a Hamamatsu CMOS Flat Panel Sensor, with a pixel size of 100 µm, revealed the presence of propagation-based phase contrast and demonstrated significant improvement of the quality of phase-contrast CT imaging compared with conventional (absorption-based) CT, at medically acceptable radiation doses.

High-efficiency aperiodic two-dimensional high-contrast-grating hologram

NASA Astrophysics Data System (ADS)

Qiao, Pengfei; Zhu, Li; Chang-Hasnain, Connie J.

2016-03-01

High efficiency phase holograms are designed and implemented using aperiodic two-dimensional (2D) high-contrast gratings (HCGs). With our design algorithm and an in-house developed rigorous coupled-wave analysis (RCWA) package for periodic 2D HCGs, the structural parameters are obtained to achieve a full 360-degree phase-tuning range of the reflected or transmitted wave, while maintaining the power efficiency above 90%. For given far-field patterns or 3D objects to reconstruct, we can generate the near-field phase distribution through an iterative process. The aperiodic HCG phase plates we design for holograms are pixelated, and the local geometric parameters for each pixel to achieve desired phase alternation are extracted from our periodic HCG designs. Our aperiodic HCG holograms are simulated using the 3D finite-difference time-domain method. The simulation results confirm that the desired far-field patterns are successfully produced under illumination at the designed wavelength. The HCG holograms are implemented on the quartz wafers, using amorphous silicon as the high-index material. We propose HCG designs at both visible and infrared wavelengths, and our simulation confirms the reconstruction of 3D objects. The high-contrast gratings allow us to realize low-cost, compact, flat, and integrable holograms with sub-micrometer thicknesses.

Noise in x-ray grating-based phase-contrast imaging

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

Weber, Thomas; Bartl, Peter; Bayer, Florian

Purpose: Grating-based x-ray phase-contrast imaging is a fast developing new modality not only for medical imaging, but as well for other fields such as material sciences. While these many possible applications arise, the knowledge of the noise behavior is essential. Methods: In this work, the authors used a least squares fitting algorithm to calculate the noise behavior of the three quantities absorption, differential phase, and dark-field image. Further, the calculated error formula of the differential phase image was verified by measurements. Therefore, a Talbot interferometer was setup, using a microfocus x-ray tube as source and a Timepix detector for photonmore » counting. Additionally, simulations regarding this topic were performed. Results: It turned out that the variance of the reconstructed phase is only dependent of the total number of photons used to generate the phase image and the visibility of the experimental setup. These results could be evaluated in measurements as well as in simulations. Furthermore, the correlation between absorption and dark-field image was calculated. Conclusions: These results provide the understanding of the noise characteristics of grating-based phase-contrast imaging and will help to improve image quality.« less

A Rotational Pressure-Correction Scheme for Incompressible Two-Phase Flows with Open Boundaries

PubMed Central

Dong, S.; Wang, X.

2016-01-01

Two-phase outflows refer to situations where the interface formed between two immiscible incompressible fluids passes through open portions of the domain boundary. We present several new forms of open boundary conditions for two-phase outflow simulations within the phase field framework, as well as a rotational pressure correction based algorithm for numerically treating these open boundary conditions. Our algorithm gives rise to linear algebraic systems for the velocity and the pressure that involve only constant and time-independent coefficient matrices after discretization, despite the variable density and variable viscosity of the two-phase mixture. By comparing simulation results with theory and the experimental data, we show that the method produces physically accurate results. We also present numerical experiments to demonstrate the long-term stability of the method in situations where large density contrast, large viscosity contrast, and backflows occur at the two-phase open boundaries. PMID:27163909

Effects of Optical-density and Phase Dispersion of an Imperfect Band-limited Occulting Mask on the Broadband Performance of a TPF Coronagraph

NASA Technical Reports Server (NTRS)

Sidiek, Erkin; Balasubramanian, Kunjithapatham

2007-01-01

Practical image-plane occulting masks required by high-contrast imaging systems such as the TPF-Coronagraph introduce phase errors into the transmitting beam., or, equivalently, diffracts the residual starlight into the area of the final image plane used for detecting exo-planets. Our group at JPL has recently proposed spatially Profiled metal masks that can be designed to have zero parasitic phase at the center wavelength of the incoming broadband light with small amounts of' 00 and phase dispersions at other wavelengths. Work is currently underway to design. fabricate and characterize such image-plane masks. In order to gain some understanding on the behaviors of these new imperfect band-limited occulting masks and clarify how such masks utilizing different metals or alloys compare with each other, we carried out some modeling and simulations on the contrast performance of the high-contrast imaging testbed (HCIT) at .JPL. In this paper we describe the details of our simulations and present our results.

Simulations of multi-contrast x-ray imaging using near-field speckles

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

Zdora, Marie-Christine; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom and Department of Physics & Astronomy, University College London, London, WC1E 6BT; Thibault, Pierre

2016-01-28

X-ray dark-field and phase-contrast imaging using near-field speckles is a novel technique that overcomes limitations inherent in conventional absorption x-ray imaging, i.e. poor contrast for features with similar density. Speckle-based imaging yields a wealth of information with a simple setup tolerant to polychromatic and divergent beams, and simple data acquisition and analysis procedures. Here, we present a simulation software used to model the image formation with the speckle-based technique, and we compare simulated results on a phantom sample with experimental synchrotron data. Thorough simulation of a speckle-based imaging experiment will help for better understanding and optimising the technique itself.

Improved image reconstruction of low-resolution multichannel phase contrast angiography

PubMed Central

P. Krishnan, Akshara; Joy, Ajin; Paul, Joseph Suresh

2016-01-01

Abstract. In low-resolution phase contrast magnetic resonance angiography, the maximum intensity projected channel images will be blurred with consequent loss of vascular details. The channel images are enhanced using a stabilized deblurring filter, applied to each channel prior to combining the individual channel images. The stabilized deblurring is obtained by the addition of a nonlocal regularization term to the reverse heat equation, referred to as nonlocally stabilized reverse diffusion filter. Unlike reverse diffusion filter, which is highly unstable and blows up noise, nonlocal stabilization enhances intensity projected parallel images uniformly. Application to multichannel vessel enhancement is illustrated using both volunteer data and simulated multichannel angiograms. Robustness of the filter applied to volunteer datasets is shown using statistically validated improvement in flow quantification. Improved performance in terms of preserving vascular structures and phased array reconstruction in both simulated and real data is demonstrated using structureness measure and contrast ratio. PMID:26835501

Using the phase-space imager to analyze partially coherent imaging systems: bright-field, phase contrast, differential interference contrast, differential phase contrast, and spiral phase contrast

NASA Astrophysics Data System (ADS)

Mehta, Shalin B.; Sheppard, Colin J. R.

2010-05-01

Various methods that use large illumination aperture (i.e. partially coherent illumination) have been developed for making transparent (i.e. phase) specimens visible. These methods were developed to provide qualitative contrast rather than quantitative measurement-coherent illumination has been relied upon for quantitative phase analysis. Partially coherent illumination has some important advantages over coherent illumination and can be used for measurement of the specimen's phase distribution. However, quantitative analysis and image computation in partially coherent systems have not been explored fully due to the lack of a general, physically insightful and computationally efficient model of image formation. We have developed a phase-space model that satisfies these requirements. In this paper, we employ this model (called the phase-space imager) to elucidate five different partially coherent systems mentioned in the title. We compute images of an optical fiber under these systems and verify some of them with experimental images. These results and simulated images of a general phase profile are used to compare the contrast and the resolution of the imaging systems. We show that, for quantitative phase imaging of a thin specimen with matched illumination, differential phase contrast offers linear transfer of specimen information to the image. We also show that the edge enhancement properties of spiral phase contrast are compromised significantly as the coherence of illumination is reduced. The results demonstrate that the phase-space imager model provides a useful framework for analysis, calibration, and design of partially coherent imaging methods.

Tandem-pulsed acousto-optics: an analytical framework of modulated high-contrast speckle patterns.

PubMed

Resink, S G; Steenbergen, W

2015-06-07

Recently we presented acousto-optic (AO) probing of scattering media using addition or subtraction of speckle patterns due to tandem nanosecond pulses. Here we present a theoretical framework for ideal (polarized, noise-free) speckle patterns with unity contrast that links ultrasound-induced optical phase modulation, the fraction of light that is tagged by ultrasound, speckle contrast, mean square difference of speckle patterns and the contrast of the summation of speckle patterns acquired at different ultrasound phases. We derive the important relations from basic assumptions and definitions, and then validate them with simulations. For ultrasound-generated phase modulation angles below 0.7 rad (assuming uniform modulation), we are now able to relate speckle pattern statistics to the acousto-optic phase modulation. Hence our theory allows quantifying speckle observations in terms of ultrasonically tagged fractions of light for near-unity-contrast speckle patterns.

Potential of phase contrast x-ray imaging for detecting tumors in dense breast: initial phantom studies

NASA Astrophysics Data System (ADS)

Omoumi, Farid H.; Wu, Di; Guo, Yuran; Ghani, Muhammad U.; Li, Yuhua; Boyce, Kari E.; Liu, Hong

2018-02-01

The objective of this study is to demonstrate the potential of using the High-energy in-line phase contrast x-ray imaging to detect lesions that are indistinguishable by conventional x-ray mammography but are detectable by supplemental ultrasound screening within dense breasts. For this study, a custom-made prototype x-ray/ultrasound dualmodality phantom that mimics dense breast is created to include embedded carbon fiber disks with multiple diameters and thicknesses. The phase contrast image is acquired using a prototype at 120kVp, 67μA, exposure time of 16.7sec and focal spot size of 18.3μm with average glandular dose (AGD) of 0.3mGy under a geometric magnification of 2.48. The conventional x-ray image is acquired with a bench top system operating at 40kVp, 300μA, exposure time of 50sec and same AGD. The results demonstrate that conventional x-ray imaging is unable to detect any of the carbon fiber disks, while phase contrast imaging and ultrasonography are able to detect most or all of the disks under the applied experimental conditions. These results illustrate phase contrast imaging is capable of detecting targets in a dual-modality phantom which simulates lesions in dense breast tissue, when the simulated lesions are not distinguishable by conventional mammography. Therefore mammographic screening with phase contrast technique could eventually replace both x-ray and ultrasonography for screening detection of small lesions with microcalcification in dense breasts where pathologic lesions are masked due to highly glandular tissue. These results encourage further investigation using high glandular density phantoms to further evaluate the effectiveness of phase contrast imaging as a single modality test, which combines the advantages of both x-ray and ultrasound imaging in cancer screening of patients with dense breasts.

Wide-field phase imaging for the endoscopic detection of dysplasia and early-stage esophageal cancer

NASA Astrophysics Data System (ADS)

Fitzpatrick, C. R. M.; Gordon, G. S. D.; Sawyer, T. W.; Wilkinson, T. D.; Bohndiek, S. E.

2018-02-01

Esophageal cancer has a 5-year survival rate below 20%, but can be curatively resected if it is detected early. At present, poor contrast for early lesions in white light imaging leads to a high miss rate in standard-of- care endoscopic surveillance. Early lesions in the esophagus, referred to as dysplasia, are characterized by an abundance of abnormal cells with enlarged nuclei. This tissue has a different refractive index profile to healthy tissue, which results in different light scattering properties and provides a source of endogenous contrast that can be exploited for advanced endoscopic imaging. For example, point measurements of such contrast can be made with scattering spectroscopy, while optical coherence tomography generates volumetric data. However, both require specialist interpretation for diagnostic decision making. We propose combining wide-field phase imaging with existing white light endoscopy in order to provide enhanced contrast for dysplasia and early-stage cancer in an image format that is familiar to endoscopists. Wide-field phase imaging in endoscopy can be achieved using coherent illumination combined with phase retrieval algorithms. Here, we present the design and simulation of a benchtop phase imaging system that is compatible with capsule endoscopy. We have undertaken preliminary optical modelling of the phase imaging setup, including aberration correction simulations and an investigation into distinguishing between different tissue phantom scattering coefficients. As our approach is based on phase retrieval rather than interferometry, it is feasible to realize a device with low-cost components for future clinical implementation.

Low Dose High Energy X-ray In-Line Phase Sensitive Imaging Prototype: Investigation of Optimal Geometric Conditions and Design Parameters

PubMed Central

Ghani, Muhammad. U.; Yan, Aimin; Wong, Molly. D.; Li, Yuhua; Ren, Liqiang; Wu, Xizeng; Liu, Hong

2016-01-01

The objective of this study was to investigate the optimization of a high energy in-line phase sensitive x-ray imaging prototype under different geometric and operating conditions for mammography application. A phase retrieval algorithm based on phase attenuation duality (PAD) was applied to the phase contrast images acquired by the prototype. Imaging performance was investigated at four magnification values of 1.67, 2, 2.5 and 3 using an acrylic edge, an American College of Radiology (ACR) mammography phantom and contrast detail (CD) phantom with tube potentials of 100, 120 and 140 kVp. The ACR and CD images were acquired at the same mean glandular dose (MGD) of 1.29 mGy with a computed radiography (CR) detector of 43.75 µm pixel pitch at a fixed source to image distance (SID) of 170 cm. The x-ray tube focal spot size was kept constant as 7 µm while a 2.5 mm thick aluminum (Al) filter was used for beam hardening. The performance of phase contrast and phase retrieved images were compared with computer simulations based on the relative phase contrast factor (RPF) at high x-ray energies. The imaging results showed that the x-ray tube operated at 100 kVp under the magnification of 2.5 exhibits superior imaging performance which is in accordance to the computer simulations. As compared to the phase contrast images, the phase retrieved images of the ACR and CD phantoms demonstrated improved imaging contrast and target discrimination. We compared the CD phantom images acquired in conventional contact mode with and without the anti-scatter grid using the same prototype at 1.295 mGy and 2.59 mGy using 40 kVp, a 25 µm rhodium (Rh) filter. At the same radiation dose, the phase sensitive images provided improved detection capabilities for both the large and small discs, while compared to the double dose image acquired in conventional mode, the observer study also indicated that the phase sensitive images provided improved detection capabilities for the large discs. This study therefore validates the potential of using high energy phase contrast x-ray imaging to improve lesion detection and reduce radiation dose for clinical applications such as mammography. PMID:26756405

Comparison of Simulated Contrast Performance of Different Phase Induced Amplitude Apodization (PIAA) Coronagraph Configurations

NASA Technical Reports Server (NTRS)

Sidick, Erkin; Kern, Brian; Kuhnert, Andreas; Shaklan, Stuart

2013-01-01

We compare the broadband contrast performances of several Phase Induced Amplitude Apodization (PIAA) coronagraph configurations through modeling and simulations. The basic optical design of the PIAA coronagraph is the same as NASA's High Contrast Imaging Testbed (HCIT) setup at the Jet Propulsion Laboratory (JPL). Using a deformable mirror and a broadband wavefront sensing and control algorithm, we create a "dark hole" in the broadband point-spread function (PSF) with an inner working angle (IWA) of 2(f lambda/D)(sub sky). We evaluate two systems in parallel. One is a perfect system having a design PIAA output amplitude and not having any wavefront error at its exit-pupil. The other is a realistic system having a design PIAA output amplitude and the measured residual wavefront error. We also investigate the effect of Lyot stops of various sizes when a postapodizer is and is not present. Our simulations show that the best 7.5%-broadband contrast value achievable with the current PIAA coronagraph is approximately 1.5x10(exp -8).

Approximated transport-of-intensity equation for coded-aperture x-ray phase-contrast imaging.

PubMed

Das, Mini; Liang, Zhihua

2014-09-15

Transport-of-intensity equations (TIEs) allow better understanding of image formation and assist in simplifying the "phase problem" associated with phase-sensitive x-ray measurements. In this Letter, we present for the first time to our knowledge a simplified form of TIE that models x-ray differential phase-contrast (DPC) imaging with coded-aperture (CA) geometry. The validity of our approximation is demonstrated through comparison with an exact TIE in numerical simulations. The relative contributions of absorption, phase, and differential phase to the acquired phase-sensitive intensity images are made readily apparent with the approximate TIE, which may prove useful for solving the inverse phase-retrieval problem associated with these CA geometry based DPC.

Phase imaging in brain using SWIFT

NASA Astrophysics Data System (ADS)

Lehto, Lauri Juhani; Garwood, Michael; Gröhn, Olli; Corum, Curtis Andrew

2015-03-01

The majority of MRI phase imaging is based on gradient recalled echo (GRE) sequences. This work studies phase contrast behavior due to small off-resonance frequency offsets in brain using SWIFT, a FID-based sequence with nearly zero acquisition delay. 1D simulations and a phantom study were conducted to describe the behavior of phase accumulation in SWIFT. Imaging experiments of known brain phase contrast properties were conducted in a perfused rat brain comparing GRE and SWIFT. Additionally, a human brain sample was imaged. It is demonstrated how SWIFT phase is orientation dependent and correlates well with GRE, linking SWIFT phase to similar off-resonance sources as GRE. The acquisition time is shown to be analogous to TE for phase accumulation time. Using experiments with and without a magnetization transfer preparation, the likely effect of myelin water pool contribution is seen as a phase increase for all acquisition times. Due to the phase accumulation during acquisition, SWIFT phase contrast can be sensitized to small frequency differences between white and gray matter using low acquisition bandwidths.

Redefining the lower statistical limit in x-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Marschner, M.; Birnbacher, L.; Willner, M.; Chabior, M.; Fehringer, A.; Herzen, J.; Noël, P. B.; Pfeiffer, F.

2015-03-01

Phase-contrast x-ray computed tomography (PCCT) is currently investigated and developed as a potentially very interesting extension of conventional CT, because it promises to provide high soft-tissue contrast for weakly absorbing samples. For data acquisition several images at different grating positions are combined to obtain a phase-contrast projection. For short exposure times, which are necessary for lower radiation dose, the photon counts in a single stepping position are very low. In this case, the currently used phase-retrieval does not provide reliable results for some pixels. This uncertainty results in statistical phase wrapping, which leads to a higher standard deviation in the phase-contrast projections than theoretically expected. For even lower statistics, the phase retrieval breaks down completely and the phase information is lost. New measurement procedures rely on a linear approximation of the sinusoidal phase stepping curve around the zero crossings. In this case only two images are acquired to obtain the phase-contrast projection. The approximation is only valid for small phase values. However, typically nearly all pixels are within this regime due to the differential nature of the signal. We examine the statistical properties of a linear approximation method and illustrate by simulation and experiment that the lower statistical limit can be redefined using this method. That means that the phase signal can be retrieved even with very low photon counts and statistical phase wrapping can be avoided. This is an important step towards enhanced image quality in PCCT with very low photon counts.

Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)].

PubMed

Miller, Thomas F; Manolopoulos, David E; Madden, Paul A; Konieczny, Martin; Oberhofer, Harald

2005-02-01

We show that the two phase points considered in the recent simulations of liquid para hydrogen by Hone and Voth lie in the liquid-vapor coexistence region of a purely classical molecular dynamics simulation. By contrast, their phase point for ortho deuterium was in the one-phase liquid region for both classical and quantum simulations. These observations are used to account for their report that quantum mechanical effects enhance the diffusion in liquid para hydrogen and decrease it in ortho deuterium.(c) 2005 American Institute of Physics.

Estimating the hemodynamic impact of interventional treatments of aneurysms: numerical simulation with experimental validation: technical case report.

PubMed

Acevedo-Bolton, Gabriel; Jou, Liang-Der; Dispensa, Bradley P; Lawton, Michael T; Higashida, Randall T; Martin, Alastair J; Young, William L; Saloner, David

2006-08-01

The goal of this study was to use phase-contrast magnetic resonance imaging and computational fluid dynamics to estimate the hemodynamic outcome that might result from different interventional options for treating a patient with a giant fusiform aneurysm. We followed a group of patients with giant intracranial aneurysms who have no clear surgical options. One patient demonstrated dramatic aneurysm growth and was selected for further analysis. The aneurysm geometry and input and output flow conditions were measured with contrast-enhanced magnetic resonance angiography and phase-contrast magnetic resonance imaging. The data was imported into a computational fluid dynamics program and the velocity fields and wall shear stress distributions were calculated for the presenting physiological condition and for cases in which the opposing vertebral arteries were either occluded or opened. These models were validated with in vitro flow experiments using a geometrically exact silicone flow phantom. Simulation indicated that altering the flow ratio in the two vertebrals would deflect the main blood jet into the aneurysm belly, and that this would likely reduce the extent of the region of low wall shear stress in the growth zone. Computational fluid dynamics flow simulations in a complex patient-specific aneurysm geometry were validated by in vivo and in vitro phase-contrast magnetic resonance imaging, and were shown to be useful in modeling the likely hemodynamic impact of interventional treatment of the aneurysm.

Isotropic differential phase contrast microscopy for quantitative phase bio-imaging.

PubMed

Chen, Hsi-Hsun; Lin, Yu-Zi; Luo, Yuan

2018-05-16

Quantitative phase imaging (QPI) has been investigated to retrieve optical phase information of an object and applied to biological microscopy and related medical studies. In recent examples, differential phase contrast (DPC) microscopy can recover phase image of thin sample under multi-axis intensity measurements in wide-field scheme. Unlike conventional DPC, based on theoretical approach under partially coherent condition, we propose a new method to achieve isotropic differential phase contrast (iDPC) with high accuracy and stability for phase recovery in simple and high-speed fashion. The iDPC is simply implemented with a partially coherent microscopy and a programmable thin-film transistor (TFT) shield to digitally modulate structured illumination patterns for QPI. In this article, simulation results show consistency of our theoretical approach for iDPC under partial coherence. In addition, we further demonstrate experiments of quantitative phase images of a standard micro-lens array, as well as label-free live human cell samples. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative characterization of edge enhancement in phase contrast x-ray imaging.

PubMed

Monnin, P; Bulling, S; Hoszowska, J; Valley, J F; Meuli, R; Verdun, F R

2004-06-01

The aim of this study was to model the edge enhancement effect in in-line holography phase contrast imaging. A simple analytical approach was used to quantify refraction and interference contrasts in terms of beam energy and imaging geometry. The model was applied to predict the peak intensity and frequency of the edge enhancement for images of cylindrical fibers. The calculations were compared with measurements, and the relationship between the spatial resolution of the detector and the amplitude of the phase contrast signal was investigated. Calculations using the analytical model were in good agreement with experimental results for nylon, aluminum and copper wires of 50 to 240 microm diameter, and with numerical simulations based on Fresnel-Kirchhoff theory. A relationship between the defocusing distance and the pixel size of the image detector was established. This analytical model is a useful tool for optimizing imaging parameters in phase contrast in-line holography, including defocusing distance, detector resolution and beam energy.

MTF evaluation of in-line phase contrast imaging system

NASA Astrophysics Data System (ADS)

Sun, Xiaoran; Gao, Feng; Zhao, Huijuan; Zhang, Limin; Li, Jiao; Zhou, Zhongxing

2017-02-01

X-ray phase contrast imaging (XPCI) is a novel method that exploits the phase shift for the incident X-ray to form an image. Various XPCI methods have been proposed, among which, in-line phase contrast imaging (IL-PCI) is regarded as one of the most promising clinical methods. The contrast of the interface is enhanced due to the introduction of the boundary fringes in XPCI, thus it is generally used to evaluate the image quality of XPCI. But the contrast is a comprehensive index and it does not reflect the information of image quality in the frequency range. The modulation transfer function (MTF), which is the Fourier transform of the system point spread function, is recognized as the metric to characterize the spatial response of conventional X-ray imaging system. In this work, MTF is introduced into the image quality evaluation of the IL-PCI system. Numerous simulations based on Fresnel - Kirchhoff diffraction theory are performed with varying system settings and the corresponding MTFs were calculated for comparison. The results show that MTF can provide more comprehensive information of image quality comparing to contrast in IL-PCI.

Analyser-based mammography using single-image reconstruction.

PubMed

Briedis, Dahliyani; Siu, Karen K W; Paganin, David M; Pavlov, Konstantin M; Lewis, Rob A

2005-08-07

We implement an algorithm that is able to decode a single analyser-based x-ray phase-contrast image of a sample, converting it into an equivalent conventional absorption-contrast radiograph. The algorithm assumes the projection approximation for x-ray propagation in a single-material object embedded in a substrate of approximately uniform thickness. Unlike the phase-contrast images, which have both directional bias and a bias towards edges present in the sample, the reconstructed images are directly interpretable in terms of the projected absorption coefficient of the sample. The technique was applied to a Leeds TOR[MAM] phantom, which is designed to test mammogram quality by the inclusion of simulated microcalcifications, filaments and circular discs. This phantom was imaged at varying doses using three modalities: analyser-based synchrotron phase-contrast images converted to equivalent absorption radiographs using our algorithm, slot-scanned synchrotron imaging and imaging using a conventional mammography unit. Features in the resulting images were then assigned a quality score by volunteers. The single-image reconstruction method achieved higher scores at equivalent and lower doses than the conventional mammography images, but no improvement of visualization of the simulated microcalcifications, and some degradation in image quality at reduced doses for filament features.

Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation.

PubMed

Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

2017-02-21

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation

PubMed Central

Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

2017-01-01

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance. PMID:28772570

Phase gradient imaging for positive contrast generation to superparamagnetic iron oxide nanoparticle-labeled targets in magnetic resonance imaging.

PubMed

Zhu, Haitao; Demachi, Kazuyuki; Sekino, Masaki

2011-09-01

Positive contrast imaging methods produce enhanced signal at large magnetic field gradient in magnetic resonance imaging. Several postprocessing algorithms, such as susceptibility gradient mapping and phase gradient mapping methods, have been applied for positive contrast generation to detect the cells targeted by superparamagnetic iron oxide nanoparticles. In the phase gradient mapping methods, smoothness condition has to be satisfied to keep the phase gradient unwrapped. Moreover, there has been no discussion about the truncation artifact associated with the algorithm of differentiation that is performed in k-space by the multiplication with frequency value. In this work, phase gradient methods are discussed by considering the wrapping problem when the smoothness condition is not satisfied. A region-growing unwrapping algorithm is used in the phase gradient image to solve the problem. In order to reduce the truncation artifact, a cosine function is multiplied in the k-space to eliminate the abrupt change at the boundaries. Simulation, phantom and in vivo experimental results demonstrate that the modified phase gradient mapping methods may produce improved positive contrast effects by reducing truncation or wrapping artifacts. Copyright © 2011 Elsevier Inc. All rights reserved.

A beam hardening and dispersion correction for x-ray dark-field radiography.

PubMed

Pelzer, Georg; Anton, Gisela; Horn, Florian; Rieger, Jens; Ritter, André; Wandner, Johannes; Weber, Thomas; Michel, Thilo

2016-06-01

X-ray dark-field imaging promises information on the small angle scattering properties even of large samples. However, the dark-field image is correlated with the object's attenuation and phase-shift if a polychromatic x-ray spectrum is used. A method to remove part of these correlations is proposed. The experimental setup for image acquisition was modeled in a wave-field simulation to quantify the dark-field signals originating solely from a material's attenuation and phase-shift. A calibration matrix was simulated for ICRU46 breast tissue. Using the simulated data, a dark-field image of a human mastectomy sample was corrected for the finger print of attenuation- and phase-image. Comparing the simulated, attenuation-based dark-field values to a phantom measurement, a good agreement was found. Applying the proposed method to mammographic dark-field data, a reduction of the dark-field background and anatomical noise was achieved. The contrast between microcalcifications and their surrounding background was increased. The authors show that the influence of and dispersion can be quantified by simulation and, thus, measured image data can be corrected. The simulation allows to determine the corresponding dark-field artifacts for a wide range of setup parameters, like tube-voltage and filtration. The application of the proposed method to mammographic dark-field data shows an increase in contrast compared to the original image, which might simplify a further image-based diagnosis.

Simulation of a compact analyzer-based imaging system with a regular x-ray source

NASA Astrophysics Data System (ADS)

Caudevilla, Oriol; Zhou, Wei; Stoupin, Stanislav; Verman, Boris; Brankov, J. G.

2017-03-01

Analyzer-based Imaging (ABI) belongs to a broader family of phase-contrast (PC) X-ray techniques. PC measures X-ray deflection phenomena when interacting with a sample, which is known to provide higher contrast images of soft tissue than other X-ray methods. This is of high interest in the medical field, in particular for mammogram applications. This paper presents a simulation tool for table-top ABI systems using a conventional polychromatic X-ray source.

Measurement of absolute regional lung air volumes from near-field x-ray speckles.

PubMed

Leong, Andrew F T; Paganin, David M; Hooper, Stuart B; Siew, Melissa L; Kitchen, Marcus J

2013-11-18

Propagation-based phase contrast x-ray (PBX) imaging yields high contrast images of the lung where airways that overlap in projection coherently scatter the x-rays, giving rise to a speckled intensity due to interference effects. Our previous works have shown that total and regional changes in lung air volumes can be accurately measured from two-dimensional (2D) absorption or phase contrast images when the subject is immersed in a water-filled container. In this paper we demonstrate how the phase contrast speckle patterns can be used to directly measure absolute regional lung air volumes from 2D PBX images without the need for a water-filled container. We justify this technique analytically and via simulation using the transport-of-intensity equation and calibrate the technique using our existing methods for measuring lung air volume. Finally, we show the full capabilities of this technique for measuring regional differences in lung aeration.

Feasibility of measuring renal blood flow by phase-contrast magnetic resonance imaging in patients with autosomal dominant polycystic kidney disease.

PubMed

Spithoven, E M; Meijer, E; Borns, C; Boertien, W E; Gaillard, C A J M; Kappert, P; Greuter, M J W; van der Jagt, E; Vart, P; de Jong, P E; Gansevoort, R T

2016-03-01

Renal blood flow (RBF) has been shown to predict disease progression in autosomal dominant polycystic kidney disease (ADPKD). We investigated the feasibility and accuracy of phase-contrast RBF by MRI (RBFMRI) in ADPKD patients with a wide range of estimated glomerular filtration rate (eGFR) values. First, we validated RBFMRI measurement using phantoms simulating renal artery hemodynamics. Thereafter, we investigated in a test-set of 21 patients intra- and inter-observer coefficient of variation of RBFMRI. After validation, we measured RBFMRI in a cohort of 91 patients and compared the variability explained by characteristics indicative for disease severity for RBFMRI and RBF measured by continuous hippuran infusion. The correlation in flow measurement using phantoms by phase-contrast MRI was high and fluid collection was high (CCC=0.969). Technical problems that precluded RBFMRI measurement occurred predominantly in patients with a lower eGFR (34% vs. 16%). In subjects with higher eGFRs, variability in RBF explained by disease characteristics was similar for RBFMRI compared to RBFHip, whereas in subjects with lower eGFRs, this was significantly less for RBFMRI. Our study shows that RBF can be measured accurately in ADPKD patients by phase-contrast, but this technique may be less feasible in subjects with a lower eGFR. Renal blood flow (RBF) can be accurately measured by phase-contrast MRI in ADPKD patients. RBF measured by phase-contrast is associated with ADPKD disease severity. RBF measurement by phase-contrast MRI may be less feasible in patients with an impaired eGFR.

An active coronagraph using a liquid crystal array for exoplanet imaging: principle and testing

NASA Astrophysics Data System (ADS)

Zhang, Xi; Ren, De-Qing; Zhu, Yong-Tian; Dou, Jiang-Pei

2012-05-01

High-contrast imaging coronagraphs, used for the detection of exoplanets, have always adopted passive coronagraph optical components. It is therefore impossible to actively optimize the coronagraphs to achieve their best performance. To solve this problem, we propose a novel high-contrast imaging coronagraph which combines a liquid crystal array (LCA) for active pupil apodization and a deformable mirror (DM) for phase correction. The LCA we use is an amplitude-only spatial light modulator. The LCA is well calibrated and compensates for its amplitude non-uniformity and nonlinear intensity responsivity. We measured the imaging contrasts of the coronagraph system with the LCA only and without the DM deployed. Imaging contrasts of 10-4 and 10-5 can be reached at an inner working angular distance of 2.5 and 5λ/D, respectively. A simulation shows that the phase errors on the coronagraph pupil limit the contrast performance. The contrast could be further improved if a DM is deployed to correct the phase errors induced by the LCA and coronagraph optics.

Comparison of High-Fidelity Simulation Versus Didactic Instruction as a Reinforcement Intervention in a Comprehensive Curriculum for Radiology Trainees in Learning Contrast Reaction Management: Does It Matter How We Refresh?

PubMed

Picard, Melissa; Curry, Nancy; Collins, Heather; Soma, LaShonda; Hill, Jeanne

2015-10-01

Simulation-based training has been shown to be a useful adjunct to standard didactic lecture in teaching residents appropriate management of adverse contrast reactions. In addition, it has been suggested that a biannual refresher is needed; however, the type of refresher education has not been assessed. This was a prospective study involving 31 radiology residents across all years in a university program. All residents underwent standard didactic lecture followed by high-fidelity simulation-based training. At approximately 6 months, residents were randomized into a didactic versus simulation group for a refresher. At approximately 9 months, all residents returned to the simulation center for performance testing. Knowledge and confidence assessments were obtained from all participants before and after each phase. Performance testing was obtained at each simulation session and scored based on predefined critical actions. There was significant improvement in knowledge (P < .002) and confidence (P < .001) after baseline education of combined didactic and simulation-based training. There was no statistical difference between the simulation and didactic groups in knowledge or confidence at any phase of the study. There was no significant difference in tested performance between the groups in either performance testing session. This study suggests that a curriculum consisting of an annual didactic lecture combined with simulation-based training followed by a didactic refresher at 6 months is an effective and efficient (both cost-effective and time-effective) method of educating radiology residents in the management of adverse contrast reactions. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Measurements of Mode Converted Ion Cyclotron Wave with Phase Contrast Imaging in Alcator C-Mod and Comparisons with Synthetic PCI Simulations in TORIC

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

Tsujii, N.; Porkolab, M.; Edlund, E. M.

2009-11-26

Mode converted ion cyclotron wave (ICW) has been observed with phase contrast imaging (PCI) in D-{sup 3}He plasmas in Alcator C-Mod. The measurements were carried out with the optical heterodyne technique using acousto-optic modulators which modulate the CO2 laser beam intensity near the ion cyclotron frequency. With recently improved calibration of the PCI system using a calibrated sound wave source, the measurements have been compared with the full-wave code TORIC, as interpreted by a synthetic diagnostic. Because of the line-integrated nature of the PCI signal, the predictions are sensitive to the exact wave field pattern. The simulations are found tomore » be in qualitative agreement with the measurements.« less

A reconstruction method for cone-beam differential x-ray phase-contrast computed tomography.

PubMed

Fu, Jian; Velroyen, Astrid; Tan, Renbo; Zhang, Junwei; Chen, Liyuan; Tapfer, Arne; Bech, Martin; Pfeiffer, Franz

2012-09-10

Most existing differential phase-contrast computed tomography (DPC-CT) approaches are based on three kinds of scanning geometries, described by parallel-beam, fan-beam and cone-beam. Due to the potential of compact imaging systems with magnified spatial resolution, cone-beam DPC-CT has attracted significant interest. In this paper, we report a reconstruction method based on a back-projection filtration (BPF) algorithm for cone-beam DPC-CT. Due to the differential nature of phase contrast projections, the algorithm restrains from differentiation of the projection data prior to back-projection, unlike BPF algorithms commonly used for absorption-based CT data. This work comprises a numerical study of the algorithm and its experimental verification using a dataset measured with a three-grating interferometer and a micro-focus x-ray tube source. Moreover, the numerical simulation and experimental results demonstrate that the proposed method can deal with several classes of truncated cone-beam datasets. We believe that this feature is of particular interest for future medical cone-beam phase-contrast CT imaging applications.

Low dose reconstruction algorithm for differential phase contrast imaging.

PubMed

Wang, Zhentian; Huang, Zhifeng; Zhang, Li; Chen, Zhiqiang; Kang, Kejun; Yin, Hongxia; Wang, Zhenchang; Marco, Stampanoni

2011-01-01

Differential phase contrast imaging computed tomography (DPCI-CT) is a novel x-ray inspection method to reconstruct the distribution of refraction index rather than the attenuation coefficient in weakly absorbing samples. In this paper, we propose an iterative reconstruction algorithm for DPCI-CT which benefits from the new compressed sensing theory. We first realize a differential algebraic reconstruction technique (DART) by discretizing the projection process of the differential phase contrast imaging into a linear partial derivative matrix. In this way the compressed sensing reconstruction problem of DPCI reconstruction can be transformed to a resolved problem in the transmission imaging CT. Our algorithm has the potential to reconstruct the refraction index distribution of the sample from highly undersampled projection data. Thus it can significantly reduce the dose and inspection time. The proposed algorithm has been validated by numerical simulations and actual experiments.

An iterative method for near-field Fresnel region polychromatic phase contrast imaging

NASA Astrophysics Data System (ADS)

Carroll, Aidan J.; van Riessen, Grant A.; Balaur, Eugeniu; Dolbnya, Igor P.; Tran, Giang N.; Peele, Andrew G.

2017-07-01

We present an iterative method for polychromatic phase contrast imaging that is suitable for broadband illumination and which allows for the quantitative determination of the thickness of an object given the refractive index of the sample material. Experimental and simulation results suggest the iterative method provides comparable image quality and quantitative object thickness determination when compared to the analytical polychromatic transport of intensity and contrast transfer function methods. The ability of the iterative method to work over a wider range of experimental conditions means the iterative method is a suitable candidate for use with polychromatic illumination and may deliver more utility for laboratory-based x-ray sources, which typically have a broad spectrum.

Pump-probe nonlinear phase dispersion spectroscopy.

PubMed

Robles, Francisco E; Samineni, Prathyush; Wilson, Jesse W; Warren, Warren S

2013-04-22

Pump-probe microscopy is an imaging technique that delivers molecular contrast of pigmented samples. Here, we introduce pump-probe nonlinear phase dispersion spectroscopy (PP-NLDS), a method that leverages pump-probe microscopy and spectral-domain interferometry to ascertain information from dispersive and resonant nonlinear effects. PP-NLDS extends the information content to four dimensions (phase, amplitude, wavelength, and pump-probe time-delay) that yield unique insight into a wider range of nonlinear interactions compared to conventional methods. This results in the ability to provide highly specific molecular contrast of pigmented and non-pigmented samples. A theoretical framework is described, and experimental results and simulations illustrate the potential of this method. Implications for biomedical imaging are discussed.

Pump-probe nonlinear phase dispersion spectroscopy

PubMed Central

Robles, Francisco E.; Samineni, Prathyush; Wilson, Jesse W.; Warren, Warren S.

2013-01-01

Pump-probe microscopy is an imaging technique that delivers molecular contrast of pigmented samples. Here, we introduce pump-probe nonlinear phase dispersion spectroscopy (PP-NLDS), a method that leverages pump-probe microscopy and spectral-domain interferometry to ascertain information from dispersive and resonant nonlinear effects. PP-NLDS extends the information content to four dimensions (phase, amplitude, wavelength, and pump-probe time-delay) that yield unique insight into a wider range of nonlinear interactions compared to conventional methods. This results in the ability to provide highly specific molecular contrast of pigmented and non-pigmented samples. A theoretical framework is described, and experimental results and simulations illustrate the potential of this method. Implications for biomedical imaging are discussed. PMID:23609646

Comparison of velocity patterns in an AComA aneurysm measured with 2D phase contrast MRI and simulated with CFD.

PubMed

Karmonik, Christof; Klucznik, Richard; Benndorf, Goetz

2008-01-01

Computational Fluid Dynamic (CFD) is increasingly being used for modeling hemodynamics in intracranial aneurysms. While CFD techniques are well established, need for validation of the results remains. By quantifying features in velocity patterns measured with 2D phase contrast magnetic resonance (pcMRI) in vivo and simulated with CFD, the role of pcMRI for providing reference data for the CFD simulation is explored. Unsteady CFD simulations were performed with inflow boundary conditions obtained from 2D pcMRI measurements of an aneurysm of the anterior communication artery. Intra-aneurysmal velocity profiles were recorded with 2D pcMRI and calculated with CFD. Relative areas of positive and negative velocity were calculated in these profiles for maximum and minimum inflow. Areas of positive and of negative velocity similar in shape were found in the velocity profiles obtained with both methods. Relative difference in size of the relative areas for the whole cardiac cycle ranged from 1%-25% (average 12%). 2D pcMRI is able to record velocity profiles in an aneurysm of the anterior commuting artery in vivo. These velocity profiles can serve as reference data for validation of CFD simulations. Further studies are needed to explore the role of pcMRI in the context of CFD simulations.

High energy x-ray phase contrast CT using glancing-angle grating interferometers

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

Sarapata, A., E-mail: adrian.sarapata@tum.de; Stayman, J. W.; Siewerdsen, J. H.

Purpose: The authors present initial progress toward a clinically compatible x-ray phase contrast CT system, using glancing-angle x-ray grating interferometry to provide high contrast soft tissue images at estimated by computer simulation dose levels comparable to conventional absorption based CT. Methods: DPC-CT scans of a joint phantom and of soft tissues were performed in order to answer several important questions from a clinical setup point of view. A comparison between high and low fringe visibility systems is presented. The standard phase stepping method was compared with sliding window interlaced scanning. Using estimated dose values obtained with a Monte-Carlo code themore » authors studied the dependence of the phase image contrast on exposure time and dose. Results: Using a glancing angle interferometer at high x-ray energy (∼45 keV mean value) in combination with a conventional x-ray tube the authors achieved fringe visibility values of nearly 50%, never reported before. High fringe visibility is shown to be an indispensable parameter for a potential clinical scanner. Sliding window interlaced scanning proved to have higher SNRs and CNRs in a region of interest and to also be a crucial part of a low dose CT system. DPC-CT images of a soft tissue phantom at exposures in the range typical for absorption based CT of musculoskeletal extremities were obtained. Assuming a human knee as the CT target, good soft tissue phase contrast could be obtained at an estimated absorbed dose level around 8 mGy, similar to conventional CT. Conclusions: DPC-CT with glancing-angle interferometers provides improved soft tissue contrast over absorption CT even at clinically compatible dose levels (estimated by a Monte-Carlo computer simulation). Further steps in image processing, data reconstruction, and spectral matching could make the technique fully clinically compatible. Nevertheless, due to its increased scan time and complexity the technique should be thought of not as replacing, but as complimentary to conventional CT, to be used in specific applications.« less

Probing polariton dynamics in trapped ions with phase-coherent two-dimensional spectroscopy

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

Gessner, Manuel; Schlawin, Frank; Buchleitner, Andreas

2015-06-07

We devise a phase-coherent three-pulse protocol to probe the polariton dynamics in a trapped-ion quantum simulation. In contrast to conventional nonlinear signals, the presented scheme does not change the number of excitations in the system, allowing for the investigation of the dynamics within an N-excitation manifold. In the particular case of a filling factor one (N excitations in an N-ion chain), the proposed interaction induces coherent transitions between a delocalized phonon superfluid and a localized atomic insulator phase. Numerical simulations of a two-ion chain demonstrate that the resulting two-dimensional spectra allow for the unambiguous identification of the distinct phases, andmore » the two-dimensional line shapes efficiently characterize the relevant decoherence mechanism.« less

A geometrical shift results in erroneous appearance of low frequency tissue eddy current induced phase maps.

PubMed

Mandija, Stefano; van Lier, Astrid L H M W; Katscher, Ulrich; Petrov, Petar I; Neggers, Sebastian F W; Luijten, Peter R; van den Berg, Cornelis A T

2016-09-01

Knowledge on low frequency (LF) tissue conductivity is relevant for various biomedical purposes. To obtain this information, LF phase maps arising from time-varying imaging gradients have been demonstrated to create a LF conductivity contrast. Essential in this methodology is the subtraction of phase images acquired with opposite gradient polarities to separate LF and RF phase effects. Here we demonstrate how sensitive these subtractions are with respect to geometrical distortions. The effect of geometrical distortions on LF phase maps is mathematically defined. After quantifying typical geometrical distortions, their effects on LF phase maps are evaluated using conductive phantoms. For validation, electromagnetic simulations of LF phase maps were performed. Even sub-voxel distortions of 10% of the voxel size, measured for a typical LF MR sequence, cause leakage of RF phase into LF phase of several milli-radians, leading to a misleading pattern of LF phase maps. This leakage is mathematically confirmed, while simulations indicate that the expected LF phase should be in order of micro-radians. The conductivity scaling of LF phase maps is attributable to the RF phase leakage, thus dependent on the RF conductivity. In fact, simulations show that the LF phase is not measurable. Magn Reson Med 76:905-912, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Theta EEG dynamics of the error-related negativity.

PubMed

Trujillo, Logan T; Allen, John J B

2007-03-01

The error-related negativity (ERN) is a response-locked brain potential (ERP) occurring 80-100ms following response errors. This report contrasts three views of the genesis of the ERN, testing the classic view that time-locked phasic bursts give rise to the ERN against the view that the ERN arises from a pure phase-resetting of ongoing theta (4-7Hz) EEG activity and the view that the ERN is generated - at least in part - by a phase-resetting and amplitude enhancement of ongoing theta EEG activity. Time-domain ERP analyses were augmented with time-frequency investigations of phase-locked and non-phase-locked spectral power, and inter-trial phase coherence (ITPC) computed from individual EEG trials, examining time courses and scalp topographies. Simulations based on the assumptions of the classic, pure phase-resetting, and phase-resetting plus enhancement views, using parameters from each subject's empirical data, were used to contrast the time-frequency findings that could be expected if one or more of these hypotheses adequately modeled the data. Error responses produced larger amplitude activity than correct responses in time-domain ERPs immediately following responses, as expected. Time-frequency analyses revealed that significant error-related post-response increases in total spectral power (phase- and non-phase-locked), phase-locked power, and ITPC were primarily restricted to the theta range, with this effect located over midfrontocentral sites, with a temporal distribution from approximately 150-200ms prior to the button press and persisting up to 400ms post-button press. The increase in non-phase-locked power (total power minus phase-locked power) was larger than phase-locked power, indicating that the bulk of the theta event-related dynamics were not phase-locked to response. Results of the simulations revealed a good fit for data simulated according to the phase-locking with amplitude enhancement perspective, and a poor fit for data simulated according to the classic view and the pure phase-resetting view. Error responses produce not only phase-locked increases in theta EEG activity, but also increases in non-phase-locked theta, both of which share a similar topography. The findings are thus consistent with the notion advanced by Luu et al. [Luu P, Tucker DM, Makeig S. Frontal midline theta and the error-related negativity; neurophysiological mechanisms of action regulation. Clin Neurophysiol 2004;115:1821-35] that the ERN emerges, at least in part, from a phase-resetting and phase-locking of ongoing theta-band activity, in the context of a general increase in theta power following errors.

Low cost label-free live cell imaging for biological samples

NASA Astrophysics Data System (ADS)

Seniya, C.; Towers, C. E.; Towers, D. P.

2017-02-01

This paper reports the progress to develop a practical phase measuring microscope offering new capabilities in terms of phase measurement accuracy and quantification of cell:cell interactions over the longer term. A novel, low cost phase interference microscope for imaging live cells (label-free) is described. The method combines the Zernike phase contrast approach with a dual mirror design to enable phase modulation between the scattered and un-scattered optical fields. Two designs are proposed and demonstrated, one of which retains the common path nature of Zernike's original microscopy concept. In both setups the phase shift is simple to control via a piezoelectric driven mirror in the back focal plane of the imaging system. The approach is significantly cheaper to implement than those based on spatial light modulators (SLM) at approximately 20% of the cost. A quantitative assessment of the performance of a set of phase shifting algorithms is also presented, specifically with regard to broad bandwidth illumination in phase contrast microscopy. The simulation results show that the phase measurement accuracy is strongly dependent on the algorithm selected and the optical path difference in the sample.

Ideal-observer detectability in photon-counting differential phase-contrast imaging using a linear-systems approach

PubMed Central

Fredenberg, Erik; Danielsson, Mats; Stayman, J. Webster; Siewerdsen, Jeffrey H.; Åslund, Magnus

2012-01-01

Purpose: To provide a cascaded-systems framework based on the noise-power spectrum (NPS), modulation transfer function (MTF), and noise-equivalent number of quanta (NEQ) for quantitative evaluation of differential phase-contrast imaging (Talbot interferometry) in relation to conventional absorption contrast under equal-dose, equal-geometry, and, to some extent, equal-photon-economy constraints. The focus is a geometry for photon-counting mammography. Methods: Phase-contrast imaging is a promising technology that may emerge as an alternative or adjunct to conventional absorption contrast. In particular, phase contrast may increase the signal-difference-to-noise ratio compared to absorption contrast because the difference in phase shift between soft-tissue structures is often substantially larger than the absorption difference. We have developed a comprehensive cascaded-systems framework to investigate Talbot interferometry, which is a technique for differential phase-contrast imaging. Analytical expressions for the MTF and NPS were derived to calculate the NEQ and a task-specific ideal-observer detectability index under assumptions of linearity and shift invariance. Talbot interferometry was compared to absorption contrast at equal dose, and using either a plane wave or a spherical wave in a conceivable mammography geometry. The impact of source size and spectrum bandwidth was included in the framework, and the trade-off with photon economy was investigated in some detail. Wave-propagation simulations were used to verify the analytical expressions and to generate example images. Results: Talbot interferometry inherently detects the differential of the phase, which led to a maximum in NEQ at high spatial frequencies, whereas the absorption-contrast NEQ decreased monotonically with frequency. Further, phase contrast detects differences in density rather than atomic number, and the optimal imaging energy was found to be a factor of 1.7 higher than for absorption contrast. Talbot interferometry with a plane wave increased detectability for 0.1-mm tumor and glandular structures by a factor of 3–4 at equal dose, whereas absorption contrast was the preferred method for structures larger than ∼0.5 mm. Microcalcifications are small, but differ from soft tissue in atomic number more than density, which is favored by absorption contrast, and Talbot interferometry was barely beneficial at all within the resolution limit of the system. Further, Talbot interferometry favored detection of “sharp” as opposed to “smooth” structures, and discrimination tasks by about 50% compared to detection tasks. The technique was relatively insensitive to spectrum bandwidth, whereas the projected source size was more important. If equal photon economy was added as a restriction, phase-contrast efficiency was reduced so that the benefit for detection tasks almost vanished compared to absorption contrast, but discrimination tasks were still improved close to a factor of 2 at the resolution limit. Conclusions: Cascaded-systems analysis enables comprehensive and intuitive evaluation of phase-contrast efficiency in relation to absorption contrast under requirements of equal dose, equal geometry, and equal photon economy. The benefit of Talbot interferometry was highly dependent on task, in particular detection versus discrimination tasks, and target size, shape, and material. Requiring equal photon economy weakened the benefit of Talbot interferometry in mammography. PMID:22957600

Motile bacteria in a critical fluid mixture

NASA Astrophysics Data System (ADS)

Koumakis, Nick; Devailly, Clémence; Poon, Wilson C. K.

2018-06-01

We studied the swimming of Escherichia coli bacteria in the vicinity of the critical point in a solution of the nonionic surfactant C12E5 in buffer solution. In phase-contrast microscopy, each swimming cell produces a transient trail behind itself lasting several seconds. Comparing quantitative image analysis with simulations show that these trails are due to local phase reorganization triggered by differential adsorption. This contrasts with similar trails seen in bacteria swimming in liquid crystals, which are due to shear effects. We show how our trails are controlled, and use them to probe the structure and dynamics of critical fluctuations in the fluid medium.

Application of adaptive optics in complicated and integrated spatial multisensor system and its measurement analysis

NASA Astrophysics Data System (ADS)

Ding, Quanxin; Guo, Chunjie; Cai, Meng; Liu, Hua

2007-12-01

Adaptive Optics Expand System is a kind of new concept spatial equipment, which concerns system, cybernetics and informatics deeply, and is key way to improve advanced sensors ability. Traditional Zernike Phase Contrast Method is developed, and Accelerated High-level Phase Contrast Theory is established. Integration theory and mathematical simulation is achieved. Such Equipment, which is based on some crucial components, such as, core optical system, multi mode wavefront sensor and so on, is established for AOES advantageous configuration and global design. Studies on Complicated Spatial Multisensor System Integratation and measurement Analysis including error analysis are carried out.

Bilateral filtering using the full noise covariance matrix applied to x-ray phase-contrast computed tomography.

PubMed

Allner, S; Koehler, T; Fehringer, A; Birnbacher, L; Willner, M; Pfeiffer, F; Noël, P B

2016-05-21

The purpose of this work is to develop an image-based de-noising algorithm that exploits complementary information and noise statistics from multi-modal images, as they emerge in x-ray tomography techniques, for instance grating-based phase-contrast CT and spectral CT. Among the noise reduction methods, image-based de-noising is one popular approach and the so-called bilateral filter is a well known algorithm for edge-preserving filtering. We developed a generalization of the bilateral filter for the case where the imaging system provides two or more perfectly aligned images. The proposed generalization is statistically motivated and takes the full second order noise statistics of these images into account. In particular, it includes a noise correlation between the images and spatial noise correlation within the same image. The novel generalized three-dimensional bilateral filter is applied to the attenuation and phase images created with filtered backprojection reconstructions from grating-based phase-contrast tomography. In comparison to established bilateral filters, we obtain improved noise reduction and at the same time a better preservation of edges in the images on the examples of a simulated soft-tissue phantom, a human cerebellum and a human artery sample. The applied full noise covariance is determined via cross-correlation of the image noise. The filter results yield an improved feature recovery based on enhanced noise suppression and edge preservation as shown here on the example of attenuation and phase images captured with grating-based phase-contrast computed tomography. This is supported by quantitative image analysis. Without being bound to phase-contrast imaging, this generalized filter is applicable to any kind of noise-afflicted image data with or without noise correlation. Therefore, it can be utilized in various imaging applications and fields.

Physics of near-wavelength high contrast gratings.

PubMed

Karagodsky, Vadim; Chang-Hasnain, Connie J

2012-05-07

We present a simple theory explaining the extraordinary features of high-contrast optical gratings in the near-wavelength regime, particularly the very broadband high reflectivity (>99%) and the ultra-high quality factor resonances (Q>10(7)). We present, for the first time, an intuitive explanation for both features using a simple phase selection rule, and reveal the anti-crossing and crossing effects between the grating modes. Our analytical results agree well with simulations and the experimental data obtained from vertical cavity surface emitting lasers incorporating a high contrast grating as top reflector.

New innovations for contrast enhancement in electron microscopy

NASA Astrophysics Data System (ADS)

Mohan, A.

In this study two techniques for producing and improving contrast in Electron Microscopy are discussed. The first technique deals with the production of secondary contrast in a Variable Pressure SEM under poor vacuum conditions using the specimen current signal. A review of the prior work in this field shows that the presence of the gas ions in the microscope column results in the amplification of the specimen current signal which is enriched in secondary content. The focus of this study is to establish practical conditions for imaging samples in the microscope using specimen current with gas amplification. This is done by understanding the different variables in the microscope which affect the image formation process and then finding out optimum conditions for obtaining the best possible image, i.e., the image most enhanced in secondary contrast. A few 'real life' samples analyzed using this technique show that the gas amplified specimen current images contain secondary information and, in some cases, provide clear advantages to imaging with conventional secondary and backscattered detectors. The second technique dealing with the production of phase contrast in the TEM for extremely thin, electron transparent samples, is analyzed. A review of the literature regarding prior work in the field shows that, while the theoretical aspects of production of phase contrast in the TEM using a phase plate are well understood, there have been problems in practically implementing this in the microscope. One major assumption with most of the studies is that a fiber, partially coated with gold, results in the formation of point charges which is an essential requirement for symmetrically shifting the phase of the electron beam. The focus of this portion of the dissertation is to image the type of fields associated with such a phase plate using the technique of electron holography. It is found that there are two types of fields associated with a phase plate of this sort. One is a cylindrical field which extends along the length of the fiber while the other is a localized spherically symmetric field. A series of simulations show that the spherical field can produce phase contrast in the TEM and also improve the contrast transfer properties of the microscope.

High Resolution X-Ray Phase Contrast Imaging With Acoustic Tissue-Selective Contrast Enhancement

DTIC Science & Technology

2006-06-01

1999). 17. Sarvazyan, A. P. Shear Wave Elasticity Imaging: A New Ultrasonic Technology of Medical Diagnostics. Ultrasound in Medicine and Biology 24... elastography 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON USAMRMC a...Body Figure 2 shows the results of a set of experiments involving a simulated breast . The phantom (purchased from CIR, Inc.) was designed to

A Monte Carlo study of the spin-1 Blume-Emery-Griffiths phase diagrams within biquadratic exchange anisotropy

NASA Astrophysics Data System (ADS)

Dani, Ibtissam; Tahiri, Najim; Ez-Zahraouy, Hamid; Benyoussef, Abdelilah

2014-08-01

The effect of the bi-quadratic exchange coupling anisotropy on the phase diagram of the spin-1 Blume-Emery-Griffiths model on simple-cubic lattice is investigated using mean field theory (MFT) and Monte Carlo simulation (MC). It is found that the anisotropy of the biquadratic coupling favors the stability of the ferromagnetic phase. By decreasing the parallel and/or perpendicular bi-quadratic coupling, the ferrimagnetic and the antiquadrupolar phases broaden in contrast, the ferromagnetic and the disordered phases become narrow. The behavior of magnetization and quadrupolar moment as a function of temperature is also computed, especially in the ferrimagnetic phase.

Simulations of arctic mixed-phase clouds in forecasts with CAM3 and AM2 for M-PACE

DOE PAGES

Xie, Shaocheng; Boyle, James; Klein, Stephen A.; ...

2008-02-27

[1] Simulations of mixed-phase clouds in forecasts with the NCAR Atmosphere Model version 3 (CAM3) and the GFDL Atmospheric Model version 2 (AM2) for the Mixed-Phase Arctic Cloud Experiment (M-PACE) are performed using analysis data from numerical weather prediction centers. CAM3 significantly underestimates the observed boundary layer mixed-phase cloud fraction and cannot realistically simulate the variations of liquid water fraction with temperature and cloud height due to its oversimplified cloud microphysical scheme. In contrast, AM2 reasonably reproduces the observed boundary layer cloud fraction while its clouds contain much less cloud condensate than CAM3 and the observations. The simulation of themore » boundary layer mixed-phase clouds and their microphysical properties is considerably improved in CAM3 when a new physically based cloud microphysical scheme is used (CAM3LIU). The new scheme also leads to an improved simulation of the surface and top of the atmosphere longwave radiative fluxes. Sensitivity tests show that these results are not sensitive to the analysis data used for model initialization. Increasing model horizontal resolution helps capture the subgrid-scale features in Arctic frontal clouds but does not help improve the simulation of the single-layer boundary layer clouds. AM2 simulated cloud fraction and LWP are sensitive to the change in cloud ice number concentrations used in the Wegener-Bergeron-Findeisen process while CAM3LIU only shows moderate sensitivity in its cloud fields to this change. Furthermore, this paper shows that the Wegener-Bergeron-Findeisen process is important for these models to correctly simulate the observed features of mixed-phase clouds.« less

Simulations of Arctic mixed-phase clouds in forecasts with CAM3 and AM2 for M-PACE

NASA Astrophysics Data System (ADS)

Xie, Shaocheng; Boyle, James; Klein, Stephen A.; Liu, Xiaohong; Ghan, Steven

2008-02-01

Simulations of mixed-phase clouds in forecasts with the NCAR Atmosphere Model version 3 (CAM3) and the GFDL Atmospheric Model version 2 (AM2) for the Mixed-Phase Arctic Cloud Experiment (M-PACE) are performed using analysis data from numerical weather prediction centers. CAM3 significantly underestimates the observed boundary layer mixed-phase cloud fraction and cannot realistically simulate the variations of liquid water fraction with temperature and cloud height due to its oversimplified cloud microphysical scheme. In contrast, AM2 reasonably reproduces the observed boundary layer cloud fraction while its clouds contain much less cloud condensate than CAM3 and the observations. The simulation of the boundary layer mixed-phase clouds and their microphysical properties is considerably improved in CAM3 when a new physically based cloud microphysical scheme is used (CAM3LIU). The new scheme also leads to an improved simulation of the surface and top of the atmosphere longwave radiative fluxes. Sensitivity tests show that these results are not sensitive to the analysis data used for model initialization. Increasing model horizontal resolution helps capture the subgrid-scale features in Arctic frontal clouds but does not help improve the simulation of the single-layer boundary layer clouds. AM2 simulated cloud fraction and LWP are sensitive to the change in cloud ice number concentrations used in the Wegener-Bergeron-Findeisen process while CAM3LIU only shows moderate sensitivity in its cloud fields to this change. This paper shows that the Wegener-Bergeron-Findeisen process is important for these models to correctly simulate the observed features of mixed-phase clouds.

Numerical simulation of pseudoelastic shape memory alloys using the large time increment method

NASA Astrophysics Data System (ADS)

Gu, Xiaojun; Zhang, Weihong; Zaki, Wael; Moumni, Ziad

2017-04-01

The paper presents a numerical implementation of the large time increment (LATIN) method for the simulation of shape memory alloys (SMAs) in the pseudoelastic range. The method was initially proposed as an alternative to the conventional incremental approach for the integration of nonlinear constitutive models. It is adapted here for the simulation of pseudoelastic SMA behavior using the Zaki-Moumni model and is shown to be especially useful in situations where the phase transformation process presents little or lack of hardening. In these situations, a slight stress variation in a load increment can result in large variations of strain and local state variables, which may lead to difficulties in numerical convergence. In contrast to the conventional incremental method, the LATIN method solve the global equilibrium and local consistency conditions sequentially for the entire loading path. The achieved solution must satisfy the conditions of static and kinematic admissibility and consistency simultaneously after several iterations. 3D numerical implementation is accomplished using an implicit algorithm and is then used for finite element simulation using the software Abaqus. Computational tests demonstrate the ability of this approach to simulate SMAs presenting flat phase transformation plateaus and subjected to complex loading cases, such as the quasi-static behavior of a stent structure. Some numerical results are contrasted to those obtained using step-by-step incremental integration.

Multiphase mean curvature flows with high mobility contrasts: A phase-field approach, with applications to nanowires

NASA Astrophysics Data System (ADS)

Bretin, Elie; Danescu, Alexandre; Penuelas, José; Masnou, Simon

2018-07-01

The structure of many multiphase systems is governed by an energy that penalizes the area of interfaces between phases weighted by surface tension coefficients. However, interface evolution laws depend also on interface mobility coefficients. Having in mind some applications where highly contrasted or even degenerate mobilities are involved, for which classical phase field models are inapplicable, we propose a new effective phase field approach to approximate multiphase mean curvature flows with mobilities. The key aspect of our model is to incorporate the mobilities not in the phase field energy (which is conventionally the case) but in the metric which determines the gradient flow. We show the consistency of such an approach by a formal analysis of the sharp interface limit. We also propose an efficient numerical scheme which allows us to illustrate the advantages of the model on various examples, as the wetting of droplets on solid surfaces or the simulation of nanowires growth generated by the so-called vapor-liquid-solid method.

The Accuracy and Precision of Flow Measurements Using Phase Contrast Techniques

NASA Astrophysics Data System (ADS)

Tang, Chao

Quantitative volume flow rate measurements using the magnetic resonance imaging technique are studied in this dissertation because the volume flow rates have a special interest in the blood supply of the human body. The method of quantitative volume flow rate measurements is based on the phase contrast technique, which assumes a linear relationship between the phase and flow velocity of spins. By measuring the phase shift of nuclear spins and integrating velocity across the lumen of the vessel, we can determine the volume flow rate. The accuracy and precision of volume flow rate measurements obtained using the phase contrast technique are studied by computer simulations and experiments. The various factors studied include (1) the partial volume effect due to voxel dimensions and slice thickness relative to the vessel dimensions; (2) vessel angulation relative to the imaging plane; (3) intravoxel phase dispersion; (4) flow velocity relative to the magnitude of the flow encoding gradient. The partial volume effect is demonstrated to be the major obstacle to obtaining accurate flow measurements for both laminar and plug flow. Laminar flow can be measured more accurately than plug flow in the same condition. Both the experiment and simulation results for laminar flow show that, to obtain the accuracy of volume flow rate measurements to within 10%, at least 16 voxels are needed to cover the vessel lumen. The accuracy of flow measurements depends strongly on the relative intensity of signal from stationary tissues. A correction method is proposed to compensate for the partial volume effect. The correction method is based on a small phase shift approximation. After the correction, the errors due to the partial volume effect are compensated, allowing more accurate results to be obtained. An automatic program based on the correction method is developed and implemented on a Sun workstation. The correction method is applied to the simulation and experiment results. The results show that the correction significantly reduces the errors due to the partial volume effect. We apply the correction method to the data of in vivo studies. Because the blood flow is not known, the results of correction are tested according to the common knowledge (such as cardiac output) and conservation of flow. For example, the volume of blood flowing to the brain should be equal to the volume of blood flowing from the brain. Our measurement results are very convincing.

Characterization of LiBC by phase-contrast scanning transmission electron microscopy.

PubMed

Krumeich, Frank; Wörle, Michael; Reibisch, Philipp; Nesper, Reinhard

2014-08-01

LiBC was used as a model compound for probing the applicability of phase-contrast (PC) imaging in an aberration-corrected scanning transmission electron microscope (STEM) to visualize lithium distributions. In the LiBC structure, boron and carbon are arranged to hetero graphite layers between which lithium is incorporated. The crystal structure is reflected in the PC-STEM images recorded perpendicular to the layers. The experimental images and their defocus dependence match with multi-slice simulations calculated utilizing the reciprocity principle. The observation that a part of the Li positions is not occupied is likely an effect of the intense electron beam triggering Li displacement. Copyright © 2013 Elsevier Ltd. All rights reserved.

Astronomical Near-neighbor Detection with a Four-quadrant Phase Mask (FQPM) Coronagraph

NASA Technical Reports Server (NTRS)

Haguenauer, Pierre; Serabyn, Eugene; Mennesson, Bertrand; Wallace, James K.; Gappinger, Robert O.; Troy, Mitchell; Bloemhof, Eric E.; Moore, Jim; Koresko, Chris D.

2006-01-01

Direct detection of planets around nearby stars requires the development of high-contrast imaging techniques, because of their very different respective fluxes. We thus investigated the innovative coronagraphic approach based on the use of a four-quadrant phase mask (FQPM). Simulations showed that, combined with high-level wavefront correction on an unobscured off-axis section of a large telescope, this method allows high-contrast imaging very close to stars, with detection capability superior to that of a traditional coronagraph. A FQPM instrument was thus built to test the feasibility of near-neighbor observations with our new off-axis approach on a ground-based telescope. In June 2005, we deployed our instrument to the Palomar 200-inch telescope, using existing facilities as much as possible for rapid implementation. In these initial observations, using data processing techniques specific to FQPM coronagraphs, we reached extinction levels of the order of 200:1. Here we discuss our simulations and on-sky results obtained so far.

Validity of computational hemodynamics in human arteries based on 3D time-of-flight MR angiography and 2D electrocardiogram gated phase contrast images

NASA Astrophysics Data System (ADS)

Yu, Huidan (Whitney); Chen, Xi; Chen, Rou; Wang, Zhiqiang; Lin, Chen; Kralik, Stephen; Zhao, Ye

2015-11-01

In this work, we demonstrate the validity of 4-D patient-specific computational hemodynamics (PSCH) based on 3-D time-of-flight (TOF) MR angiography (MRA) and 2-D electrocardiogram (ECG) gated phase contrast (PC) images. The mesoscale lattice Boltzmann method (LBM) is employed to segment morphological arterial geometry from TOF MRA, to extract velocity profiles from ECG PC images, and to simulate fluid dynamics on a unified GPU accelerated computational platform. Two healthy volunteers are recruited to participate in the study. For each volunteer, a 3-D high resolution TOF MRA image and 10 2-D ECG gated PC images are acquired to provide the morphological geometry and the time-varying flow velocity profiles for necessary inputs of the PSCH. Validation results will be presented through comparisons of LBM vs. 4D Flow Software for flow rates and LBM simulation vs. MRA measurement for blood flow velocity maps. Indiana University Health (IUH) Values Fund.

Studies of Turbulence and Transport in Alcator C-Mod H-Mode Plasmas with Phase Contrast Imaging and Comparisons with GYRO

NASA Astrophysics Data System (ADS)

Porkolab, M.; Lin, L.; Edlund, E. M.; Rost, J. C.; Fiore, C. L.; Greenwald, M.; Mikkelsen, D.

2008-11-01

We present recent experimental measurements of turbulence and transport in C-Mod H-Mode plasmas with and without internal transport barriers (ITB) using the phase contrast imaging (PCI) diagnostic and compare the results with GYRO predictions. In plasmas without ITB, the fluctuation above 300 kHz observed by PCI agrees with ITG in GYRO simulation, including the direction of propagation, wavenumber spectrum, and absolute intensity within experimental uncertainly (+/-75%). After transition to ITBs, the observed overall fluctuation intensity increases. GYRO simulation in the core shows that ITG dominates in ITBs but its intensity is lower than the overall experimental measurements which may also include contributions from the plasma edge. These results, as well as the impact of varying ∇Ti, ∇n, and ExB shear on turbulence will be discussed. C.L. Fiore et al., Fusion Sci. Technol., 51, 303 (2007). M. Porkolab et al., IEEE Trans. Plasma Sci. 34, 229 (2006). J. Candy et al., Phys. Rev. Lett., 91, 045001 (2003).

Flow Cytometry with Gold Nanoparticles and their Clusters as scattering Contrast Agents: FDTD Simulation of Light-Cell Interaction

PubMed Central

Tanev, Stoyan; Sun, Wenbo; Pond, James; Tuchin, Valery V.; Zharov, Vladimir P.

2010-01-01

The formulation of the Finite-Difference Time-Domain (FDTD) approach is presented in the framework of its potential applications to in vivo flow cytometry based on light scattering. The consideration is focused on comparison of light scattering by a single biological cell alone in controlled refractive index matching conditions and by cells labeled by gold nanoparticles. The optical schematics including phase contrast (OPCM) microscopy as a prospective modality for in vivo flow cytometry is also analyzed. The validation of the FDTD approach for the simulation of flow cytometry may open a new avenue in the development of advanced cytometric techniques based on scattering effects from nanoscale targets. PMID:19670359

X-ray grating interferometer for materials-science imaging at a low-coherent wiggler source

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

Herzen, Julia; Physics Department and Institute for Medical Engineering, Technische Universitaet Muenchen, 85748 Garching; Donath, Tilman

2011-11-15

X-ray phase-contrast radiography and tomography enable to increase contrast for weakly absorbing materials. Recently, x-ray grating interferometers were developed that extend the possibility of phase-contrast imaging from highly brilliant radiation sources like third-generation synchrotron sources to non-coherent conventional x-ray tube sources. Here, we present the first installation of a three grating x-ray interferometer at a low-coherence wiggler source at the beamline W2 (HARWI II) operated by the Helmholtz-Zentrum Geesthacht at the second-generation synchrotron storage ring DORIS (DESY, Hamburg, Germany). Using this type of the wiggler insertion device with a millimeter-sized source allows monochromatic phase-contrast imaging of centimeter sized objects withmore » high photon flux. Thus, biological and materials-science imaging applications can highly profit from this imaging modality. The specially designed grating interferometer currently works in the photon energy range from 22 to 30 keV, and the range will be increased by using adapted x-ray optical gratings. Our results of an energy-dependent visibility measurement in comparison to corresponding simulations demonstrate the performance of the new setup.« less

Sensitivity analysis for future space missions with segmented telescopes for high-contrast imaging

NASA Astrophysics Data System (ADS)

Leboulleux, Lucie; Pueyo, Laurent; Sauvage, Jean-François; Mazoyer, Johan; Soummer, Remi; Fusco, Thierry; Sivaramakrishnan, Anand

2018-01-01

The detection and analysis of biomarkers on earth-like planets using direct-imaging will require both high-contrast imaging and spectroscopy at very close angular separation (10^10 star to planet flux ratio at a few 0.1”). This goal can only be achieved with large telescopes in space to overcome atmospheric turbulence, often combined with a coronagraphic instrument with wavefront control. Large segmented space telescopes such as studied for the LUVOIR mission will generate segment-level instabilities and cophasing errors in addition to local mirror surface errors and other aberrations of the overall optical system. These effects contribute directly to the degradation of the final image quality and contrast. We present an analytical model that produces coronagraphic images of a segmented pupil telescope in the presence of segment phasing aberrations expressed as Zernike polynomials. This model relies on a pair-based projection of the segmented pupil and provides results that match an end-to-end simulation with an rms error on the final contrast of ~3%. This analytical model can be applied both to static and dynamic modes, and either in monochromatic or broadband light. It retires the need for end-to-end Monte-Carlo simulations that are otherwise needed to build a rigorous error budget, by enabling quasi-instantaneous analytical evaluations. The ability to invert directly the analytical model provides direct constraints and tolerances on all segments-level phasing and aberrations.

Complex-based OCT angiography algorithm recovers microvascular information better than amplitude- or phase-based algorithms in phase-stable systems

NASA Astrophysics Data System (ADS)

Xu, Jingjiang; Song, Shaozhen; Li, Yuandong; Wang, Ruikang K.

2018-01-01

Optical coherence tomography angiography (OCTA) is increasingly becoming a popular inspection tool for biomedical imaging applications. By exploring the amplitude, phase and complex information available in OCT signals, numerous algorithms have been proposed that contrast functional vessel networks within microcirculatory tissue beds. However, it is not clear which algorithm delivers optimal imaging performance. Here, we investigate systematically how amplitude and phase information have an impact on the OCTA imaging performance, to establish the relationship of amplitude and phase stability with OCT signal-to-noise ratio (SNR), time interval and particle dynamics. With either repeated A-scan or repeated B-scan imaging protocols, the amplitude noise increases with the increase of OCT SNR; however, the phase noise does the opposite, i.e. it increases with the decrease of OCT SNR. Coupled with experimental measurements, we utilize a simple Monte Carlo (MC) model to simulate the performance of amplitude-, phase- and complex-based algorithms for OCTA imaging, the results of which suggest that complex-based algorithms deliver the best performance when the phase noise is  <  ~40 mrad. We also conduct a series of in vivo vascular imaging in animal models and human retina to verify the findings from the MC model through assessing the OCTA performance metrics of vessel connectivity, image SNR and contrast-to-noise ratio. We show that for all the metrics assessed, the complex-based algorithm delivers better performance than either the amplitude- or phase-based algorithms for both the repeated A-scan and the B-scan imaging protocols, which agrees well with the conclusion drawn from the MC simulations.

Complex-based OCT angiography algorithm recovers microvascular information better than amplitude- or phase-based algorithms in phase-stable systems.

PubMed

Xu, Jingjiang; Song, Shaozhen; Li, Yuandong; Wang, Ruikang K

2017-12-19

Optical coherence tomography angiography (OCTA) is increasingly becoming a popular inspection tool for biomedical imaging applications. By exploring the amplitude, phase and complex information available in OCT signals, numerous algorithms have been proposed that contrast functional vessel networks within microcirculatory tissue beds. However, it is not clear which algorithm delivers optimal imaging performance. Here, we investigate systematically how amplitude and phase information have an impact on the OCTA imaging performance, to establish the relationship of amplitude and phase stability with OCT signal-to-noise ratio (SNR), time interval and particle dynamics. With either repeated A-scan or repeated B-scan imaging protocols, the amplitude noise increases with the increase of OCT SNR; however, the phase noise does the opposite, i.e. it increases with the decrease of OCT SNR. Coupled with experimental measurements, we utilize a simple Monte Carlo (MC) model to simulate the performance of amplitude-, phase- and complex-based algorithms for OCTA imaging, the results of which suggest that complex-based algorithms deliver the best performance when the phase noise is  <  ~40 mrad. We also conduct a series of in vivo vascular imaging in animal models and human retina to verify the findings from the MC model through assessing the OCTA performance metrics of vessel connectivity, image SNR and contrast-to-noise ratio. We show that for all the metrics assessed, the complex-based algorithm delivers better performance than either the amplitude- or phase-based algorithms for both the repeated A-scan and the B-scan imaging protocols, which agrees well with the conclusion drawn from the MC simulations.

Polarimetric Radar Characteristics of Simulated and Observed Intense Convection Between Continental and Maritime Environment

NASA Astrophysics Data System (ADS)

Matsui, T.; Dolan, B.; Tao, W. K.; Rutledge, S. A.; Iguchi, T.; Barnum, J. I.; Lang, S. E.

2017-12-01

This study presents polarimetric radar characteristics of intense convective cores derived from observations as well as a polarimetric-radar simulator from cloud resolving model (CRM) simulations from Midlatitude Continental Convective Clouds Experiment (MC3E) May 23 case over Oklahoma and a Tropical Warm Pool-International Cloud Experiment (TWP-ICE) Jan 23 case over Darwin, Australia to highlight the contrast between continental and maritime convection. The POLArimetric Radar Retrieval and Instrument Simulator (POLARRIS) is a state-of-art T-matrix-Mueller-Matrix-based polarimetric radar simulator that can generate synthetic polarimetric radar signals (reflectivity, differential reflectivity, specific differential phase, co-polar correlation) as well as synthetic radar retrievals (precipitation, hydrometeor type, updraft velocity) through the consistent treatment of cloud microphysics and dynamics from CRMs. The Weather Research and Forecasting (WRF) model is configured to simulate continental and maritime severe storms over the MC3E and TWP-ICE domains with the Goddard bulk 4ICE single-moment microphysics and HUCM spectra-bin microphysics. Various statistical diagrams of polarimetric radar signals, hydrometeor types, updraft velocity, and precipitation intensity are investigated for convective and stratiform precipitation regimes and directly compared between MC3E and TWP-ICE cases. The result shows MC3E convection is characterized with very strong reflectivity (up to 60dBZ), slight negative differential reflectivity (-0.8 0 dB) and near-zero specific differential phase above the freezing levels. On the other hand, TWP-ICE convection shows strong reflectivity (up to 50dBZ), slight positive differential reflectivity (0 1.0 dB) and differential phase (0 0.8 dB/km). Hydrometeor IDentification (HID) algorithm from the observation and simulations detect hail-dominant convection core in MC3E, while graupel-dominant convection core in TWP-ICE. This land-ocean contrast agrees with the previous studies using the radar and radiometer signals from TRMM satellite climatology associated with warm-cloud depths and vertical structure of buoyancy.

Motility-Induced Phase Separation

NASA Astrophysics Data System (ADS)

Cates, Michael E.; Tailleur, Julien

2015-03-01

Self-propelled particles include both self-phoretic synthetic colloids and various microorganisms. By continually consuming energy, they bypass the laws of equilibrium thermodynamics. These laws enforce the Boltzmann distribution in thermal equilibrium: The steady state is then independent of kinetic parameters. In contrast, self-propelled particles tend to accumulate where they move more slowly. They may also slow down at high density for either biochemical or steric reasons. This creates positive feedback, which can lead to motility-induced phase separation (MIPS) between dense and dilute fluid phases. At leading order in gradients, a mapping relates variable-speed, self-propelled particles to passive particles with attractions. This deep link to equilibrium phase separation is confirmed by simulations but generally breaks down at higher order in gradients: New effects, with no equilibrium counterpart, then emerge. We give a selective overview of the fast-developing field of MIPS, focusing on theory and simulation but including a brief speculative survey of its experimental implications.

Electron ptychographic phase imaging of light elements in crystalline materials using Wigner distribution deconvolution

DOE PAGES

Yang, Hao; MacLaren, Ian; Jones, Lewys; ...

2017-04-01

Recent development in fast pixelated detector technology has allowed a two dimensional diffraction pattern to be recorded at every probe position of a two dimensional raster scan in a scanning transmission electron microscope (STEM), forming an information-rich four dimensional (4D) dataset. Electron ptychography has been shown to enable efficient coherent phase imaging of weakly scattering objects from a 4D dataset recorded using a focused electron probe, which is optimised for simultaneous incoherent Z-contrast imaging and spectroscopy in STEM. Thus coherent phase contrast and incoherent Z-contrast imaging modes can be efficiently combined to provide a good sensitivity of both light andmore » heavy elements at atomic resolution. Here, we explore the application of electron ptychography for atomic resolution imaging of strongly scattering crystalline specimens, and present experiments on imaging crystalline specimens including samples containing defects, under dynamical channelling conditions using an aberration corrected microscope. A ptychographic reconstruction method called Wigner distribution deconvolution (WDD) was implemented. Our experimental results and simulation results suggest that ptychography provides a readily interpretable phase image and great sensitivity for imaging light elements at atomic resolution in relatively thin crystalline materials.« less

On the performance of digital phase locked loops in the threshold region

NASA Technical Reports Server (NTRS)

Hurst, G. T.; Gupta, S. C.

1974-01-01

Extended Kalman filter algorithms are used to obtain a digital phase lock loop structure for demodulation of angle modulated signals. It is shown that the error variance equations obtained directly from this structure enable one to predict threshold if one retains higher frequency terms. This is in sharp contrast to the similar analysis of the analog phase lock loop, where the higher frequency terms are filtered out because of the low pass filter in the loop. Results are compared to actual simulation results and threshold region results obtained previously.

Simulation-based validation and arrival-time correction for Patlak analyses of Perfusion-CT scans

NASA Astrophysics Data System (ADS)

Bredno, Jörg; Hom, Jason; Schneider, Thomas; Wintermark, Max

2009-02-01

Blood-brain-barrier (BBB) breakdown is a hypothesized mechanism for hemorrhagic transformation in acute stroke. The Patlak analysis of a Perfusion Computed Tomography (PCT) scan measures the BBB permeability, but the method yields higher estimates when applied to the first pass of the contrast bolus compared to a delayed phase. We present a numerical phantom that simulates vascular and parenchymal time-attenuation curves to determine the validity of permeability measurements obtained with different acquisition protocols. A network of tubes represents the major cerebral arteries ipsi- and contralateral to an ischemic event. These tubes branch off into smaller segments that represent capillary beds. Blood flow in the phantom is freely defined and simulated as non-Newtonian tubular flow. Diffusion of contrast in the vessels and permeation through vessel walls is part of the simulation. The phantom allows us to compare the results of a permeability measurement to the simulated vessel wall status. A Patlak analysis reliably detects areas with BBB breakdown for acquisitions of 240s duration, whereas results obtained from the first pass are biased in areas of reduced blood flow. Compensating for differences in contrast arrival times reduces this bias and gives good estimates of BBB permeability for PCT acquisitions of 90-150s duration.

Tailoring magnetic domains in Gd-Fe thin films

NASA Astrophysics Data System (ADS)

Talapatra, A.; Chelvane, J. Arout; Mohanty, J.

2018-05-01

This paper presents the global modification of magnetic domains and magnetic properties in amorphous Gd19Fe81 thin films with rapid thermal processing at two distinct temperatures (250oC and 450oC), and with different time intervals viz., 2, 5, 10 and 20 minutes. 100 nm thick as-prepared films display nano-scale meandering stripe domains with high magnetic phase contrast which is the signature of perpendicular magnetic anisotropy. The films processed at 250oC for various time intervals show successive reduction in magnetic phase contrast and domain size. The domain pattern completely disappeared, and topography dominated mixed magnetic phase has been obtained for the films processed at 450oC for time intervals greater than 2 minutes. The magnetization measurements indicate the reduction in perpendicular magnetic anisotropy with increase in saturation magnetization for all the rapid thermal processed films. The experimental outputs have been used to simulate the domain pattern. Reduction in uniaxial anisotropy along with the increase in saturation magnetization successfully explain the experimental trend of decrease in domain size and magnetic contrast.

First evidence of phase-contrast imaging with laboratory sources and active pixel sensors

NASA Astrophysics Data System (ADS)

Olivo, A.; Arvanitis, C. D.; Bohndiek, S. E.; Clark, A. T.; Prydderch, M.; Turchetta, R.; Speller, R. D.

2007-11-01

The aim of the present work is to achieve a first step towards combining the advantages of an innovative X-ray imaging technique—phase-contrast imaging (XPCi)—with those of a new class of sensors, i.e. CMOS-based active pixel sensors (APSs). The advantages of XPCi are well known and include increased image quality and detection of details invisible to conventional techniques, with potential application fields encompassing the medical, biological, industrial and security areas. Vanilla, one of the APSs developed by the MI-3 collaboration (see http://mi3.shef.ac.uk), was thoroughly characterised and an appropriate scintillator was selected to provide X-ray sensitivity. During this process, a set of phase-contrast images of different biological samples was acquired by means of the well-established free-space propagation XPCi technique. The obtained results are very encouraging and are in optimum agreement with the predictions of a simulation recently developed by some of the authors thus further supporting its reliability. This paper presents these preliminary results in detail and discusses in brief both the background to this work and its future developments.

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

Liu, Zhao; Chen-Wiegart, Yu-chen K.; Wang, Jun

Three-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO 2electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO 2particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surface area,more » feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. In conclusion, the electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.« less

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

Liu, Zhao; Chen-Wiegart, Yu-chen K.; Wang, Jun

Abstract Three-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO 2electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO 2particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surfacemore » area, feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. The electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.« less

Phase-contrast x-ray imaging of microstructure and fatigue-crack propagation in single-crystal nickel-base superalloys

NASA Astrophysics Data System (ADS)

Husseini, Naji Sami

Single-crystal nickel-base superalloys are ubiquitous in demanding turbine-blade applications, and they owe their remarkable resilience to their dendritic, hierarchical microstructure and complex composition. During normal operations, they endure rapid low-stress vibrations that may initiate fatigue cracks. This failure mode in the very high-cycle regime is poorly understood, in part due to inadequate testing and diagnostic equipment. Phase-contrast imaging with coherent synchrotron x rays, however, is an emergent technique ideally suited for dynamic processes such as crack initiation and propagation. A specially designed portable ultrasonic-fatigue apparatus, coupled with x-ray radiography, allows real-time, in situ imaging while simulating service conditions. Three contrast mechanisms - absorption, diffraction, and phase contrast - span the immense breadth of microstructural features in superalloys. Absorption contrast is sensitive to composition and crack displacements, and diffraction contrast illuminates dislocation aggregates and crystallographic misorientations. Phase contrast enhances electron-density gradients and is particularly useful for fatigue-crack studies, sensitive to internal crack tips and openings less than one micrometer. Superalloy samples were imaged without external stresses to study microstructure and mosaicity. Maps of rhenium and tungsten concentrations revealed strong segregation to the center of dendrites, as manifested by absorption contrast. Though nominally single crystals, dendrites were misoriented from the bulk by a few degrees, as revealed by diffraction contrast. For dynamic studies of cyclic fatigue, superalloys were mounted in the portable ultrasonic-fatigue apparatus, subjected to a mean tensile stress of ˜50-150 MPa, and cycled in tension to initiate and propagate fatigue cracks. Radiographs were recorded every thousand cycles over the multimillion-cycle lifetime to measure micron-scale crack growth. Crack openings were very small, as determined by absorption and phase contrast, and suggested multiple fracture modes for propagation along {111} planes at room temperature, which was verified by finite element analysis. With increasing temperature, cracks became Mode I (perpendicular to the loading axis) in character and more sensitive to the microstructure. Advancing plastic zones ahead of crack tips altered the crystallographic quality, from which diffraction contrast anticipated initiation and propagation. These studies demonstrate the extreme sensitivity of x-ray radiography for detailed studies of superalloys and crack growth processes.

Performance evaluation of spatial compounding in the presence of aberration and adaptive imaging

NASA Astrophysics Data System (ADS)

Dahl, Jeremy J.; Guenther, Drake; Trahey, Gregg E.

2003-05-01

Spatial compounding has been used for years to reduce speckle in ultrasonic images and to resolve anatomical features hidden behind the grainy appearance of speckle. Adaptive imaging restores image contrast and resolution by compensating for beamforming errors caused by tissue-induced phase errors. Spatial compounding represents a form of incoherent imaging, whereas adaptive imaging attempts to maintain a coherent, diffraction-limited aperture in the presence of aberration. Using a Siemens Antares scanner, we acquired single channel RF data on a commercially available 1-D probe. Individual channel RF data was acquired on a cyst phantom in the presence of a near field electronic phase screen. Simulated data was also acquired for both a 1-D and a custom built 8x96, 1.75-D probe (Tetrad Corp.). The data was compounded using a receive spatial compounding algorithm; a widely used algorithm because it takes advantage of parallel beamforming to avoid reductions in frame rate. Phase correction was also performed by using a least mean squares algorithm to estimate the arrival time errors. We present simulation and experimental data comparing the performance of spatial compounding to phase correction in contrast and resolution tasks. We evaluate spatial compounding and phase correction, and combinations of the two methods, under varying aperture sizes, aperture overlaps, and aberrator strength to examine the optimum configuration and conditions in which spatial compounding will provide a similar or better result than adaptive imaging. We find that, in general, phase correction is hindered at high aberration strengths and spatial frequencies, whereas spatial compounding is helped by these aberrators.

Phase-contrast MRI versus numerical simulation to quantify hemodynamical changes in cerebral aneurysms after flow diverter treatment

PubMed Central

Frolov, Sergey; Prothmann, Sascha; Liepsch, Dieter; Balasso, Andrea; Berg, Philipp; Kaczmarz, Stephan; Kirschke, Jan Stefan

2018-01-01

Cerebral aneurysms are a major risk factor for intracranial bleeding with devastating consequences for the patient. One recently established treatment is the implantation of flow-diverters (FD). Methods to predict their treatment success before or directly after implantation are not well investigated yet. The aim of this work was to quantitatively study hemodynamic parameters in patient-specific models of treated cerebral aneurysms and its correlation with the clinical outcome. Hemodynamics were evaluated using both computational fluid dynamics (CFD) and phase contrast (PC) MRI. CFD simulations and in vitro MRI measurements were done under similar flow conditions and results of both methods were comparatively analyzed. For preoperative and postoperative distribution of hemodynamic parameters, CFD simulations and PC-MRI velocity measurements showed similar results. In both cases where no occlusion of the aneurysm was observed after six months, a flow reduction of about 30-50% was found, while in the clinically successful case with complete occlusion of the aneurysm after 6 months, the flow reduction was about 80%. No vortex was observed in any of the three models after treatment. The results are in agreement with recent studies suggesting that CFD simulations can predict post-treatment aneurysm flow alteration already before implantation of a FD and PC-MRI could validate the predicted hemodynamic changes right after implantation of a FD. PMID:29304062

Wave-optical evaluation of interference fringes and wavefront phase in a hard-x-ray beam totally reflected by mirror optics.

PubMed

Yamauchi, Kazuto; Yamamura, Kazuya; Mimura, Hidekazu; Sano, Yasuhisa; Saito, Akira; Endo, Katsuyoshi; Souvorov, Alexei; Yabashi, Makina; Tamasaku, Kenji; Ishikawa, Tetsuya; Mori, Yuzo

2005-11-10

The intensity flatness and wavefront shape in a coherent hard-x-ray beam totally reflected by flat mirrors that have surface bumps modeled by Gaussian functions were investigated by use of a wave-optical simulation code. Simulated results revealed the necessity for peak-to-valley height accuracy of better than 1 nm at a lateral resolution near 0.1 mm to remove high-contrast interference fringes and appreciable wavefront phase errors. Three mirrors that had different surface qualities were tested at the 1 km-long beam line at the SPring-8/Japan Synchrotron Radiation Research Institute. Interference fringes faded when the surface figure was corrected below the subnanometer level to a spatial resolution close to 0.1 mm, as indicated by the simulated results.

Three-Phase 3D Reconstruction of a LiCoO 2 Cathode via FIB-SEM Tomography

DOE PAGES

Liu, Zhao; Chen-Wiegart, Yu-chen K.; Wang, Jun; ...

2016-01-14

Three-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO 2electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO 2particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surface area,more » feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. In conclusion, the electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.« less

Quantitative evaluation of phase processing approaches in susceptibility weighted imaging

NASA Astrophysics Data System (ADS)

Li, Ningzhi; Wang, Wen-Tung; Sati, Pascal; Pham, Dzung L.; Butman, John A.

2012-03-01

Susceptibility weighted imaging (SWI) takes advantage of the local variation in susceptibility between different tissues to enable highly detailed visualization of the cerebral venous system and sensitive detection of intracranial hemorrhages. Thus, it has been increasingly used in magnetic resonance imaging studies of traumatic brain injury as well as other intracranial pathologies. In SWI, magnitude information is combined with phase information to enhance the susceptibility induced image contrast. Because of global susceptibility variations across the image, the rate of phase accumulation varies widely across the image resulting in phase wrapping artifacts that interfere with the local assessment of phase variation. Homodyne filtering is a common approach to eliminate this global phase variation. However, filter size requires careful selection in order to preserve image contrast and avoid errors resulting from residual phase wraps. An alternative approach is to apply phase unwrapping prior to high pass filtering. A suitable phase unwrapping algorithm guarantees no residual phase wraps but additional computational steps are required. In this work, we quantitatively evaluate these two phase processing approaches on both simulated and real data using different filters and cutoff frequencies. Our analysis leads to an improved understanding of the relationship between phase wraps, susceptibility effects, and acquisition parameters. Although homodyne filtering approaches are faster and more straightforward, phase unwrapping approaches perform more accurately in a wider variety of acquisition scenarios.

Preliminary research on dual-energy X-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Han, Hua-Jie; Wang, Sheng-Hao; Gao, Kun; Wang, Zhi-Li; Zhang, Can; Yang, Meng; Zhang, Kai; Zhu, Pei-Ping

2016-04-01

Dual-energy X-ray absorptiometry (DEXA) has been widely applied to measure the bone mineral density (BMD) and soft-tissue composition of the human body. However, the use of DEXA is greatly limited for low-Z materials such as soft tissues due to their weak absorption, while X-ray phase-contrast imaging (XPCI) shows significantly improved contrast in comparison with the conventional standard absorption-based X-ray imaging for soft tissues. In this paper, we propose a novel X-ray phase-contrast method to measure the area density of low-Z materials, including a single-energy method and a dual-energy method. The single-energy method is for the area density calculation of one low-Z material, while the dual-energy method aims to calculate the area densities of two low-Z materials simultaneously. Comparing the experimental and simulation results with the theoretical ones, the new method proves to have the potential to replace DEXA in area density measurement. The new method sets the prerequisites for a future precise and low-dose area density calculation method for low-Z materials. Supported by Major State Basic Research Development Program (2012CB825800), Science Fund for Creative Research Groups (11321503) and National Natural Science Foundation of China (11179004, 10979055, 11205189, 11205157)

Binocular contrast discrimination needs monocular multiplicative noise

PubMed Central

Ding, Jian; Levi, Dennis M.

2016-01-01

The effects of signal and noise on contrast discrimination are difficult to separate because of a singularity in the signal-detection-theory model of two-alternative forced-choice contrast discrimination (Katkov, Tsodyks, & Sagi, 2006). In this article, we show that it is possible to eliminate the singularity by combining that model with a binocular combination model to fit monocular, dichoptic, and binocular contrast discrimination. We performed three experiments using identical stimuli to measure the perceived phase, perceived contrast, and contrast discrimination of a cyclopean sine wave. In the absence of a fixation point, we found a binocular advantage in contrast discrimination both at low contrasts (<4%), consistent with previous studies, and at high contrasts (≥34%), which has not been previously reported. However, control experiments showed no binocular advantage at high contrasts in the presence of a fixation point or for observers without accommodation. We evaluated two putative contrast-discrimination mechanisms: a nonlinear contrast transducer and multiplicative noise (MN). A binocular combination model (the DSKL model; Ding, Klein, & Levi, 2013b) was first fitted to both the perceived-phase and the perceived-contrast data sets, then combined with either the nonlinear contrast transducer or the MN mechanism to fit the contrast-discrimination data. We found that the best model combined the DSKL model with early MN. Model simulations showed that, after going through interocular suppression, the uncorrelated noise in the two eyes became anticorrelated, resulting in less binocular noise and therefore a binocular advantage in the discrimination task. Combining a nonlinear contrast transducer or MN with a binocular combination model (DSKL) provides a powerful method for evaluating the two putative contrast-discrimination mechanisms. PMID:26982370

Binocular contrast discrimination needs monocular multiplicative noise.

PubMed

Ding, Jian; Levi, Dennis M

2016-01-01

The effects of signal and noise on contrast discrimination are difficult to separate because of a singularity in the signal-detection-theory model of two-alternative forced-choice contrast discrimination (Katkov, Tsodyks, & Sagi, 2006). In this article, we show that it is possible to eliminate the singularity by combining that model with a binocular combination model to fit monocular, dichoptic, and binocular contrast discrimination. We performed three experiments using identical stimuli to measure the perceived phase, perceived contrast, and contrast discrimination of a cyclopean sine wave. In the absence of a fixation point, we found a binocular advantage in contrast discrimination both at low contrasts (<4%), consistent with previous studies, and at high contrasts (≥34%), which has not been previously reported. However, control experiments showed no binocular advantage at high contrasts in the presence of a fixation point or for observers without accommodation. We evaluated two putative contrast-discrimination mechanisms: a nonlinear contrast transducer and multiplicative noise (MN). A binocular combination model (the DSKL model; Ding, Klein, & Levi, 2013b) was first fitted to both the perceived-phase and the perceived-contrast data sets, then combined with either the nonlinear contrast transducer or the MN mechanism to fit the contrast-discrimination data. We found that the best model combined the DSKL model with early MN. Model simulations showed that, after going through interocular suppression, the uncorrelated noise in the two eyes became anticorrelated, resulting in less binocular noise and therefore a binocular advantage in the discrimination task. Combining a nonlinear contrast transducer or MN with a binocular combination model (DSKL) provides a powerful method for evaluating the two putative contrast-discrimination mechanisms.

In vivo differentiation of complementary contrast media at dual-energy CT.

PubMed

Mongan, John; Rathnayake, Samira; Fu, Yanjun; Wang, Runtang; Jones, Ella F; Gao, Dong-Wei; Yeh, Benjamin M

2012-10-01

To evaluate the feasibility of using a commercially available clinical dual-energy computed tomographic (CT) scanner to differentiate the in vivo enhancement due to two simultaneously administered contrast media with complementary x-ray attenuation ratios. Approval from the institutional animal care and use committee was obtained, and National Institutes of Health guidelines for the care and use of laboratory animals were observed. Dual-energy CT was performed in a set of iodine and tungsten solution phantoms and in a rabbit in which iodinated intravenous and bismuth subsalicylate oral contrast media were administered. In addition, a second rabbit was studied after intravenous administration of iodinated and tungsten cluster contrast media. Images were processed to produce virtual monochromatic images that simulated the appearance of conventional single-energy scans, as well as material decomposition images that separate the attenuation due to each contrast medium. Clear separation of each of the contrast media pairs was seen in the phantom and in both in vivo animal models. Separation of bowel lumen from vascular contrast medium allowed visualization of bowel wall enhancement that was obscured by intraluminal bowel contrast medium on conventional CT scans. Separation of two vascular contrast media in different vascular phases enabled acquisition of a perfectly coregistered CT angiogram and venous phase-enhanced CT scan simultaneously in a single examination. Commercially available clinical dual-energy CT scanners can help differentiate the enhancement of selected pairs of complementary contrast media in vivo. © RSNA, 2012.

Steady-state hydrodynamic instabilities of active liquid crystals: hybrid lattice Boltzmann simulations.

PubMed

Marenduzzo, D; Orlandini, E; Cates, M E; Yeomans, J M

2007-09-01

We report hybrid lattice Boltzmann (HLB) simulations of the hydrodynamics of an active nematic liquid crystal sandwiched between confining walls with various anchoring conditions. We confirm the existence of a transition between a passive phase and an active phase, in which there is spontaneous flow in the steady state. This transition is attained for sufficiently "extensile" rods, in the case of flow-aligning liquid crystals, and for sufficiently "contractile" ones for flow-tumbling materials. In a quasi-one-dimensional geometry, deep in the active phase of flow-aligning materials, our simulations give evidence of hysteresis and history-dependent steady states, as well as of spontaneous banded flow. Flow-tumbling materials, in contrast, rearrange themselves so that only the two boundary layers flow in steady state. Two-dimensional simulations, with periodic boundary conditions, show additional instabilities, with the spontaneous flow appearing as patterns made up of "convection rolls." These results demonstrate a remarkable richness (including dependence on anchoring conditions) in the steady-state phase behavior of active materials, even in the absence of external forcing; they have no counterpart for passive nematics. Our HLB methodology, which combines lattice Boltzmann for momentum transport with a finite difference scheme for the order parameter dynamics, offers a robust and efficient method for probing the complex hydrodynamic behavior of active nematics.

The Roles of Magnetosphere-Ionosphere Coupling on Ring Current development: Comparison of TWINS Measurements and CIMI Simulations for the 7-10 September 2015 Geomagnetic Storm

NASA Astrophysics Data System (ADS)

Edmond, J. A.; Hill, S. C.; Xu, H.; Perez, J. D.; Fok, M. C. H.; Goldstein, J.; McComas, D. J.; Valek, P. W.

2017-12-01

The Two Wide-Angle Imaging Neutral-Atom Spectrometers (TWINS) mission obtained energetic neutral atom (ENA) images during a 4 day storm on 7-10 September 2015. The storm has two separate SYM/H minima, so we divide the storm into four intervals: first main phase, first recovery phase, second main phase, and second recovery phase. Simulations with the Comprehensive Inner Magnetosphere-Ionosphere Model (CIMI) are compared and contrasted with the TWINS observations. We find good agreement in most aspects of the storm. E. G. (1) the location of the ion pressure peaks are most often in the dusk-midnight sector, (2) the pitch angle distributions at the pressure peaks most often display perpendicular anisotropy, and (3) the energy spectra at the pressure peaks have similar maximum energies. There are, however, some exceptions to these general features. We describe and interpret these notable events. We also have examined particle paths determined from the CIMI model simulations to assist in the interpretation of the notable events.In this poster, we focus upon the features of the CIMI simulations with a self-consistent electric field and with the semi-empirical Weimer electric potential in relationship to the TWINS observations.

Phase contrast STEM for thin samples: Integrated differential phase contrast.

PubMed

Lazić, Ivan; Bosch, Eric G T; Lazar, Sorin

2016-01-01

It has been known since the 1970s that the movement of the center of mass (COM) of a convergent beam electron diffraction (CBED) pattern is linearly related to the (projected) electrical field in the sample. We re-derive a contrast transfer function (CTF) for a scanning transmission electron microscopy (STEM) imaging technique based on this movement from the point of view of image formation and continue by performing a two-dimensional integration on the two images based on the two components of the COM movement. The resulting integrated COM (iCOM) STEM technique yields a scalar image that is linear in the phase shift caused by the sample and therefore also in the local (projected) electrostatic potential field of a thin sample. We confirm that the differential phase contrast (DPC) STEM technique using a segmented detector with 4 quadrants (4Q) yields a good approximation for the COM movement. Performing a two-dimensional integration, just as for the COM, we obtain an integrated DPC (iDPC) image which is approximately linear in the phase of the sample. Beside deriving the CTFs of iCOM and iDPC, we clearly point out the objects of the two corresponding imaging techniques, and highlight the differences to objects corresponding to COM-, DPC-, and (HA) ADF-STEM. The theory is validated with simulations and we present first experimental results of the iDPC-STEM technique showing its capability for imaging both light and heavy elements with atomic resolution and a good signal to noise ratio (SNR). Copyright © 2015 Elsevier B.V. All rights reserved.

Selection of higher eigenmode amplitude based on dissipated power and virial contrast in bimodal atomic force microscopy

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

Diaz, Alfredo J.; Eslami, Babak; López-Guerra, Enrique A.

2014-09-14

This paper explores the effect of the amplitude ratio of the higher to the fundamental eigenmode in bimodal atomic force microscopy (AFM) on the phase contrast and the dissipated power contrast of the higher eigenmode. We explore the optimization of the amplitude ratio in order to maximize the type of contrast that is most relevant to the particular study. Specifically, we show that the trends in the contrast range behave differently for different quantities, especially the dissipated power and the phase, with the former being more meaningful than the latter (a similar analysis can be carried out using the virial,more » for which we also provide a brief example). Our work is based on numerical simulations using two different conservative-dissipative tip-sample models, including the standard linear solid and the combination of a dissipation coefficient with a conservative model, as well as experimental images of thin film Nafion{sup ®} proton exchange polymers. We focus on the original bimodal AFM method, where the higher eigenmode is driven with constant amplitude and frequency (i.e., in “open loop”).« less

Far-from-equilibrium bidirectional transport system with constrained entrances competing for pool of limited resources

NASA Astrophysics Data System (ADS)

Verma, Atul Kumar; Sharma, Natasha; Gupta, Arvind Kumar

2018-02-01

Motivated by the wide occurrence of limited resources in many real-life systems, we investigate two-lane totally asymmetric simple exclusion process with constrained entrances under finite supply of particles. We analyze the system within the framework of mean-field theory and examine various complex phenomena, including phase separation, phase transition, and symmetry breaking. Based on the theoretical analysis, we analytically derive the phase boundaries for various symmetric as well as asymmetric phases. It has been observed that the symmetry-breaking phenomenon initiates even for very small number of particles in the system. The phases with broken symmetry originates as shock-low density phase under limited resources, which is in contrast to the scenario with infinite number of particles. As expected, the symmetry breaking continues to persist even for higher values of system particles. Seven stationary phases are observed, with three of them exhibiting symmetry-breaking phenomena. The critical values of a total number of system particles, beyond which various symmetrical and asymmetrical phases appear and disappear are identified. Theoretical outcomes are supported by extensive Monte Carlo simulations. Finally, the size-scaling effect and symmetry-breaking phenomenon on the simulation results have also been examined based on particle density histograms.

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

Meiser, Jerome; Urbassek, Herbert M., E-mail: urbassek@rhrk.uni-kl.de

Using classical molecular dynamics simulations and the Meyer-Entel interaction potential, we study the martensitic transformation pathway in a pure iron bi-crystal containing a symmetric tilt grain boundary. Upon cooling the system from the austenitic phase, the transformation starts with the nucleation of the martensitic phase near the grain boundary in a plate-like arrangement. The Kurdjumov-Sachs orientation relations are fulfilled at the plates. During further cooling, the plates expand and merge. In contrast to the orientation relation in the plate structure, the complete transformation proceeds via the Pitsch pathway.

Pathogenesis of primary foot-and-mouth disease virus infection in the nasopharynx of vaccinated and non-vaccinated cattle

USDA-ARS?s Scientific Manuscript database

A time-course pathogenesis study was performed to compare and contrast primary foot-and-mouth disease virus (FMDV) infection in vaccinated and non-vaccinated cattle following simulated-natural virus exposure. FMDV genome and infectious virus were detected during the initial phase of infection from b...

Effective conductivity, dielectric constant, and diffusion coefficient of digitized composite media via first-passage-time equations

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

Torquato, S.; Kim, I.C.; Cule, D.

1999-02-01

We generalize the Brownian motion simulation method of Kim and Torquato [J. Appl. Phys. {bold 68}, 3892 (1990)] to compute the effective conductivity, dielectric constant and diffusion coefficient of digitized composite media. This is accomplished by first generalizing the {ital first-passage-time equations} to treat first-passage regions of arbitrary shape. We then develop the appropriate first-passage-time equations for digitized media: first-passage squares in two dimensions and first-passage cubes in three dimensions. A severe test case to prove the accuracy of the method is the two-phase periodic checkerboard in which conduction, for sufficiently large phase contrasts, is dominated by corners that joinmore » two conducting-phase pixels. Conventional numerical techniques (such as finite differences or elements) do not accurately capture the local fields here for reasonable grid resolution and hence lead to inaccurate estimates of the effective conductivity. By contrast, we show that our algorithm yields accurate estimates of the effective conductivity of the periodic checkerboard for widely different phase conductivities. Finally, we illustrate our method by computing the effective conductivity of the random checkerboard for a wide range of volume fractions and several phase contrast ratios. These results always lie within rigorous four-point bounds on the effective conductivity. {copyright} {ital 1999 American Institute of Physics.}« less

Phase-Contrast MRI and CFD Modeling of Apparent 3He Gas Flow in Rat Pulmonary Airways

PubMed Central

Minard, Kevin R.; Kuprat, Andrew P.; Kabilan, Senthil; Jacob, Richard E.; Einstein, Daniel R.; Carson, James P.; Corley, Richard A.

2012-01-01

Phase-contrast (PC) magnetic resonance imaging (MRI) with hyperpolarized 3He is potentially useful for developing and testing patient-specific models of pulmonary airflow. One challenge, however, is that PC-MRI provides apparent values of local 3He velocity that not only depend on actual airflow but also on gas diffusion. This not only blurs laminar flow patterns in narrow airways but also introduces anomalous airflow structure that reflects gas-wall interactions. Here, both effects are predicted in a live rat using computational fluid dynamics (CFD), and for the first time, simulated patterns of apparent 3He gas velocity are compared with in-vivo PC-MRI. Results show 1) that correlations (R2) between measured and simulated airflow patterns increase from 0.23 to 0.79 simply by accounting for apparent 3He transport, and 2) that remaining differences are mainly due to uncertain airway segmentation and partial volume effects stemming from relatively coarse MRI resolution. Higher-fidelity testing of pulmonary airflow predictions should therefore be possible with future imaging improvements. PMID:22771528

Phase-contrast MRI and CFD modeling of apparent 3He gas flow in rat pulmonary airways

NASA Astrophysics Data System (ADS)

Minard, Kevin R.; Kuprat, Andrew P.; Kabilan, Senthil; Jacob, Richard E.; Einstein, Daniel R.; Carson, James P.; Corley, Richard A.

2012-08-01

Phase-contrast (PC) magnetic resonance imaging (MRI) with hyperpolarized 3He is potentially useful for developing and testing patient-specific models of pulmonary airflow. One challenge, however, is that PC-MRI provides apparent values of local 3He velocity that not only depend on actual airflow but also on gas diffusion. This not only blurs laminar flow patterns in narrow airways but also introduces anomalous airflow structure that reflects gas-wall interactions. Here, both effects are predicted in a live rat using computational fluid dynamics (CFD), and for the first time, simulated patterns of apparent 3He gas velocity are compared with in vivo PC-MRI. Results show (1) that correlations (R2) between measured and simulated airflow patterns increase from 0.23 to 0.79 simply by accounting for apparent 3He transport, and (2) that remaining differences are mainly due to uncertain airway segmentation and partial volume effects stemming from relatively coarse MRI resolution. Higher-fidelity testing of pulmonary airflow predictions should therefore be possible with future imaging improvements.

Dark-field imaging in coronary atherosclerosis.

PubMed

Hetterich, Holger; Webber, Nicole; Willner, Marian; Herzen, Julia; Birnbacher, Lorenz; Auweter, Sigrid; Schüller, Ulrich; Bamberg, Fabian; Notohamiprodjo, Susan; Bartsch, Harald; Wolf, Johannes; Marschner, Mathias; Pfeiffer, Franz; Reiser, Maximilian; Saam, Tobias

2017-09-01

Dark-field imaging based on small angle X-ray scattering has been shown to be highly sensitive for microcalcifications, e.g. in breast tissue. We hypothesized (i) that high signal areas in dark-field imaging of atherosclerotic plaque are associated with microcalcifications and (ii) that dark-field imaging is more sensitive for microcalcifications than attenuation-based imaging. Fifteen coronary artery specimens were examined at an experimental set-up consisting of X-ray tube (40kV), grating-interferometer and detector. Tomographic dark-field-, attenuation-, and phase-contrast data were simultaneously acquired. Histopathology served as standard of reference. To explore the potential of dark field imaging in a full-body CT system, simulations were carried out with spherical calcifications of different sizes to simulate small and intermediate microcalcifications. Microcalcifications were present in 10/10 (100%) cross-sections with high dark-field signal and without evidence of calcifications in attenuation- or phase contrast. In positive controls with high signal areas in all three modalities, 10/10 (100%) cross-sections showed macrocalcifications. In negative controls without high signal areas, no calcifications were detected. Simulations showed that the microcalcifications generate substantially higher dark-field than attenuation signal. Dark-field imaging is highly sensitive for microcalcifications in coronary atherosclerotic plaque and might provide complementary information in the assessment of plaque instability. Copyright © 2017 Elsevier B.V. All rights reserved.

Lesion contrast and detection using sonoelastographic shear velocity imaging: preliminary results

NASA Astrophysics Data System (ADS)

Hoyt, Kenneth; Parker, Kevin J.

2007-03-01

This paper assesses lesion contrast and detection using sonoelastographic shear velocity imaging. Shear wave interference patterns, termed crawling waves, for a two phase medium were simulated assuming plane wave conditions. Shear velocity estimates were computed using a spatial autocorrelation algorithm that operates in the direction of shear wave propagation for a given kernel size. Contrast was determined by analyzing shear velocity estimate transition between mediums. Experimental results were obtained using heterogeneous phantoms with spherical inclusions (5 or 10 mm in diameter) characterized by elevated shear velocities. Two vibration sources were applied to opposing phantom edges and scanned (orthogonal to shear wave propagation) with an ultrasound scanner equipped for sonoelastography. Demodulated data was saved and transferred to an external computer for processing shear velocity images. Simulation results demonstrate shear velocity transition between contrasting mediums is governed by both estimator kernel size and source vibration frequency. Experimental results from phantoms further indicates that decreasing estimator kernel size produces corresponding decrease in shear velocity estimate transition between background and inclusion material albeit with an increase in estimator noise. Overall, results demonstrate the ability to generate high contrast shear velocity images using sonoelastographic techniques and detect millimeter-sized lesions.

The kinematics and kinetics of riding a racehorse: A quantitative comparison of a training simulator and real horses.

PubMed

Walker, A M; Applegate, C; Pfau, T; Sparkes, E L; Wilson, A M; Witte, T H

2016-10-03

Movement of a racehorse simulator differs to that of a real horse, but the effects of these differences on jockey technique have not been evaluated. We quantified and compared the kinematics and kinetics of jockeys during gallop riding on a simulator and real horses. Inertial measurement units were attached mid-shaft to the long bones of six jockeys and the sacrum of the horse or simulator. Instrumented stirrups were used to measure force. Data were collected during galloping on a synthetic gallop or while riding a racehorse simulator. Jockey kinematics varied more on a real horse compared to the simulator. Greater than double the peak stirrup force was recorded during gallop on real horses compared to the simulator. On the simulator stirrup forces were symmetrical, whereas on a real horse peak forces were higher on the opposite side to the lead limb. Asymmetric forces and lateral movement of the horse and jockey occurs away from the side of the lead leg, likely a result of horse trunk roll. Jockeys maintained a more upright trunk position on a real horse compared to simulator, with no change in pitch. The feet move in phase with the horse and simulator exhibiting similar magnitude displacements in all directions. In contrast the pelvis was in phase with the horse and simulator in the dorso-ventral and medio-lateral axes while a phase shift of 180° was seen in the cranio-caudal direction indicating an inverted pendulum action of the jockey. Copyright © 2016 Elsevier Ltd. All rights reserved.

Flow cytometry with gold nanoparticles and their clusters as scattering contrast agents: FDTD simulation of light-cell interaction.

PubMed

Tanev, Stoyan; Sun, Wenbo; Pond, James; Tuchin, Valery V; Zharov, Vladimir P

2009-09-01

The formulation of the finite-difference time-domain (FDTD) approach is presented in the framework of its potential applications to in-vivo flow cytometry based on light scattering. The consideration is focused on comparison of light scattering by a single biological cell alone in controlled refractive-index matching conditions and by cells labeled by gold nanoparticles. The optical schematics including phase contrast (OPCM) microscopy as a prospective modality for in-vivo flow cytometry is also analyzed. The validation of the FDTD approach for the simulation of flow cytometry may open up a new avenue in the development of advanced cytometric techniques based on scattering effects from nanoscale targets. 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Influence of simulated microgravity on the longevity of insect-cell culture

NASA Technical Reports Server (NTRS)

Cowger, N. L.; O'Connor, K. C.; Bivins, J. E.

1997-01-01

Simulated microgravity within the NASA High Aspect Rotating-Wall Vessel (HARV) provides a quiescent environment to culture fragile insect cells. In this vessel, the duration of stationary and death phase for cultures of Spodoptera frugiperda cells was greatly extended over that achieved in shaker-flask controls. For both HARV and control cultures, S. frugiperda cells grew to concentrations in excess of 1 x 10(7) viable cells ml-1 with viabilities greater than 90%. In the HARV, stationary phase was maintained 9-15 days in contrast to 4-5 days in the shaker flask. Furthermore, the rate of cell death was reduced in the HARV by a factor of 20-90 relative to the control culture and was characterized with a death rate constant of 0.01-0.02 day-1. Beginning in the stationary phase and continuing in the death phase, there was a significant decrease in population size in the HARV versus an increase in the shaker flask. This phenomenon could represent cell adaptation to simulated microgravity and/or a change in the ratio of apoptotic to necrotic cells. Differences observed in this research between the HARV and its control were attributed to a reduction in hydrodynamic forces in the microgravity vessel.

Stochastic Rotation Dynamics simulations of wetting multi-phase flows

NASA Astrophysics Data System (ADS)

Hiller, Thomas; Sanchez de La Lama, Marta; Brinkmann, Martin

2016-06-01

Multi-color Stochastic Rotation Dynamics (SRDmc) has been introduced by Inoue et al. [1,2] as a particle based simulation method to study the flow of emulsion droplets in non-wetting microchannels. In this work, we extend the multi-color method to also account for different wetting conditions. This is achieved by assigning the color information not only to fluid particles but also to virtual wall particles that are required to enforce proper no-slip boundary conditions. To extend the scope of the original SRDmc algorithm to e.g. immiscible two-phase flow with viscosity contrast we implement an angular momentum conserving scheme (SRD+mc). We perform extensive benchmark simulations to show that a mono-phase SRDmc fluid exhibits bulk properties identical to a standard SRD fluid and that SRDmc fluids are applicable to a wide range of immiscible two-phase flows. To quantify the adhesion of a SRD+mc fluid in contact to the walls we measure the apparent contact angle from sessile droplets in mechanical equilibrium. For a further verification of our wettability implementation we compare the dewetting of a liquid film from a wetting stripe to experimental and numerical studies of interfacial morphologies on chemically structured surfaces.

Phase locked multiple rings in the radiation pressure ion acceleration process

NASA Astrophysics Data System (ADS)

Wan, Y.; Hua, J. F.; Pai, C.-H.; Li, F.; Wu, Y. P.; Lu, W.; Zhang, C. J.; Xu, X. L.; Joshi, C.; Mori, W. B.

2018-04-01

Laser contrast plays a crucial role for obtaining high quality ion beams in the radiation pressure ion acceleration (RPA) process. Through one- and two-dimensional particle-in-cell (PIC) simulations, we show that a plasma with a bi-peak density profile can be produced from a thin foil on the effects of a picosecond prepulse, and it can then lead to distinctive modulations in the ion phase space (phase locked double rings) when the main pulse interacts with the target. These fascinating ion dynamics are mainly due to the trapping effect from the ponderomotive potential well of a formed moving standing wave (i.e. the interference between the incoming pulse and the pulse reflected by a slowly moving surface) at nodes, quite different from the standard RPA process. A theoretical model is derived to explain the underlying mechanism, and good agreements have been achieved with PIC simulations.

Phase locked multiple rings in the radiation pressure ion acceleration process

DOE PAGES

Wan, Y.; Hua, J. F.; Pai, C. -H.; ...

2018-03-05

Laser contrast plays a crucial role for obtaining high quality ion beams in the radiation pressure ion acceleration (RPA) process. Through one- and two-dimensional particle-in-cell (PIC) simulations, we show that a plasma with a bi-peak density profile can be produced from a thin foil on the effects of a picosecond prepulse, and it can then lead to distinctive modulations in the ion phase space (phase locked double rings) when the main pulse interacts with the target. These fascinating ion dynamics are mainly due to the trapping effect from the ponderomotive potential well of a formed moving standing wave (i.e. themore » interference between the incoming pulse and the pulse reflected by a slowly moving surface) at nodes, quite different from the standard RPA process. Here, a theoretical model is derived to explain the underlying mechanism, and good agreements have been achieved with PIC simulations.« less

Extinction phase transitions in a model of ecological and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Barghathi, Hatem; Tackkett, Skye; Vojta, Thomas

2017-07-01

We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental conditions, i.e., temporal disorder. Using large-scale Monte-Carlo simulations of up to 3 × 107 organisms and 105 generations, we find the extinction transition in time-independent environments to be in the well-known directed percolation universality class. In contrast, temporal disorder leads to a highly unusual extinction transition characterized by logarithmically slow population decay and enormous fluctuations even for large populations. The simulations provide strong evidence for this transition to be of exotic infinite-noise type, as recently predicted by a renormalization group theory. The transition is accompanied by temporal Griffiths phases featuring a power-law dependence of the life time on the population size.

Phase locked multiple rings in the radiation pressure ion acceleration process

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

Wan, Y.; Hua, J. F.; Pai, C. -H.

Laser contrast plays a crucial role for obtaining high quality ion beams in the radiation pressure ion acceleration (RPA) process. Through one- and two-dimensional particle-in-cell (PIC) simulations, we show that a plasma with a bi-peak density profile can be produced from a thin foil on the effects of a picosecond prepulse, and it can then lead to distinctive modulations in the ion phase space (phase locked double rings) when the main pulse interacts with the target. These fascinating ion dynamics are mainly due to the trapping effect from the ponderomotive potential well of a formed moving standing wave (i.e. themore » interference between the incoming pulse and the pulse reflected by a slowly moving surface) at nodes, quite different from the standard RPA process. Here, a theoretical model is derived to explain the underlying mechanism, and good agreements have been achieved with PIC simulations.« less

Local structure of the crystalline and amorphous states of Ga2Te3 phase-change alloy without resonant bonding: A combined x-ray absorption and ab initio study

NASA Astrophysics Data System (ADS)

Kolobov, A. V.; Fons, P.; Krbal, M.; Mitrofanov, K.; Tominaga, J.; Uruga, T.

2017-02-01

Phase-change memories are usually associated with GeTe-Sb2Te3 quasibinary alloys, where the large optical contrast between the crystalline and amorphous phases is attributed to the formation of resonant bonds in the crystalline phase, which has a rocksalt-like structure. The recent findings that tetrahedrally bonded Ga2Te3 possesses a similarly large property contrast and very low thermal conductivity in the crystalline phase and undergoes low-energy switching [H. Zhu et al., Appl. Phys. Lett. 97, 083504 (2010), 10.1063/1.3483762; K. Kurosaki et al., Appl. Phys. Lett. 93, 012101 (2008), 10.1063/1.2940591] challenge the existing paradigm. In this work we report on the local structure of the crystalline and amorphous phases of Ga2Te3 obtained from x-ray absorption measurements and ab initio simulations. Based on the obtained results, a model of phase change in Ga2Te3 is proposed. We argue that efficient switching in Ga2Te3 is due to the presence of primary and secondary bonding in the crystalline phase originating from the high concentration of Ga vacancies, whereas the structural stability of both phases is ensured by polyvalency of Te atoms due to the presence of lone-pair electrons and the formation of like-atom bonds in the amorphous phase.

Program optimizations: The interplay between power, performance, and energy

DOE PAGES

Leon, Edgar A.; Karlin, Ian; Grant, Ryan E.; ...

2016-05-16

Practical considerations for future supercomputer designs will impose limits on both instantaneous power consumption and total energy consumption. Working within these constraints while providing the maximum possible performance, application developers will need to optimize their code for speed alongside power and energy concerns. This paper analyzes the effectiveness of several code optimizations including loop fusion, data structure transformations, and global allocations. A per component measurement and analysis of different architectures is performed, enabling the examination of code optimizations on different compute subsystems. Using an explicit hydrodynamics proxy application from the U.S. Department of Energy, LULESH, we show how code optimizationsmore » impact different computational phases of the simulation. This provides insight for simulation developers into the best optimizations to use during particular simulation compute phases when optimizing code for future supercomputing platforms. Here, we examine and contrast both x86 and Blue Gene architectures with respect to these optimizations.« less

Detectability comparison between a high energy x-ray phase sensitive and mammography systems in imaging phantoms with varying glandular-adipose ratios

NASA Astrophysics Data System (ADS)

Ghani, Muhammad U.; Wong, Molly D.; Wu, Di; Zheng, Bin; Fajardo, Laurie L.; Yan, Aimin; Fuh, Janis; Wu, Xizeng; Liu, Hong

2017-05-01

The objective of this study was to demonstrate the potential benefits of using high energy x-rays in comparison with the conventional mammography imaging systems for phase sensitive imaging of breast tissues with varying glandular-adipose ratios. This study employed two modular phantoms simulating the glandular (G) and adipose (A) breast tissue composition in 50 G-50 A and 70 G-30 A percentage densities. Each phantom had a thickness of 5 cm with a contrast detail test pattern embedded in the middle. For both phantoms, the phase contrast images were acquired using a micro-focus x-ray source operated at 120 kVp and 4.5 mAs, with a magnification factor (M) of 2.5 and a detector with a 50 µm pixel pitch. The mean glandular dose delivered to the 50 G-50 A and 70 G-30 A phantom sets were 1.33 and 1.3 mGy, respectively. A phase retrieval algorithm based on the phase attenuation duality that required only a single phase contrast image was applied. Conventional low energy mammography images were acquired using GE Senographe DS and Hologic Selenia systems utilizing their automatic exposure control (AEC) settings. In addition, the automatic contrast mode (CNT) was also used for the acquisition with the GE system. The AEC mode applied higher dose settings for the 70 G-30 A phantom set. As compared to the phase contrast images, the dose levels for the AEC mode acquired images were similar while the dose levels for the CNT mode were almost double. The observer study, contrast-to-noise ratio and figure of merit comparisons indicated a large improvement with the phase retrieved images in comparison to the AEC mode images acquired with the clinical systems for both density levels. As the glandular composition increased, the detectability of smaller discs decreased with the clinical systems, particularly with the GE system, even at higher dose settings. As compared to the CNT mode (double dose) images, the observer study also indicated that the phase retrieved images provided similar or improved detection for all disc sizes except for the disk diameters of 2 mm and 1 mm for the 50 G-50 A phantom and 3 mm and 0.5 mm for the 70 G-30 A phantom. This study demonstrated the potential of utilizing a high energy phase sensitive x-ray imaging system to improve lesion detection and reduce radiation dose when imaging breast tissues with varying glandular compositions.

Pairing versus phase coherence of doped holes in distinct quantum spin backgrounds

NASA Astrophysics Data System (ADS)

Zhu, Zheng; Sheng, D. N.; Weng, Zheng-Yu

2018-03-01

We examine the pairing structure of holes injected into two distinct spin backgrounds: a short-range antiferromagnetic phase versus a symmetry protected topological phase. Based on density matrix renormalization group (DMRG) simulation, we find that although there is a strong binding between two holes in both phases, phase fluctuations can significantly influence the pair-pair correlation depending on the spin-spin correlation in the background. Here the phase fluctuation is identified as an intrinsic string operator nonlocally controlled by the spins. We show that while the pairing amplitude is generally large, the coherent Cooper pairing can be substantially weakened by the phase fluctuation in the symmetry-protected topological phase, in contrast to the short-range antiferromagnetic phase. It provides an example of a non-BCS mechanism for pairing, in which the paring phase coherence is determined by the underlying spin state self-consistently, bearing an interesting resemblance to the pseudogap physics in the cuprate.

Analysis of field of view limited by a multi-line X-ray source and its improvement for grating interferometry.

PubMed

Du, Yang; Huang, Jianheng; Lin, Danying; Niu, Hanben

2012-08-01

X-ray phase-contrast imaging based on grating interferometry is a technique with the potential to provide absorption, differential phase contrast, and dark-field signals simultaneously. The multi-line X-ray source used recently in grating interferometry has the advantage of high-energy X-rays for imaging of thick samples for most clinical and industrial investigations. However, it has a drawback of limited field of view (FOV), because of the axial extension of the X-ray emission area. In this paper, we analyze the effects of axial extension of the multi-line X-ray source on the FOV and its improvement in terms of Fresnel diffraction theory. Computer simulation results show that the FOV limitation can be overcome by use of an alternative X-ray tube with a specially designed multi-step anode. The FOV of this newly designed X-ray source can be approximately four times larger than that of the multi-line X-ray source in the same emission area. This might be beneficial for the applications of X-ray phase contrast imaging in materials science, biology, medicine, and industry.

Rheology and hydrodynamic properties of Tolypocladium inflatum fermentation broth and its simulation.

PubMed

Benchapattarapong, N; Anderson, W A; Bai, F; Moo-Young, M

2005-07-01

A physico-chemical, two phase simulated pseudoplastic fermentation (SPF) broth was investigated in which Solka Floc cellulose fibre was used to simulate the filamentous biomass, and a mixture of 0.1% (w/v) carboxymethyl cellulose (CMC) and 0.15 M aqueous sodium chloride was used to simulate the liquid fraction of the fermentation broth. An investigation of the rheological behaviour and hydrodynamic properties of the SPF broth was carried out, and compared to both a fungal Tolypocladium inflatum fermentation broth and a CMC solution in a 50 L stirred tank bioreactor equipped with conventional Rushton turbines. The experimental data confirmed the ability of the two phase SPF broth to mimic both the T. inflatum broth bulk rheology as well as the mixing and mass transfer behaviour. In contrast, using a homogeneous CMC solution with a similar bulk rheology to simulate the fermentation resulted in a significant underestimation of the mass transfer and mixing times. The presence of the solid phase and its microstructure in the SPF broth appear to play a significant role in gas holdup and bubble size, thus leading to the different behaviours. The SPF broth seems to be a more accurate simulation fluid that can be used to predict the bioreactor mixing and mass transfer performance in filamentous fermentations, in comparison with CMC solutions used in some previous studies.

Binocular combination of phase and contrast explained by a gain-control and gain-enhancement model

PubMed Central

Ding, Jian; Klein, Stanley A.; Levi, Dennis M.

2013-01-01

We investigated suprathreshold binocular combination, measuring both the perceived phase and perceived contrast of a cyclopean sine wave. We used a paradigm adapted from Ding and Sperling (2006, 2007) to measure the perceived phase by indicating the apparent location (phase) of the dark trough in the horizontal cyclopean sine wave relative to a black horizontal reference line, and we used the same stimuli to measure perceived contrast by matching the binocular combined contrast to a standard contrast presented to one eye. We found that under normal viewing conditions (high contrast and long stimulus duration), perceived contrast is constant, independent of the interocular contrast ratio and the interocular phase difference, while the perceived phase shifts smoothly from one eye to the other eye depending on the contrast ratios. However, at low contrasts and short stimulus durations, binocular combination is more linear and contrast summation is phase-dependent. To account for phase-dependent contrast summation, we incorporated a fusion remapping mechanism into our model, using disparity energy to shift the monocular phases towards the cyclopean phase in order to align the two eyes' images through motor/sensory fusion. The Ding-Sperling model with motor/sensory fusion mechanism gives a reasonable account of the phase dependence of binocular contrast combination and can account for either the perceived phase or the perceived contrast of a cyclopean sine wave separately; however it requires different model parameters for the two. However, when fit to both phase and contrast data simultaneously, the Ding-Sperling model fails. Incorporating interocular gain enhancement into the model results in a significant improvement in fitting both phase and contrast data simultaneously, successfully accounting for both linear summation at low contrast energy and strong nonlinearity at high contrast energy. PMID:23397038

Toward multiscale modelings of grain-fluid systems

NASA Astrophysics Data System (ADS)

Chareyre, Bruno; Yuan, Chao; Montella, Eduard P.; Salager, Simon

2017-06-01

Computationally efficient methods have been developed for simulating partially saturated granular materials in the pendular regime. In contrast, one hardly avoid expensive direct resolutions of 2-phase fluid dynamics problem for mixed pendular-funicular situations or even saturated regimes. Following previous developments for single-phase flow, a pore-network approach of the coupling problems is described. The geometry and movements of phases and interfaces are described on the basis of a tetrahedrization of the pore space, introducing elementary objects such as bridge, meniscus, pore body and pore throat, together with local rules of evolution. As firmly established local rules are still missing on some aspects (entry capillary pressure and pore-scale pressure-saturation relations, forces on the grains, or kinetics of transfers in mixed situations) a multi-scale numerical framework is introduced, enhancing the pore-network approach with the help of direct simulations. Small subsets of a granular system are extracted, in which multiphase scenario are solved using the Lattice-Boltzman method (LBM). In turns, a global problem is assembled and solved at the network scale, as illustrated by a simulated primary drainage.

Unwrapping eddy current compensation: improved compensation of eddy current induced baseline shifts in high-resolution phase-contrast MRI at 9.4 Tesla.

PubMed

Espe, Emil K S; Zhang, Lili; Sjaastad, Ivar

2014-10-01

Phase-contrast MRI (PC-MRI) is a versatile tool allowing evaluation of in vivo motion, but is sensitive to eddy current induced phase offsets, causing errors in the measured velocities. In high-resolution PC-MRI, these offsets can be sufficiently large to cause wrapping in the baseline phase, rendering conventional eddy current compensation (ECC) inadequate. The purpose of this study was to develop an improved ECC technique (unwrapping ECC) able to handle baseline phase discontinuities. Baseline phase discontinuities are unwrapped by minimizing the spatiotemporal standard deviation of the static-tissue phase. Computer simulations were used for demonstrating the theoretical foundation of the proposed technique. The presence of baseline wrapping was confirmed in high-resolution myocardial PC-MRI of a normal rat heart at 9.4 Tesla (T), and the performance of unwrapping ECC was compared with conventional ECC. Areas of phase wrapping in static regions were clearly evident in high-resolution PC-MRI. The proposed technique successfully eliminated discontinuities in the baseline, and resulted in significantly better ECC than the conventional approach. We report the occurrence of baseline phase wrapping in PC-MRI, and provide an improved ECC technique capable of handling its presence. Unwrapping ECC offers improved correction of eddy current induced baseline shifts in high-resolution PC-MRI. Copyright © 2013 Wiley Periodicals, Inc.

Stability of the bcc phase of 4He close to the melting curve: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Belonoshko, A. B.; Koči, L.; Rosengren, A.

2012-01-01

We have investigated whether the Aziz [J. Chem. Phys.JCPSA60021-960610.1063/1.438007 70, 4330 (1979)] model for 4He renders the body-centered cubic phase more stable than the face-centered cubic phase in the proximity of the melting curve. Using molecular dynamics, we have simulated these solid phases in equilibrium with the liquid at a number of densities. In contrast to previous free energy molecular dynamics calculations, the model stabilizes the body-centered cubic phase. The stability field is just 5∘ wide below the melting curve at pressures around 140 Kbar and about 70∘ wide at pressures around 750 Kbar. Considering that the body-centered cubic phase is dynamically unstable at low temperature, this result bears striking similarities to transition metal phase diagrams.

Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

NASA Astrophysics Data System (ADS)

Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki

2016-03-01

Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and posterior eye segment as well as in skin imaging. The new estimator shows superior performance and also shows clearer image contrast.

Intramolecular hydrogen bonds: ab initio Car Parrinello simulations of arylamide torsions

NASA Astrophysics Data System (ADS)

Doerksen, Robert J.; Chen, Bin; Klein, Michael L.

2003-10-01

Gas-phase, room temperature Car-Parrinello molecular dynamics simulations using the HCTH density functional are reported for the arylamides acetanilide ( 1) and ortho-methylthioacetanilide ( 2). The simulations show that in 1, rotation around the ring-amide bond is relatively unrestricted. By contrast, in 2 the methylthio side chain encourages the amide to be directed with N-H pointing toward S, not to flip by 360°, and furthermore to remain close to coplanar with the benzene ring. Because of an intramolecular N-H⋯S hydrogen bond, the N-H stretch frequency of 2 is red-shifted by ˜78 cm -1 compared to that of 1.

Coronagraph Focal-Plane Phase Masks Based on Photonic Crystal Technology: Recent Progress and Observational Strategy

NASA Technical Reports Server (NTRS)

Murakami, Naoshi; Nishikawa, Jun; Sakamoto, Moritsugu; Ise, Akitoshi; Oka, Kazuhiko; Baba, Naoshi; Murakami, Hiroshi; Tamura, Motohide; Traub, Wesley A.; Mawet, Dimitri;

Animal-to-animal variability in the phasing of the crustacean cardiac motor pattern: an experimental and computational analysis

PubMed Central

Williams, Alex H.; Kwiatkowski, Molly A.; Mortimer, Adam L.; Marder, Eve; Zeeman, Mary Lou

2013-01-01

The cardiac ganglion (CG) of Homarus americanus is a central pattern generator that consists of two oscillatory groups of neurons: “small cells” (SCs) and “large cells” (LCs). We have shown that SCs and LCs begin their bursts nearly simultaneously but end their bursts at variable phases. This variability contrasts with many other central pattern generator systems in which phase is well maintained. To determine both the consequences of this variability and how CG phasing is controlled, we modeled the CG as a pair of Morris-Lecar oscillators coupled by electrical and excitatory synapses and constructed a database of 15,000 simulated networks using random parameter sets. These simulations, like our experimental results, displayed variable phase relationships, with the bursts beginning together but ending at variable phases. The model suggests that the variable phasing of the pattern has important implications for the functional role of the excitatory synapses. In networks in which the two oscillators had similar duty cycles, the excitatory coupling functioned to increase cycle frequency. In networks with disparate duty cycles, it functioned to decrease network frequency. Overall, we suggest that the phasing of the CG may vary without compromising appropriate motor output and that this variability may critically determine how the network behaves in response to manipulations. PMID:23446690

Geometrically tunable Fabry-Perot filters based on reflection phase shift of high contrast gratings

NASA Astrophysics Data System (ADS)

Fang, Liang; Shi, Zhendong; Cheng, Xin; Peng, Xiang; Zhang, Hui

2016-03-01

We propose tunable Fabry-Perot filters constituted by double high contrast gratings (HCGs) arrays with different periods acting as reflectors separated by a fixed short cavity, based on high reflectivity and the variety reflection phase shift of HCG array which realize dynamic regulation of the filtering condition. Single optimized HCG obtains the reflectivity of higher than 99% in a grating period ranging from 0.68μm to 0.8μm across a bandwidth of 30nm near the 1.55μm wavelength. The filters can achieve the full width at half maximum (FWHM) of spectral line of less than 0.15nm, and the linear relationship of peak wavelengths and grating periods is established. The simulation results indicate a potential new approach to design a tunable narrowband transmission filter.

Amplitude Variation of Bottom Simulating Reflection with Respect to Frequency - Transitional Base or Attenuation?

USGS Publications Warehouse

Lee, Myung W.

2007-01-01

The amplitude of a bottom simulating reflection (BSR), which occurs near the phase boundary between gas hydrate-bearing sediments and underlying gas-filled sediments, strongly depends on the frequency content of a seismic signal, as well as the impedance contrast across the phase boundary. A strong-amplitude BSR, detectable in a conventional seismic profile, is a good indicator of the presence of free gas beneath the phase boundary. However, the BSR as observed in low-frequency multichannel seismic data is generally difficult to identify in high-frequency, single-channel seismic data. To investigate the frequency dependence of BSR amplitudes, single-channel seismic data acquired with an air gun source at Blake Ridge, which is located off the shore of South Carolina, were analyzed in the frequency range of 10-240 Hz. The frequency-dependent impedance contrast caused by the velocity dispersion in partially gas saturated sediments is important to accurately analyze BSR amplitude. Analysis indicates that seismic attenuation of gas hydrate-bearing sediments, velocity dispersion, and a transitional base all contribute to the frequency-dependent BSR amplitude variation in the frequency range of 10-500 Hz. When velocity dispersion is incorporated into the BSR amplitude analysis, the frequency-dependent BSR amplitude at Blake Ridge can be explained with gas hydrate-bearing sediments having a quality factor of about 250 and a transitional base with a thickness of about 1 meter.

Simulations of x-ray speckle-based dark-field and phase-contrast imaging with a polychromatic beam

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

Zdora, Marie-Christine, E-mail: marie-christine.zdora@diamond.ac.uk; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE; Department of Physics & Astronomy, University College London, London WC1E 6BT

2015-09-21

Following the first experimental demonstration of x-ray speckle-based multimodal imaging using a polychromatic beam [I. Zanette et al., Phys. Rev. Lett. 112(25), 253903 (2014)], we present a simulation study on the effects of a polychromatic x-ray spectrum on the performance of this technique. We observe that the contrast of the near-field speckles is only mildly influenced by the bandwidth of the energy spectrum. Moreover, using a homogeneous object with simple geometry, we characterize the beam hardening artifacts in the reconstructed transmission and refraction angle images, and we describe how the beam hardening also affects the dark-field signal provided by specklemore » tracking. This study is particularly important for further implementations and developments of coherent speckle-based techniques at laboratory x-ray sources.« less

Responses of summer Asian-Pacific zonal thermal contrast and associated evolutions of atmospheric circulation to transient orbital change during the Holocene

NASA Astrophysics Data System (ADS)

Xiao, D.; Zhao, P.

2016-12-01

This study investigates the response of large-scale atmospheric circulation over the Asian-Pacific sector and precipitation over eastern China to the transient orbital changes during the Holocene summer. Corresponding to a variation of the incoming solar radiation, eddy sea level pressure (SLP) presented an out-of-phase relationship between the North Pacific and the Eurasian landmass, which is similar to the present-day Asia-Pacific Oscillation (APO) pattern and defined as the paleo-APO. Its index presented an increasing trend, which implies an enhancement of the zonal thermal contrast between Asia and North Pacific. Associated with the strengthening of thermal contrast was the westward shift of North Pacific high pressure. Accordingly, there were less summer precipitation over both the middle reach of the Yangtze River and Southwest China and more precipitation over North China during. The high-resolution stalagmite δ18O records further support this decrease in the simulated precipitation. From the negative phase of paleo-APO during the early Holocene to the recent positive phase, the eddy SLP anomalies show a decreasing/increasing trend over the Eurasian landmass/the North Pacific, with a phase change around 4.5 ka BP, and they both move westward. Meanwhile, less rainfall belt over East China shows a northward propagation from southern China.

Phase-Shifting Zernike Interferometer Wavefront Sensor

NASA Technical Reports Server (NTRS)

Wallace, J. Kent; Rao, Shanti; Jensen-Clemb, Rebecca M.; Serabyn, Gene

2011-01-01

The canonical Zernike phase-contrast technique1,2,3,4 transforms a phase object in one plane into an intensity object in the conjugate plane. This is done by applying a static pi/2 phase shift to the central core (approx. lambda/D) of the PSF which is intermediate between the input and output planes. Here we present a new architecture for this sensor. First, the optical system is simple and all reflective. Second, the phase shift in the central core of the PSF is dynamic and or arbitrary size. This common-path, all-reflective design makes it minimally sensitive to vibration, polarization and wavelength. We review the theory of operation, describe the optical system, summarize numerical simulations and sensitivities and review results from a laboratory demonstration of this novel instrument

Phase-Shifting Zernike Interferometer Wavefront Sensor

NASA Technical Reports Server (NTRS)

Wallace, J. Kent; Rao, Shanti; Jensen-Clem, Rebecca M.

2011-01-01

The canonical Zernike phase-contrast technique transforms a phase object in one plane into an intensity object in the conjugate plane. This is done by applying a static pi/2 phase shift to the central core (approx. lambda/diameter) of the PSF which is intermediate between the input and output plane. Here we present a new architecture for this sensor. First, the optical system is simple and all reflective, and second the phase shift in the central core of the PSF is dynamic and can be made arbitrarily large. This common-path, all-reflective design makes it minimally sensitive to vibration, polarization and wavelength. We review the theory of operation, describe the optical system, summarize numerical simulations and sensitivities and review results from a laboratory demonstration of this novel instrument.

Magnetic domains in Tb-Fe-Co thin films under anisotropy tilt

NASA Astrophysics Data System (ADS)

Talapatra, A.; Umadevi, K.; Arout Chelvane, J.; Mohanty, J.; Jayalakshmi, V.

2018-04-01

Tailoring of magnetic domains of Tb-Fe-Co thin films with rapid thermal processing has been reported in this paper. While the as-deposited films show elongated, inter-connected domains with high out-of-plane magnetic phase contrast, the rapid thermal processed films at 550 °C with different time intervals display deterioration of magnetic contrast. A longitudinal extension of domains has been observed with the processing time of 5 min. With subsequent increase in processing time, the domain patterns exhibit considerable decrease in magnetic phase difference combined with strong intermixing between two oppositely magnetized areas. The out-of-plane magnetic contrast is seen to be very weak for the Tb-Fe-Co film processed for 30 min. The domain morphology and the contrast variation have been modeled with micromagnetic simulations, considering the in-plane (along xz plane) tilt of anisotropy axis. The ground state energy profile and the variation in magnetic properties indicate the threshold tilt angle to be around 30 ° wherein the in-plane and out-of-plane squareness ratio and coercivities are comparable and hence the system shows a spin re-orientation behavior at higher tilt angles.

Two-Color Coherent Control of Femtosecond Above-Threshold Photoemission from a Tungsten Nanotip.

PubMed

Förster, Michael; Paschen, Timo; Krüger, Michael; Lemell, Christoph; Wachter, Georg; Libisch, Florian; Madlener, Thomas; Burgdörfer, Joachim; Hommelhoff, Peter

2016-11-18

We demonstrate coherent control of multiphoton and above-threshold photoemission from a single solid-state nanoemitter driven by a fundamental and a weak second harmonic laser pulse. Depending on the relative phase of the two pulses, electron emission is modulated with a contrast of the oscillating current signal of up to 94%. Electron spectra reveal that all observed photon orders are affected simultaneously and similarly. We confirm that photoemission takes place within 10 fs. Accompanying simulations indicate that the current modulation with its large contrast results from two interfering quantum pathways leading to electron emission.

High-contrast grating hollow-core waveguide splitter applied to optical phased array

NASA Astrophysics Data System (ADS)

Zhao, Che; Xue, Ping; Zhang, Hanxing; Chen, Te; Peng, Chao; Hu, Weiwei

2014-11-01

A novel hollow-core (HW) Y-branch waveguide splitter based on high-contrast grating (HCG) is presented. We calculated and designed the HCG-HW splitter using Rigorous Coupled Wave Analysis (RCWA). Finite-different timedomain (FDTD) simulation shows that the splitter has a broad bandwidth and the branching loss is as low as 0.23 dB. Fabrication is accomplished with standard Silicon-On-Insulator (SOI) process. The experimental measurement results indicate its good performance on beam splitting near the central wavelength λ = 1550 nm with a total insertion loss of 7.0 dB.

Performance Sensitivity Studies on the PIAA Implementation of the High-Contrast Imaging Testbed

NASA Technical Reports Server (NTRS)

Sidick, Erkin; Lou, John Z.; Shaklan, Stuart; Levine, Marie

2009-01-01

We have investigated the dependence of the High Contrast Imaging Testbed (HCIT) Phase Induced Amplitude Apodization (PIAA) coronagraph system performance on the rigid-body perturbations of various optics. The structural design of the optical system as well as the parameters of various optical elements used in the analysis are drawn from those of the PIAA/HCIT system that have been and will be implemented, and the simulation takes into account the surface errors of various optics. In this paper, we report our findings when the input light is a narrowband beam.

High-charge and multiple-star vortex coronagraphy from stacked vector vortex phase masks.

PubMed

Aleksanyan, Artur; Brasselet, Etienne

2018-02-01

Optical vortex phase masks are now installed at many ground-based large telescopes for high-contrast astronomical imaging. To date, such instrumental advances have been restricted to the use of helical phase masks of the lowest even order, while future giant telescopes will require high-order masks. Here we propose a single-stage on-axis scheme to create high-order vortex coronagraphs based on second-order vortex phase masks. By extending our approach to an off-axis design, we also explore the implementation of multiple-star vortex coronagraphy. An experimental laboratory demonstration is reported and supported by numerical simulations. These results offer a practical roadmap to the development of future coronagraphic tools with enhanced performances.

Complexity of spatiotemporal traffic phenomena in flow of identical drivers: Explanation based on fundamental hypothesis of three-phase theory

NASA Astrophysics Data System (ADS)

Kerner, Boris S.

2012-03-01

Based on numerical simulations of a stochastic three-phase traffic flow model, we reveal the physics of the fundamental hypothesis of three-phase theory that, in contrast with a fundamental diagram of classical traffic flow theories, postulates the existence of a two-dimensional (2D) region of steady states of synchronized flow where a driver makes an arbitrary choice of a space gap (time headway) to the preceding vehicle. We find that macroscopic and microscopic spatiotemporal effects of the entire complexity of traffic congestion observed up to now in real measured traffic data can be explained by simulations of traffic flow consisting of identical drivers and vehicles, if a microscopic model used in these simulations incorporates the fundamental hypothesis of three-phase theory. It is shown that the driver's choice of space gaps within the 2D region of synchronized flow associated with the fundamental hypothesis of three-phase theory can qualitatively change types of congested patterns that can emerge at a highway bottleneck. In particular, if drivers choose long enough spaces gaps associated with the fundamental hypothesis, then general patterns, which consist of synchronized flow and wide moving jams, do not emerge independent of the flow rates and bottleneck characteristics: Even at a heavy bottleneck leading to a very low speed within congested patterns, only synchronized flow patterns occur in which no wide moving jams emerge spontaneously.

Complexity of spatiotemporal traffic phenomena in flow of identical drivers: explanation based on fundamental hypothesis of three-phase theory.

PubMed

Kerner, Boris S

2012-03-01

Based on numerical simulations of a stochastic three-phase traffic flow model, we reveal the physics of the fundamental hypothesis of three-phase theory that, in contrast with a fundamental diagram of classical traffic flow theories, postulates the existence of a two-dimensional (2D) region of steady states of synchronized flow where a driver makes an arbitrary choice of a space gap (time headway) to the preceding vehicle. We find that macroscopic and microscopic spatiotemporal effects of the entire complexity of traffic congestion observed up to now in real measured traffic data can be explained by simulations of traffic flow consisting of identical drivers and vehicles, if a microscopic model used in these simulations incorporates the fundamental hypothesis of three-phase theory. It is shown that the driver's choice of space gaps within the 2D region of synchronized flow associated with the fundamental hypothesis of three-phase theory can qualitatively change types of congested patterns that can emerge at a highway bottleneck. In particular, if drivers choose long enough spaces gaps associated with the fundamental hypothesis, then general patterns, which consist of synchronized flow and wide moving jams, do not emerge independent of the flow rates and bottleneck characteristics: Even at a heavy bottleneck leading to a very low speed within congested patterns, only synchronized flow patterns occur in which no wide moving jams emerge spontaneously.

Simulations For Investigating the Contrast Mechanism of Biological Cells with High Frequency Scanning Acoustic Microscopy

NASA Astrophysics Data System (ADS)

Juntarapaso, Yada

Scanning Acoustic Microscopy (SAM) is one of the most powerful techniques for nondestructive evaluation and it is a promising tool for characterizing the elastic properties of biological tissues/cells. Exploring a single cell is important since there is a connection between single cell biomechanics and human cancer. Scanning acoustic microscopy (SAM) has been accepted and extensively utilized for acoustical cellular and tissue imaging including measurements of the mechanical and elastic properties of biological specimens. SAM provides superb advantages in that it is non-invasive, can measure mechanical properties of biological cells or tissues, and fixation/chemical staining is not necessary. The first objective of this research is to develop a program for simulating the images and contrast mechanism obtained by high-frequency SAM. Computer simulation algorithms based on MatlabRTM were built for simulating the images and contrast mechanisms. The mechanical properties of HeLa and MCF-7 cells were computed from the measurement data of the output signal amplitude as a function of distance from the focal planes of the acoustics lens which is known as V(z) . Algorithms for simulating V(z) responses involved the calculation of the reflectance function and were created based on ray theory and wave theory. The second objective is to design transducer arrays for SAM. Theoretical simulations based on Field II(c) programs of the high frequency ultrasound array designs were performed to enhance image resolution and volumetric imaging capabilities. Phased array beam forming and dynamic apodization and focusing were employed in the simulations. The new transducer array design will be state-of-the-art in improving the performance of SAM by electronic scanning and potentially providing a 4-D image of the specimen.

SU-F-R-39: Effects of Radiation Dose Reduction On Renal Cell Carcinoma Discrimination Using Multi-Phasic CT Imaging

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

Wahi-Anwar, M; Young, S; Lo, P

Purpose: A method to discriminate different types of renal cell carcinoma (RCC) was developed using attenuation values observed in multiphasic contrast-enhanced CT. This work evaluates the sensitivity of this RCC discrimination task at different CT radiation dose levels. Methods: We selected 5 cases of kidney lesion patients who had undergone four-phase CT scans covering the abdomen to the lilac crest. Through an IRB-approved study, the scans were conducted on 64-slice CT scanners (Definition AS/Definition Flash, Siemens Healthcare) using automatic tube-current modulation (TCM). The protocol included an initial baseline unenhanced scan, followed by three post-contrast injection phases. CTDIvol (32 cm phantom)more » measured between 9 to 35 mGy for any given phase. As a preliminary study, we limited the scope to the cortico-medullary phase—shown previously to be the most discriminative phase. A previously validated method was used to simulate a reduced dose acquisition via adding noise to raw CT sinogram data, emulating corresponding images at simulated doses of 50%, 25%, and 10%. To discriminate the lesion subtype, ROIs were placed in the most enhancing region of the lesion. The mean HU value of an ROI was extracted and used to discriminate to the worst-case RCC subtype, ranked in the order of clear cell, papillary, chromophobe and the benign oncocytoma. Results: Two patients exhibited a change of worst case RCC subtype between original and simulated scans, at 25% and 10% doses. In one case, the worst-case RCC subtype changed from oncocytoma to chromophobe at 10% and 25% doses, while the other case changed from oncocytoma to clear cell at 10% dose. Conclusion: Based on preliminary results from an initial cohort of 5 patients, worst-case RCC subtypes remained constant at all simulated dose levels except for 2 patients. Further study conducted on more patients will be needed to confirm our findings. Institutional research agreement, Siemens Healthcare; Past recipient, research grant support, Siemens Healthcare; Consultant, Toshiba America Medical Systems; Consultant, Samsung Electronics; NIH Grant Support from: U01 CA181156.« less

Real-time holographic deconvolution techniques for one-way image transmission through an aberrating medium: characterization, modeling, and measurements.

PubMed

Haji-Saeed, B; Sengupta, S K; Testorf, M; Goodhue, W; Khoury, J; Woods, C L; Kierstead, J

2006-05-10

We propose and demonstrate a new photorefractive real-time holographic deconvolution technique for adaptive one-way image transmission through aberrating media by means of four-wave mixing. In contrast with earlier methods, which typically required various codings of the exact phase or two-way image transmission for correcting phase distortion, our technique relies on one-way image transmission through the use of exact phase information. Our technique can simultaneously correct both amplitude and phase distortions. We include several forms of image degradation, various test cases, and experimental results. We characterize the performance as a function of the input beam ratios for four metrics: signal-to-noise ratio, normalized root-mean-square error, edge restoration, and peak-to-total energy ratio. In our characterization we use false-color graphic images to display the best beam-intensity ratio two-dimensional region(s) for each of these metrics. Test cases are simulated at the optimal values of the beam-intensity ratios. We demonstrate our results through both experiment and computer simulation.

Investigating the limitations of single breath-hold renal artery blood flow measurements using spiral phase contrast MR with R-R interval averaging.

PubMed

Steeden, Jennifer A; Muthurangu, Vivek

2015-04-01

1) To validate an R-R interval averaged golden angle spiral phase contrast magnetic resonance (RAGS PCMR) sequence against conventional cine PCMR for assessment of renal blood flow (RBF) in normal volunteers; and 2) To investigate the effects of motion and heart rate on the accuracy of flow measurements using an in silico simulation. In 20 healthy volunteers RAGS (∼6 sec breath-hold) and respiratory-navigated cine (∼5 min) PCMR were performed in both renal arteries to assess RBF. A simulation of RAGS PCMR was used to assess the effect of heart rate (30-105 bpm), vessel expandability (0-150%) and translational motion (x1.0-4.0) on the accuracy of RBF measurements. There was good agreement between RAGS and cine PCMR in the volunteer study (bias: 0.01 L/min, limits of agreement: -0.04 to +0.06 L/min, P = 0.0001). The simulation demonstrated a positive linear relationship between heart rate and error (r = 0.9894, P < 0.0001), a negative linear relationship between vessel expansion and error (r = -0.9484, P < 0.0001), and a nonlinear, heart rate-dependent relationship between vessel translation and error. We have demonstrated that RAGS PCMR accurately measures RBF in vivo. However, the simulation reveals limitations in this technique at extreme heart rates (<40 bpm, >100 bpm), or when there is significant motion (vessel expandability: >80%, vessel translation: >x2.2). © 2014 Wiley Periodicals, Inc.

Assessment by Monte Carlo computer simulations of the phase behavior of hard spherocylinders confined within cylindrical cavities.

PubMed

Viveros-Méndez, Perla X; Gil-Villegas, Alejandro; Aranda Espinoza, Said

2017-12-21

The phase behavior of hard spherocylinders (HSCs) confined in cylindrical cavities is studied using Monte Carlo simulations in the canonical ensemble. Results are presented for different values of the particles' aspect ratio l/σ, where l and σ are the length and diameter of the cylinder and hemispherical caps, respectively. Finite cavities with periodic boundary conditions along the principal axis of the cavities have been considered, where the cavity's principal axis is along the z-direction. We first focus our study in the structure induced by varying the degree of confinement, determining the HSC phase diagram for aspect ratios l/σ = 3, 5, 7, and 9, at a fixed packing fraction η = 0.071. By compressing the cavities along the radial direction, the isotropic phase becomes stable before the nematic phase as the length of the cavities is increased, resulting in a second-order transition. The occurrence of phase transitions has also been determined by varying η for constant values of the cavity's length L. Systems with low aspect ratios, l/σ = 3, 5, 7, and 9, exhibit first-order transitions with chiral, paranematic, and isotropic phases, whereas for larger HSCs, l/σ = 50, 70, and 100, the transitions are second order with paranematic, nematic, and isotropic phases, in contrast with the behavior of non-confined systems, with first-order transitions for isotropic, nematic, smectic-A, and solid phases.

Simulating the onset of spring vegetation growth across the Northern Hemisphere.

PubMed

Liu, Qiang; Fu, Yongshuo H; Liu, Yongwen; Janssens, Ivan A; Piao, Shilong

2018-03-01

Changes in the spring onset of vegetation growth in response to climate change can profoundly impact climate-biosphere interactions. Thus, robust simulation of spring onset is essential to accurately predict ecosystem responses and feedback to ongoing climate change. To date, the ability of vegetation phenology models to reproduce spatiotemporal patterns of spring onset at larger scales has not been thoroughly investigated. In this study, we took advantage of phenology observations via remote sensing to calibrate and evaluated six models, including both one-phase (considering only forcing temperatures) and two-phase (involving forcing, chilling, and photoperiod) models across the Northern Hemisphere between 1982 and 2012. Overall, we found that the model that integrated the photoperiod effect performed best at capturing spatiotemporal patterns of spring phenology in boreal and temperate forests. By contrast, all of the models performed poorly in simulating the onset of growth in grasslands. These results suggest that the photoperiod plays a role in controlling the onset of growth in most Northern Hemisphere forests, whereas other environmental factors (e.g., precipitation) should be considered when simulating the onset of growth in grasslands. We also found that the one-phase model performed as well as the two-phase models in boreal forests, which implies that the chilling requirement is probably fulfilled across most of the boreal zone. Conversely, two-phase models performed better in temperate forests than the one-phase model, suggesting that photoperiod and chilling play important roles in these temperate forests. Our results highlight the significance of including chilling and photoperiod effects in models of the spring onset of forest growth at large scales, and indicate that the consideration of additional drivers may be required for grasslands. © 2017 John Wiley & Sons Ltd.

Volumetric velocity measurements in restricted geometries using spiral sampling: a phantom study.

PubMed

Nilsson, Anders; Revstedt, Johan; Heiberg, Einar; Ståhlberg, Freddy; Bloch, Karin Markenroth

2015-04-01

The aim of this study was to evaluate the accuracy of maximum velocity measurements using volumetric phase-contrast imaging with spiral readouts in a stenotic flow phantom. In a phantom model, maximum velocity, flow, pressure gradient, and streamline visualizations were evaluated using volumetric phase-contrast magnetic resonance imaging (MRI) with velocity encoding in one (extending on current clinical practice) and three directions (for characterization of the flow field) using spiral readouts. Results of maximum velocity and pressure drop were compared to computational fluid dynamics (CFD) simulations, as well as corresponding low-echo-time (TE) Cartesian data. Flow was compared to 2D through-plane phase contrast (PC) upstream from the restriction. Results obtained with 3D through-plane PC as well as 4D PC at shortest TE using a spiral readout showed excellent agreements with the maximum velocity values obtained with CFD (<1 % for both methods), while larger deviations were seen using Cartesian readouts (-2.3 and 13 %, respectively). Peak pressure drop calculations from 3D through-plane PC and 4D PC spiral sequences were respectively 14 and 13 % overestimated compared to CFD. Identification of the maximum velocity location, as well as the accurate velocity quantification can be obtained in stenotic regions using short-TE spiral volumetric PC imaging.

Deciphering complex, functional structures with synchrotron-based absorption and phase contrast tomographic microscopy

NASA Astrophysics Data System (ADS)

Stampanoni, M.; Reichold, J.; Weber, B.; Haberthür, D.; Schittny, J.; Eller, J.; Büchi, F. N.; Marone, F.

2010-09-01

Nowadays, thanks to the high brilliance available at modern, third generation synchrotron facilities and recent developments in detector technology, it is possible to record volumetric information at the micrometer scale within few minutes. High signal-to-noise ratio, quantitative information on very complex structures like the brain micro vessel architecture, lung airways or fuel cells can be obtained thanks to the combination of dedicated sample preparation protocols, in-situ acquisition schemes and cutting-edge imaging analysis instruments. In this work we report on recent experiments carried out at the TOMCAT beamline of the Swiss Light Source [1] where synchrotron-based tomographic microscopy has been successfully used to obtain fundamental information on preliminary models for cerebral fluid flow [2], to provide an accurate mesh for 3D finite-element simulation of the alveolar structure of the pulmonary acinus [3] and to investigate the complex functional mechanism of fuel cells [4]. Further, we introduce preliminary results on the combination of absorption and phase contrast microscopy for the visualization of high-Z nanoparticles in soft tissues, a fundamental information when designing modern drug delivery systems [5]. As an outlook we briefly discuss the new possibilities offered by high sensitivity, high resolution grating interferomtery as well as Zernike Phase contrast nanotomography [6].

Advances in Focal Plane Wavefront Estimation for Directly Imaging Exoplanets

NASA Astrophysics Data System (ADS)

Eldorado Riggs, A. J.; Kasdin, N. Jeremy; Groff, Tyler Dean

2015-01-01

To image cold exoplanets directly in visible light, an instrument on a telescope needs to suppress starlight by about 9 orders of magnitude at small separations from the star. A coronagraph changes the point spread function to create regions of high contrast where exoplanets or disks can be seen. Aberrations on the optics degrade the contrast by several orders of magnitude, so all high-contrast imaging systems incorporate one or more deformable mirrors (DMs) to recover regions of high contrast. With a coronagraphic instrument planned for the WFIRST-AFTA space telescope, there is a pressing need for faster, more robust estimation and control schemes for the DMs. Non-common path aberrations limit conventional phase conjugation schemes to medium star-to-planet contrast ratios of about 1e-6. High-contrast imaging requires estimation and control of both phase and amplitude in the same beam path as the science camera. Field estimation is a challenge since only intensity is measured; the most common approach, including that planned for WFIRST-AFTA, is to use DMs to create diversity, via pairs of small probe shapes, thereby allowing disambiguation of the electric field. Most implementations of DM Diversity require at least five images per electric field estimate and require narrowband measurements. This paper describes our new estimation algorithms that improve the speed (by using fewer images) and bandwidth of focal plane wavefront estimation. For narrowband estimation, we are testing nonlinear, recursive algorithms such as an iterative extended Kalman filter (IEKF) to use three images each iteration and build better, more robust estimates. We are also exploring the use of broadband estimation without the need for narrowband sub-filters and measurements. Here we present simulations of these algorithms with realistic noise and small signals to show how they might perform for WFIRST-AFTA. Once validated in simulations, we will test these algorithms experimentally in Princeton's HCIL and in the Jet Propulsion Laboratory's (JPL's) High Contrast Imaging Testbed (HCIT). Developing these faster, more robust wavefront estimators is a crucial for increasing the science yield of the WFIRST-AFTA coronagraphic instrument.

Communications: Complete description of re-entrant phase behavior in a charge variable colloidal model system.

PubMed

Wette, Patrick; Klassen, Ina; Holland-Moritz, Dirk; Herlach, Dieter M; Schöpe, Hans Joachim; Lorenz, Nina; Reiber, Holger; Palberg, Thomas; Roth, Stephan V

2010-04-07

In titration experiments with NaOH, we have determined the full phase diagram of charged colloidal spheres in dependence on the particle density n, the particle effective charge Z(eff) and the concentration of screening electrolyte c using microscopy, light and ultrasmall angle x-ray scattering (USAXS). For sufficiently large n, the system crystallizes upon increasing Z(eff) at constant c and melts upon increasing c at only slightly altered Z(eff). In contrast to earlier work, equilibrium phase boundaries are consistent with a universal melting line prediction from computer simulation, if the elasticity effective charge is used. This charge accounts for both counterion condensation and many-body effects.

Quantitative phase and amplitude imaging using Differential-Interference Contrast (DIC) microscopy

NASA Astrophysics Data System (ADS)

Preza, Chrysanthe; O'Sullivan, Joseph A.

2009-02-01

We present an extension of the development of an alternating minimization (AM) method for the computation of a specimen's complex transmittance function (magnitude and phase) from DIC images. The ability to extract both quantitative phase and amplitude information from two rotationally-diverse DIC images (i.e., acquired by rotating the sample) extends previous efforts in computational DIC microscopy that have focused on quantitative phase imaging only. Simulation results show that the inverse problem at hand is sensitive to noise as well as to the choice of the AM algorithm parameters. The AM framework allows constraints and penalties on the magnitude and phase estimates to be incorporated in a principled manner. Towards this end, Green and De Pierro's "log-cosh" regularization penalty is applied to the magnitude of differences of neighboring values of the complex-valued function of the specimen during the AM iterations. The penalty is shown to be convex in the complex space. A procedure to approximate the penalty within the iterations is presented. In addition, a methodology to pre-compute AM parameters that are optimal with respect to the convergence rate of the AM algorithm is also presented. Both extensions of the AM method are investigated with simulations.

Direct numerical simulation of incompressible multiphase flow with phase change

NASA Astrophysics Data System (ADS)

Lee, Moon Soo; Riaz, Amir; Aute, Vikrant

2017-09-01

Simulation of multiphase flow with phase change is challenging because of the potential for unphysical pressure oscillations, spurious velocity fields and mass flux errors across the interface. The resulting numerical errors may become critical when large density contrasts are present. To address these issues, we present a new approach for multiphase flow with phase change that features, (i) a smooth distribution of sharp velocity jumps and mass flux within a narrow region surrounding the interface, (ii) improved mass flux projection from the implicit interface onto the uniform Cartesian grid and (iii) post-advection velocity correction step to ensure accurate velocity divergence in interfacial cells. These new features are implemented in combination with a sharp treatment of the jumps in pressure and temperature gradient. A series of 1-D, 2-D, axisymmetric and 3-D problems are solved to verify the improvements afforded by the new approach. Axisymmetric film boiling results are also presented, which show good qualitative agreement with heat transfer correlations as well as experimental observations of bubble shapes.

Zirconia ceramics for excess weapons plutonium waste

NASA Astrophysics Data System (ADS)

Gong, W. L.; Lutze, W.; Ewing, R. C.

2000-01-01

We synthesized a zirconia (ZrO 2)-based single-phase ceramic containing simulated excess weapons plutonium waste. ZrO 2 has large solubility for other metallic oxides. More than 20 binary systems A xO y-ZrO 2 have been reported in the literature, including PuO 2, rare-earth oxides, and oxides of metals contained in weapons plutonium wastes. We show that significant amounts of gadolinium (neutron absorber) and yttrium (additional stabilizer of the cubic modification) can be dissolved in ZrO 2, together with plutonium (simulated by Ce 4+, U 4+ or Th 4+) and impurities (e.g., Ca, Mg, Fe, Si). Sol-gel and powder methods were applied to make homogeneous, single-phase zirconia solid solutions. Pu waste impurities were completely dissolved in the solid solutions. In contrast to other phases, e.g., zirconolite and pyrochlore, zirconia is extremely radiation resistant and does not undergo amorphization. Baddeleyite (ZrO 2) is suggested as the natural analogue to study long-term radiation resistance and chemical durability of zirconia-based waste forms.

Origins of the anomalous stress behavior in charged colloidal suspensions under shear.

PubMed

Kumar, Amit; Higdon, Jonathan J L

2010-11-01

Numerical simulations are conducted to determine microstructure and rheology of sheared suspensions of charged colloidal particles at a volume fraction of ϕ=0.33. Over broad ranges of repulsive force strength F0 and Péclet number Pe, dynamic simulations show coexistence of ordered and disordered stable states with the state dependent on the initial condition. In contrast to the common view, at low shear rates, the disordered phase exhibits a lower viscosity (μ(r)) than the ordered phase, while this behavior is reversed at higher shear rates. Analysis shows the stress reversal is associated with different shear induced microstructural distortions in the ordered and disordered systems. Viscosity vs shear rate data over a wide range of F0 and Pe collapses well upon rescaling with the long-time self-diffusivity. Shear thinning viscosity in the ordered phase scaled as μ(r)∼Pe(-0.81) at low shear rates. The microstructural dynamics revealed in these studies explains the anomalous behavior and hysteresis loops in stress data reported in the literature.

Gel phase formation in dilute triblock copolyelectrolyte complexes

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

Srivastava, Samanvaya; Andreev, Marat; Levi, Adam E.

Assembly of oppositely charged triblock copolyelectrolytes into phase-separated gels at low polymer concentrations (<1% by mass) has been observed in scattering experiments and molecular dynamics simulations. Here we show that in contrast to uncharged, amphiphilic block copolymers that form discrete micelles at low concentrations and enter a phase of strongly interacting micelles in a gradual manner with increasing concentration, the formation of a dilute phase of individual micelles is prevented in polyelectrolyte complexation-driven assembly of triblock copolyelectrolytes. Gel phases form and phase separate almost instantaneously on solvation of the copolymers. Furthermore, molecular models of self-assembly demonstrate the presence of oligo-chainmore » aggregates in early stages of copolyelectrolyte assembly, at experimentally unobservable polymer concentrations. Our discoveries contribute to the fundamental understanding of the structure and pathways of complexation-driven assemblies, and raise intriguing prospects for gel formation at extraordinarily low concentrations, with applications in tissue engineering, agriculture, water purification and theranostics.« less

Gel phase formation in dilute triblock copolyelectrolyte complexes

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

Srivastava, Samanvaya; Andreev, Marat; Levi, Adam E.

Assembly of oppositely charged triblock copolyelectrolytes into phase-separated gels at low polymer concentrations (<1% by mass) has been observed in scattering experiments and molecular dynamics simulations. Here we show that in contrast to uncharged, amphiphilic block copolymers that form discrete micelles at low concentrations and enter a phase of strongly interacting micelles in a gradual manner with increasing concentration, the formation of a dilute phase of individual micelles is prevented in polyelectrolyte complexation-driven assembly of triblock copolyelectrolytes. Gel phases form and phase separate almost instantaneously on solvation of the copolymers. Furthermore, molecular models of self-assembly demonstrate the presence of oligo-chainmore » aggregates in early stages of copolyelectrolyte assembly, at experimentally unobservable polymer concentrations. Finally, our discoveries contribute to the fundamental understanding of the structure and pathways of complexation-driven assemblies, and raise intriguing prospects for gel formation at extraordinarily low concentrations, with applications in tissue engineering, agriculture, water purification and theranostics.« less

Gel phase formation in dilute triblock copolyelectrolyte complexes

DOE PAGES

Srivastava, Samanvaya; Andreev, Marat; Levi, Adam E.; ...

2017-02-23

Assembly of oppositely charged triblock copolyelectrolytes into phase-separated gels at low polymer concentrations (<1% by mass) has been observed in scattering experiments and molecular dynamics simulations. Here we show that in contrast to uncharged, amphiphilic block copolymers that form discrete micelles at low concentrations and enter a phase of strongly interacting micelles in a gradual manner with increasing concentration, the formation of a dilute phase of individual micelles is prevented in polyelectrolyte complexation-driven assembly of triblock copolyelectrolytes. Gel phases form and phase separate almost instantaneously on solvation of the copolymers. Furthermore, molecular models of self-assembly demonstrate the presence of oligo-chainmore » aggregates in early stages of copolyelectrolyte assembly, at experimentally unobservable polymer concentrations. Finally, our discoveries contribute to the fundamental understanding of the structure and pathways of complexation-driven assemblies, and raise intriguing prospects for gel formation at extraordinarily low concentrations, with applications in tissue engineering, agriculture, water purification and theranostics.« less

Gel Phase Formation in Dilute Triblock Copolyelectrolyte Complexes

NASA Astrophysics Data System (ADS)

Srivastava, Samanvaya; Andreev, Marat; Prabhu, Vivek; de Pablo, Juan; Tirrell, Matthew

Assembly of oppositely charged triblock copolyelectrolytes into phase-separated gels at extremely low polymer concentrations (<1 % by mass) has been observed in scattering experiments and molecular dynamics simulations. In contrast to uncharged, amphiphilic block copolymers that form discrete micelles at low concentrations and enter a phase of strongly interacting micelles in a gradual manner with increasing polymer concentrations, the formation of a dilute phase of individual micelles is prevented in polyelectrolyte complexation-driven assemblies of triblock copolyelectrolytes. Gel phases form and phase separate almost instantaneously upon solvation of the copolymers. Furthermore, molecular models of self-assembly demonstrate the presence of oligo-chain aggregates in early stages of triblock copolyelectrolyte assembly, at experimentally unobservable polymer concentrations. Our discoveries not only contribute to our fundamental understanding of the structure and pathways of complexation driven assemblies, but also raise intriguing prospects for formation of gel structures at extraordinarily low concentrations, with applications in tissue engineering, agriculture, water purification and theranostics.

Gel phase formation in dilute triblock copolyelectrolyte complexes

NASA Astrophysics Data System (ADS)

Srivastava, Samanvaya; Andreev, Marat; Levi, Adam E.; Goldfeld, David J.; Mao, Jun; Heller, William T.; Prabhu, Vivek M.; de Pablo, Juan J.; Tirrell, Matthew V.

2017-02-01

Assembly of oppositely charged triblock copolyelectrolytes into phase-separated gels at low polymer concentrations (<1% by mass) has been observed in scattering experiments and molecular dynamics simulations. Here we show that in contrast to uncharged, amphiphilic block copolymers that form discrete micelles at low concentrations and enter a phase of strongly interacting micelles in a gradual manner with increasing concentration, the formation of a dilute phase of individual micelles is prevented in polyelectrolyte complexation-driven assembly of triblock copolyelectrolytes. Gel phases form and phase separate almost instantaneously on solvation of the copolymers. Furthermore, molecular models of self-assembly demonstrate the presence of oligo-chain aggregates in early stages of copolyelectrolyte assembly, at experimentally unobservable polymer concentrations. Our discoveries contribute to the fundamental understanding of the structure and pathways of complexation-driven assemblies, and raise intriguing prospects for gel formation at extraordinarily low concentrations, with applications in tissue engineering, agriculture, water purification and theranostics.

Molecular simulation of excess isotherm and excess enthalpy change in gas-phase adsorption.

PubMed

Do, D D; Do, H D; Nicholson, D

2009-01-29

We present a new approach to calculating excess isotherm and differential enthalpy of adsorption on surfaces or in confined spaces by the Monte Carlo molecular simulation method. The approach is very general and, most importantly, is unambiguous in its application to any configuration of solid structure (crystalline, graphite layer or disordered porous glass), to any type of fluid (simple or complex molecule), and to any operating conditions (subcritical or supercritical). The behavior of the adsorbed phase is studied using the partial molar energy of the simulation box. However, to characterize adsorption for comparison with experimental data, the isotherm is best described by the excess amount, and the enthalpy of adsorption is defined as the change in the total enthalpy of the simulation box with the change in the excess amount, keeping the total number (gas + adsorbed phases) constant. The excess quantities (capacity and energy) require a choice of a reference gaseous phase, which is defined as the adsorptive gas phase occupying the accessible volume and having a density equal to the bulk gas density. The accessible volume is defined as the mean volume space accessible to the center of mass of the adsorbate under consideration. With this choice, the excess isotherm passes through a maximum but always remains positive. This is in stark contrast to the literature where helium void volume is used (which is always greater than the accessible volume) and the resulting excess can be negative. Our definition of enthalpy change is equivalent to the difference between the partial molar enthalpy of the gas phase and the partial molar enthalpy of the adsorbed phase. There is no need to assume ideal gas or negligible molar volume of the adsorbed phase as is traditionally done in the literature. We illustrate this new approach with adsorption of argon, nitrogen, and carbon dioxide under subcritical and supercritical conditions.

Coalescence preference and droplet size inequality during fluid phase segregation

NASA Astrophysics Data System (ADS)

Roy, Sutapa

2018-02-01

Using molecular dynamics simulations and scaling arguments, we investigate the coalescence preference dynamics of liquid droplets in a phase-segregating off-critical, single-component fluid. It is observed that the preferential distance of the product drop from its larger parent, during a coalescence event, gets smaller for large parent size inequality. The relative coalescence position exhibits a power-law dependence on the parent size ratio with an exponent q ≃ 3.1 . This value of q is in strong contrast with earlier reports 2.1 and 5.1 in the literature. The dissimilarity is explained by considering the underlying coalescence mechanisms.

The phase slip factor of the electrostatic cryogenic storage ring CSR

NASA Astrophysics Data System (ADS)

Grieser, Manfred; von Hahn, Robert; Vogel, Stephen; Wolf, Andreas

2017-07-01

To determine the momentum spread of an ion beam from the measured revolution frequency distribution, the knowledge of the phase slip factor of the storage ring is necessary. The slip factor was measured for various working points of the cryogenic storage ring CSR at MPI for Nuclear Physics, Heidelberg and was compared with simulations. The predicted functional relationship of the slip factor and the horizontal tune depends on the different islands of stability, which has been experimentally verified. This behavior of the slip factor is in clear contrast to that of magnetic storage rings.

Chaos, ergodic convergence, and fractal instability for a thermostated canonical harmonic oscillator

NASA Astrophysics Data System (ADS)

Hoover, Wm. G.; Hoover, Carol G.; Isbister, Dennis J.

2001-02-01

The authors thermostat a qp harmonic oscillator using the two additional control variables ζ and ξ to simulate Gibbs' canonical distribution. In contrast to the motion of purely Hamiltonian systems, the thermostated oscillator motion is completely ergodic, covering the full four-dimensional \\{q,p,ζ,ξ\\} phase space. The local Lyapunov spectrum (instantaneous growth rates of a comoving corotating phase-space hypersphere) exhibits singularities like those found earlier for Hamiltonian chaos, reinforcing the notion that chaos requires kinetic-as opposed to statistical-study, both at and away from equilibrium. The exponent singularities appear to have a fractal character.

When will Low-Contrast Features be Visible in a STEM X-Ray Spectrum Image?

PubMed

Parish, Chad M

2015-06-01

When will a small or low-contrast feature, such as an embedded second-phase particle, be visible in a scanning transmission electron microscopy (STEM) X-ray map? This work illustrates a computationally inexpensive method to simulate X-ray maps and spectrum images (SIs), based upon the equations of X-ray generation and detection. To particularize the general procedure, an example of nanostructured ferritic alloy (NFA) containing nm-sized Y2Ti2O7 embedded precipitates in ferritic stainless steel matrix is chosen. The proposed model produces physically appearing simulated SI data sets, which can either be reduced to X-ray dot maps or analyzed via multivariate statistical analysis. Comparison to NFA X-ray maps acquired using three different STEM instruments match the generated simulations quite well, despite the large number of simplifying assumptions used. A figure of merit of electron dose multiplied by X-ray collection solid angle is proposed to compare feature detectability from one data set (simulated or experimental) to another. The proposed method can scope experiments that are feasible under specific analysis conditions on a given microscope. Future applications, such as spallation proton-neutron irradiations, core-shell nanoparticles, or dopants in polycrystalline photovoltaic solar cells, are proposed.

High-performance liquid chromatography - Ultraviolet method for the determination of total specific migration of nine ultraviolet absorbers in food simulants based on 1,1,3,3-Tetramethylguanidine and organic phase anion exchange solid phase extraction to remove glyceride.

PubMed

Wang, Jianling; Xiao, Xiaofeng; Chen, Tong; Liu, Tingfei; Tao, Huaming; He, Jun

2016-06-17

The glyceride in oil food simulant usually causes serious interferences to target analytes and leads to failure of the normal function of the RP-HPLC column. In this work, a convenient HPLC-UV method for the determination of the total specific migration of nine ultraviolet (UV) absorbers in food simulants was developed based on 1,1,3,3-tetramethylguanidine (TMG) and organic phase anion exchange (OPAE) SPE to efficiently remove glyceride in olive oil simulant. In contrast to the normal ion exchange carried out in an aqueous solution or aqueous phase environment, the OPAE SPE was performed in the organic phase environments, and the time-consuming and challenging extraction of the nine UV absorbers from vegetable oil with aqueous solution could be readily omitted. The method was proved to have good linearity (r≥0.99992), precision (intra-day RSD≤3.3%), and accuracy(91.0%≤recoveries≤107%); furthermore, the lower limit of quantifications (0.05-0.2mg/kg) in five types of food simulants(10% ethanol, 3% acetic acid, 20% ethanol, 50% ethanol and olive oil) was observed. The method was found to be well suited for quantitative determination of the total specific migration of the nine UV absorbers both in aqueous and vegetable oil simulant according to Commission Regulation (EU) No. 10/2011. Migration levels of the nine UV absorbers were determined in 31 plastic samples, and UV-24, UV-531, HHBP and UV-326 were frequently detected, especially in olive oil simulant for UV-326 in PE samples. In addition, the OPAE SPE procedure was also been applied to efficiently enrich or purify seven antioxidants in olive oil simulant. Results indicate that this procedure will have more extensive applications in the enriching or purification of the extremely weak acidic compounds with phenol hydroxyl group that are relatively stable in TMG n-hexane solution and that can be barely extracted from vegetable oil. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

PubMed

Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

2016-05-12

An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

Comparison of phase-contrast MR and flow simulations for the study of CSF dynamics in the cervical spine.

PubMed

Lindstrøm, Erika Kristina; Schreiner, Jakob; Ringstad, Geir Andre; Haughton, Victor; Eide, Per Kristian; Mardal, Kent-Andre

2018-06-01

Background Investigators use phase-contrast magnetic resonance (PC-MR) and computational fluid dynamics (CFD) to assess cerebrospinal fluid dynamics. We compared qualitative and quantitative results from the two methods. Methods Four volunteers were imaged with a heavily T2-weighted volume gradient echo scan of the brain and cervical spine at 3T and with PC-MR. Velocities were calculated from PC-MR for each phase in the cardiac cycle. Mean pressure gradients in the PC-MR acquisition through the cardiac cycle were calculated with the Navier-Stokes equations. Volumetric MR images of the brain and upper spine were segmented and converted to meshes. Models of the subarachnoid space were created from volume images with the Vascular Modeling Toolkit. CFD simulations were performed with a previously verified flow solver. The flow patterns, velocities and pressures were compared in PC-MR and CFD flow images. Results PC-MR images consistently revealed more inhomogeneous flow patterns than CFD, especially in the anterolateral subarachnoid space where spinal nerve roots are located. On average, peak systolic and diastolic velocities in PC-MR exceeded those in CFD by 31% and 41%, respectively. On average, systolic and diastolic pressure gradients calculated from PC-MR exceeded those of CFD by 11% and 39%, respectively. Conclusions PC-MR shows local flow disturbances that are not evident in typical CFD. The velocities and pressure gradients calculated from PC-MR are systematically larger than those calculated from CFD.

Collapse transition in polymer models with multiple monomers per site and multiple bonds per edge

NASA Astrophysics Data System (ADS)

Rodrigues, Nathann T.; Oliveira, Tiago J.

2017-12-01

We present results from extensive Monte Carlo simulations of polymer models where each lattice site can be visited by up to K monomers and no restriction is imposed on the number of bonds on each lattice edge. These multiple monomer per site (MMS) models are investigated on the square and cubic lattices, for K =2 and 3, by associating Boltzmann weights ω0=1 , ω1=eβ1 , and ω2=eβ2 to sites visited by 1, 2, and 3 monomers, respectively. Two versions of the MMS models are considered for which immediate reversals of the walks are allowed (RA) or forbidden (RF). In contrast to previous simulations of these models, we find the same thermodynamic behavior for both RA and RF versions. In three dimensions, the phase diagrams, in space β2×β1 , are featured by coil and globule phases separated by a line of Θ points, as thoroughly demonstrated by the metric νt, crossover ϕt, and entropic γt exponents. The existence of the Θ lines is also confirmed by the second virial coefficient. This shows that no discontinuous collapse transition exists in these models, in contrast to previous claims based on a weak bimodality observed in some distributions, which indeed exists in a narrow region very close to the Θ line when β1<0 . Interestingly, in two dimensions, only a crossover is found between the coil and globule phases.

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

Berenguer de la Cuesta, Felisa; Wenger, Marco P.E.; Bean, Richard J.

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patternsmore » from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60-70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the 'speckled' nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques.« less

Coherent X-ray diffraction from collagenous soft tissues

PubMed Central

Berenguer de la Cuesta, Felisa; Wenger, Marco P. E.; Bean, Richard J.; Bozec, Laurent; Horton, Michael A.; Robinson, Ian K.

2009-01-01

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patterns from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60–70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the ‘speckled’ nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques. PMID:19706395

Coherent X-ray diffraction from collagenous soft tissues.

PubMed

Berenguer de la Cuesta, Felisa; Wenger, Marco P E; Bean, Richard J; Bozec, Laurent; Horton, Michael A; Robinson, Ian K

2009-09-08

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patterns from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60-70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the 'speckled' nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques.

High Resolution X-Ray Phase Contrast Imaging with Acoustic Tissue-Selective Contrast Enhancement

DTIC Science & Technology

2005-06-01

Ultrasonics Symp 1319 (1999). 17. Sarvazyan, A. P. Shear Wave Elasticity Imaging: A New Ultrasonic Technology of Medical Diagnostics. Ultrasound in...samples using acoustically modulated X-ray phase contrast imaging. 15. SUBJECT TERMS x-ray, ultrasound, phase contrast, imaging, elastography 16...x-rays, phase contrast imaging is based on phase changes as x-rays traverse a body resulting in wave interference that result in intensity changes in

A Physical Model for Three-Phase Compaction in Silicic Magma Reservoirs

NASA Astrophysics Data System (ADS)

Huber, Christian; Parmigiani, Andrea

2018-04-01

We develop a model for phase separation in magma reservoirs containing a mixture of silicate melt, crystals, and fluids (exsolved volatiles). The interplay between the three phases controls the dynamics of phase separation and consequently the chemical and physical evolution of magma reservoirs. The model we propose is based on the two-phase damage theory approach of Bercovici et al. (2001, https://doi.org/10.1029/2000JB900430) and Bercovici and Ricard (2003, https://doi.org/10.1046/j.1365-246X.2003.01854.x) because it offers the leverage of considering interface (in the macroscopic limit) between phases that can deform depending on the mechanical work and phase changes taking place locally in the magma. Damage models also offer the advantage that pressure is defined uniquely to each phase and does not need to be equal among phases, which will enable us to consider, in future studies, the large capillary pressure at which fluids are mobilized in mature, crystal-rich, magma bodies. In this first analysis of three-phase compaction, we solve the three-phase compaction equations numerically for a simple 1-D problem where we focus on the effect of fluids on the efficiency of melt-crystal separation considering the competition between viscous and buoyancy stresses only. We contrast three sets of simulations to explore the behavior of three-phase compaction, a melt-crystal reference compaction scenario (two-phase compaction), a three-phase scenario without phase changes, and finally a three-phase scenario with a parameterized second boiling (crystallization-induced exsolution). The simulations show a dramatic difference between two-phase (melt crystals) and three-phase (melt-crystals-exsolved volatiles) compaction-driven phase separation. We find that the presence of a lighter, significantly less viscous fluid hinders melt-crystal separation.

Experimentally enhanced model-based deconvolution of propagation-based phase-contrast data

NASA Astrophysics Data System (ADS)

Pichotka, M.; Palma, K.; Hasn, S.; Jakubek, J.; Vavrik, D.

2016-12-01

In recent years phase-contrast has become a much investigated modality in radiographic imaging. The radiographic setups employed in phase-contrast imaging are typically rather costly and complex, e.g. high performance Talbot-Laue interferometers operated at synchrotron light sources. In-line phase-contrast imaging states the most pedestrian approach towards phase-contrast enhancement. Utilizing small angle deflection within the imaged sample and the entailed interference of the deflected and un-deflected beam during spatial propagation, in-line phase-contrast imaging only requires a well collimated X-ray source with a high contrast & high resolution detector. Employing high magnification the above conditions are intrinsically fulfilled in cone-beam micro-tomography. As opposed of 2D imaging, where contrast enhancement is generally considered beneficial, in tomographic modalities the in-line phase-contrast effect can be quite a nuisance since it renders the inverse problem posed by tomographic reconstruction inconsistent, thus causing reconstruction artifacts. We present an experimentally enhanced model-based approach to disentangle absorption and in-line phase-contrast. The approach employs comparison of transmission data to a system model computed iteratively on-line. By comparison of the forward model to absorption data acquired in continuous rotation strong local deviations of the data residual are successively identified as likely candidates for in-line phase-contrast. By inducing minimal vibrations (few mrad) to the sample around the peaks of such deviations the transmission signal can be decomposed into a constant absorptive fraction and an oscillating signal caused by phase-contrast which again allows to generate separate maps for absorption and phase-contrast. The contributions of phase-contrast and the corresponding artifacts are subsequently removed from the tomographic dataset. In principle, if a 3D handling of the sample is available, this method also allows to track discontinuities throughout the volume and therefore states a powerful tool in 3D defectoscopy.

Demonstration of Broadband Contrast at 1.2 Lambda/D for the EXCEDE Phase-Induced Amplitude Apodization Coronagraph

NASA Technical Reports Server (NTRS)

Sirbu, Dan; Thomas, Sandrine J.; Belikov, Ruslan; Lozi, Julien; Bendek, Eduardo; Pluzhnik, Eugene; Lynch, Dana H.; Hix, Troy; Zell, Peter; Schneider, Glenn;

Cell segmentation in phase contrast microscopy images via semi-supervised classification over optics-related features.

PubMed

Su, Hang; Yin, Zhaozheng; Huh, Seungil; Kanade, Takeo

2013-10-01

Phase-contrast microscopy is one of the most common and convenient imaging modalities to observe long-term multi-cellular processes, which generates images by the interference of lights passing through transparent specimens and background medium with different retarded phases. Despite many years of study, computer-aided phase contrast microscopy analysis on cell behavior is challenged by image qualities and artifacts caused by phase contrast optics. Addressing the unsolved challenges, the authors propose (1) a phase contrast microscopy image restoration method that produces phase retardation features, which are intrinsic features of phase contrast microscopy, and (2) a semi-supervised learning based algorithm for cell segmentation, which is a fundamental task for various cell behavior analysis. Specifically, the image formation process of phase contrast microscopy images is first computationally modeled with a dictionary of diffraction patterns; as a result, each pixel of a phase contrast microscopy image is represented by a linear combination of the bases, which we call phase retardation features. Images are then partitioned into phase-homogeneous atoms by clustering neighboring pixels with similar phase retardation features. Consequently, cell segmentation is performed via a semi-supervised classification technique over the phase-homogeneous atoms. Experiments demonstrate that the proposed approach produces quality segmentation of individual cells and outperforms previous approaches. Copyright © 2013 Elsevier B.V. All rights reserved.

Fizeau simultaneous phase-shifting interferometry based on extended source

NASA Astrophysics Data System (ADS)

Wang, Shanshan; Zhu, Qiudong; Hou, Yinlong; Cao, Zheng

2016-09-01

Coaxial Fizeau simultaneous phase-shifting interferometer plays an important role in many fields for its characteristics of long optical path, miniaturization, and elimination of reference surface high-frequency error. Based on the matching of coherence between extended source and interferometer, orthogonal polarization reference wave and measurement wave can be obtained by Fizeau interferometry with Michelson interferometer preposed. Through matching spatial coherence length between preposed interferometer and primary interferometer, high contrast interference fringes can be obtained and additional interference fringes can be eliminated. Thus, the problem of separation of measurement and reference surface in the common optical path Fizeau interferometer is solved. Numerical simulation and principle experiment is conducted to verify the feasibility of extended source interferometer. Simulation platform is established by using the communication technique of DDE (dynamic data exchange) to connect Zemax and Matlab. The modeling of the extended source interferometer is realized by using Zemax. Matlab codes are programmed to automatically rectify the field parameters of the optical system and conveniently calculate the visibility of interference fringes. Combined with the simulation, the experimental platform of the extended source interferometer is established. After experimental research on the influence law of scattering screen granularity to interference fringes, the granularity of scattering screen is determined. Based on the simulation platform and experimental platform, the impacts on phase measurement accuracy of the imaging system aberration and collimation system aberration of the interferometer are analyzed. Compared the visibility relation curves between experimental measurement and simulation result, the experimental result is in line with the theoretical result.

Phase contrast MR angiography techniques.

PubMed

Dumoulin, C L

1995-08-01

Phase contrast MR methods encode information from macroscopic motion into the phase of the MR signal. Phase contrast methods can be applied with small and large fields-of-view, can give quantitative measures of velocity, and provide excellent suppression of signals from stationary tissue. Unlike time-of-flight methods, phase contrast methods directly measure flow and thus are not hindered by the artifactual appearance of tissue having short T1. Phase contrast angiograms can be two-dimensional (thin slice or projectile), three-dimensional, and/or time resolved and have applications throughout the body.

Improved specimen reconstruction by Hilbert phase contrast tomography.

PubMed

Barton, Bastian; Joos, Friederike; Schröder, Rasmus R

2008-11-01

The low signal-to-noise ratio (SNR) in images of unstained specimens recorded with conventional defocus phase contrast makes it difficult to interpret 3D volumes obtained by electron tomography (ET). The high defocus applied for conventional tilt series generates some phase contrast but leads to an incomplete transfer of object information. For tomography of biological weak-phase objects, optimal image contrast and subsequently an optimized SNR are essential for the reconstruction of details such as macromolecular assemblies at molecular resolution. The problem of low contrast can be partially solved by applying a Hilbert phase plate positioned in the back focal plane (BFP) of the objective lens while recording images in Gaussian focus. Images recorded with the Hilbert phase plate provide optimized positive phase contrast at low spatial frequencies, and the contrast transfer in principle extends to the information limit of the microscope. The antisymmetric Hilbert phase contrast (HPC) can be numerically converted into isotropic contrast, which is equivalent to the contrast obtained by a Zernike phase plate. Thus, in-focus HPC provides optimal structure factor information without limiting effects of the transfer function. In this article, we present the first electron tomograms of biological specimens reconstructed from Hilbert phase plate image series. We outline the technical implementation of the phase plate and demonstrate that the technique is routinely applicable for tomography. A comparison between conventional defocus tomograms and in-focus HPC volumes shows an enhanced SNR and an improved specimen visibility for in-focus Hilbert tomography.

Optimization of intermolecular potential parameters for the CO2/H2O mixture.

PubMed

Orozco, Gustavo A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

2014-10-02

Monte Carlo simulations in the Gibbs ensemble were used to obtain optimized intermolecular potential parameters to describe the phase behavior of the mixture CO2/H2O, over a range of temperatures and pressures relevant for carbon capture and sequestration processes. Commonly used fixed-point-charge force fields that include Lennard-Jones 12-6 (LJ) or exponential-6 (Exp-6) terms were used to describe CO2 and H2O intermolecular interactions. For force fields based on the LJ functional form, changes of the unlike interactions produced higher variations in the H2O-rich phase than in the CO2-rich phase. A major finding of the present study is that for these potentials, no combination of unlike interaction parameters is able to adequately represent properties of both phases. Changes to the partial charges of H2O were found to produce significant variations in both phases and are able to fit experimental data in both phases, at the cost of inaccuracies for the pure H2O properties. By contrast, for the Exp-6 case, optimization of a single parameter, the oxygen-oxygen unlike-pair interaction, was found sufficient to give accurate predictions of the solubilities in both phases while preserving accuracy in the pure component properties. These models are thus recommended for future molecular simulation studies of CO2/H2O mixtures.

Relaxometry model of strong dipolar perturbers for balanced-SSFP: application to quantification of SPIO loaded cells.

PubMed

Lebel, R Marc; Menon, Ravi S; Bowen, Chris V

2006-03-01

Magnetic resonance microscopy using magnetically labeled cells is an emerging discipline offering the potential for non-destructive studies targeting numerous cellular events in medical research. The present work develops a technique to quantify superparamagnetic iron-oxide (SPIO) loaded cells using fully balanced steady state free precession (b-SSFP) imaging. An analytic model based on phase cancellation was derived for a single particle and extended to predict mono-exponential decay versus echo time in the presence of multiple randomly distributed particles. Numerical models verified phase incoherence as the dominant contrast mechanism and evaluated the model using a full range of tissue decay rates, repetition times, and flip angles. Numerical simulations indicated a relaxation rate enhancement (DeltaR(2b)=0.412 gamma . LMD) proportional to LMD, the local magnetic dose (the additional sample magnetization due to the SPIO particles), a quantity related to the concentration of contrast agent. A phantom model of SPIO loaded cells showed excellent agreement with simulations, demonstrated comparable sensitivity to gradient echo DeltaR(*) (2) enhancements, and 14 times the sensitivity of spin echo DeltaR(2) measurements. We believe this model can be used to facilitate the generation of quantitative maps of targeted cell populations. Magn Reson Med, 2006. (c) 2006 Wiley-Liss, Inc.

Modeling the imprint of Milankovitch cycles on early Pleistocene ice volume

NASA Astrophysics Data System (ADS)

Roychowdhury, R.; DeConto, R.; Pollard, D.

2017-12-01

Global climate during Quaternary and Late Pliocene (present-3.1 Ma) is characterized by alternating glacial and interglacial conditions. Several proposed theories associate these cycles with variations in the Earth's orbital configuration. In this study, we attempt to address the anomalously strong obliquity forcing in the Late Pliocene/Early Pleistocene ice volume records (41 kyr world), which stands in sharp contrast to the primary cyclicity of insolation, which is at precessional periods (23 kyr). Model results from GCM simulations show that at low eccentricities (e<0.015), the effect of precession is minimal, and the integrated insolation metrics (such as summer metric, PDD, etc.) vary in-phase between the two hemispheres. At higher eccentricities (e>0.015), precessional response is important, and the insolation metrics vary out-of-phase between the two hemispheres. Using simulations from a GCM-driven ice sheet model, we simulate time continuous ice volume changes from Northern and Southern Hemispheres. Under eccentricities lower than 0.015, ice sheets in both hemispheres respond only to obliquity cycle, and grow and melt together (in-phase). If the ice sheet is simulated with eccentricity higher than 0.015, both hemispheres become more sensitive to precessional variation, and vary out-of-phase with each other, which is consistent with proxy observations from the late Pleistocene glaciations. We use the simulated ice volumes from 2.0 to 1.0 ma to empirically calculate global benthic δ18O variations based on the assumption that relationships between collapse and growth of ice-sheets and sea level is linear and symmetric and that the isotopic signature of the individual ice-sheets has not changed with time. Our modeled global benthic δ18O values are broadly consistent with the paleoclimate proxy records such as the LR04 stack.

Leaching of cadmium and tellurium from cadmium telluride (CdTe) thin-film solar panels under simulated landfill conditions

PubMed Central

Ramos-Ruiz, Adriana; Wilkening, Jean V.; Field, James A.; Sierra-Alvarez, Reyes

2017-01-01

A crushed non-encapsulated CdTe thin-film solar cell was subjected to two standardized batch leaching tests (i.e., Toxicity Characteristic Leaching Procedure (TCLP) and California Waste Extraction Test (WET)) and to a continuous-flow column test to assess cadmium (Cd) and tellurium (Te) dissolution under conditions simulating the acidic- and the methanogenic phases of municipal solid waste landfills. Low levels of Cd and Te were solubilized in both batch leaching tests (<8.2% and <3.6% of added Cd and Te, respectively). On the other hand, over the course of 30 days, 73% of the Cd and 21% of the Te were released to the synthetic leachate of a continuous-flow column simulating the acidic landfill phase. The dissolved Cd concentration was 3.24-fold higher than the TCLP limit (1 mg L-1), and 650-fold higher than the maximum contaminant level established by the US-EPA for this metal in drinking water (0.005 mg L-1). In contrast, the release of Cd and Te to the effluent of the continuous-flow column simulating the methanogenic phase of a landfill was negligible. The remarkable difference in the leaching behavior of CdTe in the columns is related to different aqueous pH and redox conditions promoted by the microbial communities in the columns, and is in agreement with thermodynamic predictions. PMID:28472709

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces

DOE PAGES

Gruber, J.; Zhou, X. W.; Jones, R. E.; ...

2017-05-15

Here, we investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and (11more » $$\\bar{2}$$0) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of InxGa1-xN-alloy compositions (0 ≤ x ≤ 0.4) and homologous growth temperatures [0.50 ≤ T/T* m(x) ≤ 0.90], where T* m(x) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar (11$$\\bar{2}$$0) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. Finally, while the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.« less

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces

NASA Astrophysics Data System (ADS)

Gruber, J.; Zhou, X. W.; Jones, R. E.; Lee, S. R.; Tucker, G. J.

2017-05-01

We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ( 11 2 ¯ 0 ) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of InxGa1-xN-alloy compositions (0 ≤ x ≤ 0.4) and homologous growth temperatures [0.50 ≤ T/T*m(x) ≤ 0.90], where T*m(x) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ( 11 2 ¯ 0 ) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces.

PubMed

Gruber, J; Zhou, X W; Jones, R E; Lee, S R; Tucker, G J

2017-05-21

We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ([Formula: see text]) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of In x Ga 1-x N-alloy compositions (0 ≤  x  ≤ 0.4) and homologous growth temperatures [0.50 ≤  T/T * m ( x ) ≤ 0.90], where T * m ( x ) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ([Formula: see text]) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.

Molecular dynamics simulation of the plastic behavior anisotropy of shock-compressed monocrystal nickel

NASA Astrophysics Data System (ADS)

Chen, Ya-Zhou; Zhou, Liu-Cheng; He, Wei-Feng; Sun, Yu; Li, Ying-Hong; Jiao, Yang; Luo, Si-Hai

2017-01-01

Molecular dynamics simulations were used to study the plastic behavior of monocrystalline nickel under shock compression along the [100] and [110] orientations. The shock Hugoniot relation, local stress curve, and process of microstructure development were determined. Results showed the apparent anisotropic behavior of monocrystalline nickel under shock compression. The separation of elastic and plastic waves was also obvious. Plastic deformation was more severely altered along the [110] direction than the [100] direction. The main microstructure phase transformed from face-centered cubic to body-centered cubic and generated a large-scale and low-density stacking fault along the family of { 111 } crystal planes under shock compression along the [100] direction. By contrast, the main mechanism of plastic deformation in the [110] direction was the nucleation of the hexagonal, close-packed phase, which generated a high density of stacking faults along the [110] and [1̅10] directions.

Chiral spin liquids at finite temperature in a three-dimensional Kitaev model

NASA Astrophysics Data System (ADS)

Kato, Yasuyuki; Kamiya, Yoshitomo; Nasu, Joji; Motome, Yukitoshi

2017-11-01

Chiral spin liquids (CSLs) in three dimensions and thermal phase transitions to paramagnet are studied by unbiased Monte Carlo simulations. For an extension of the Kitaev model to a three-dimensional tricoordinate network dubbed the hypernonagon lattice, we derive low-energy effective models in two different anisotropic limits. We show that the effective interactions between the emergent Z2 degrees of freedom called fluxes are unfrustrated in one limit, while highly frustrated in the other. In both cases, we find a first-order phase transition to the CSL, where both time-reversal and parity symmetries are spontaneously broken. In the frustrated case, however, the CSL state is highly exotic—the flux configuration is subextensively degenerate while showing a directional order with broken C3 rotational symmetry. Our results provide two contrasting archetypes of CSLs in three dimensions, both of which allow approximation-free simulation for investigating the thermodynamics.

Effects of diffusion in competitive contact processes on bipartite lattices

NASA Astrophysics Data System (ADS)

de Oliveira, M. M.; Fiore, C. E.

2017-05-01

We investigate the influence of particle diffusion in the two-dimension contact process (CP) with a competitive dynamics in bipartite sublattices, proposed in de Oliveira and Dickman (2011 Phys. Rev. E 84 011125). The particle creation depends on its first and second neighbors and the extinction increases according to the local density. In contrast to the standard CP model, mean-field theory and numerical simulations predict three stable phases: inactive (absorbing), active symmetric and active asymmetric, signed by distinct sublattice particle occupations. Our results from MFT and Monte Carlo simulations reveal that low diffusion rates do not destroy sublattice ordering, ensuring the maintenance of the asymmetric phase. On the other hand, for diffusion larger than a threshold value D c , the sublattice ordering is suppressed and only the usual active (symmetric)-inactive transition is presented. We also show the critical behavior and universality classes are not affected by the diffusion.

Monte Carlo Simulations of Arterial Imaging with Optical Coherence Tomography

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

Amendt, P.; Estabrook, K.; Everett, M.

2000-02-01

The laser-tissue interaction code LATIS [London et al., Appl. Optics 36, 9068 ( 1998)] is used to analyze photon scattering histories representative of optical coherence tomography (OCT) experiment performed at Lawrence Livermore National Laboratory. Monte Carlo photonics with Henyey-Greenstein anisotropic scattering is implemented and used to simulate signal discrimination of intravascular structure. An analytic model is developed and used to obtain a scaling law relation for optimization of the OCT signal and to validate Monte Carlo photonics. The appropriateness of the Henyey-Greenstein phase function is studied by direct comparison with more detailed Mie scattering theory using an ensemble of sphericalmore » dielectric scatterers. Modest differences are found between the two prescriptions for describing photon angular scattering in tissue. In particular, the Mie scattering phase functions provide less overall reflectance signal but more signal contrast compared to the Henyey-Greenstein formulation.« less

Quantitative phase microscopy via optimized inversion of the phase optical transfer function.

PubMed

Jenkins, Micah H; Gaylord, Thomas K

2015-10-01

Although the field of quantitative phase imaging (QPI) has wide-ranging biomedical applicability, many QPI methods are not well-suited for such applications due to their reliance on coherent illumination and specialized hardware. By contrast, methods utilizing partially coherent illumination have the potential to promote the widespread adoption of QPI due to their compatibility with microscopy, which is ubiquitous in the biomedical community. Described herein is a new defocus-based reconstruction method that utilizes a small number of efficiently sampled micrographs to optimally invert the partially coherent phase optical transfer function under assumptions of weak absorption and slowly varying phase. Simulation results are provided that compare the performance of this method with similar algorithms and demonstrate compatibility with large phase objects. The accuracy of the method is validated experimentally using a microlens array as a test phase object. Lastly, time-lapse images of live adherent cells are obtained with an off-the-shelf microscope, thus demonstrating the new method's potential for extending QPI capability widely in the biomedical community.

Grating-based tomography applications in biomedical engineering

NASA Astrophysics Data System (ADS)

Schulz, Georg; Thalmann, Peter; Khimchenko, Anna; Müller, Bert

2017-10-01

For the investigation of soft tissues or tissues consisting of soft and hard tissues on the microscopic level, hard X-ray phase tomography has become one of the most suitable imaging techniques. Besides other phase contrast methods grating interferometry has the advantage of higher sensitivity than inline methods and the quantitative results. One disadvantage of the conventional double-grating setup (XDGI) compared to inline methods is the limitation of the spatial resolution. This limitation can be overcome by removing the analyser grating resulting in a single-grating setup (XSGI). In order to verify the performance of XSGI concerning contrast and spatial resolution, a quantitative comparison of XSGI and XDGI tomograms of a human nerve was performed. Both techniques provide sufficient contrast to allow for the distinction of tissue types. The spatial resolution of the two-fold binned XSGI data set is improved by a factor of two in comparison to XDGI which underlies its performance in tomography of soft tissues. Another application for grating-based X-ray phase tomography is the simultaneous visualization of soft and hard tissues of a plaque-containing coronary artery. The simultaneous visualization of both tissues is important for the segmentation of the lumen. The segmented data can be used for flow simulations in order to obtain information about the three-dimensional wall shear stress distribution needed for the optimization of mechano-sensitive nanocontainers used for drug delivery.

Ultrasonic bubbles in medicine: influence of the shell.

PubMed

Postema, Michiel; Schmitz, Georg

2007-04-01

Ultrasound contrast agents consist of microscopically small bubbles encapsulated by an elastic shell. These microbubbles oscillate upon ultrasound insonification, and demonstrate highly nonlinear behavior, ameliorating their detectability. (Potential) medical applications involving the ultrasonic disruption of contrast agent microbubble shells include release-burst imaging, localized drug delivery, and noninvasive blood pressure measurement. To develop and enhance these techniques, predicting the cracking behavior of ultrasound-insonified encapsulated microbubbles has been of importance. In this paper, we explore microbubble behavior in an ultrasound field, with special attention to the influence of the bubble shell. A bubble in a sound field can be considered a forced damped harmonic oscillator. For encapsulated microbubbles, the presence of a shell has to be taken into account. In models, an extra damping parameter and a shell stiffness parameter have been included, assuming that Hooke's Law holds for the bubble shell. At high acoustic amplitudes, disruptive phenomena have been observed, such as microbubble fragmentation and ultrasonic cracking. We analyzed the occurrence of ultrasound contrast agent fragmentation, by simulating the oscillating behavior of encapsulated microbubbles with various sizes in a harmonic acoustic field. Fragmentation occurs exclusively during the collapse phase and occurs if the kinetic energy of the collapsing microbubble is greater than the instantaneous bubble surface energy, provided that surface instabilities have grown big enough to allow for break-up. From our simulations it follows that the Blake critical radius is not a good approximation for a fragmentation threshold. We demonstrated how the phase angle differences between a damped radially oscillating bubble and an incident sound field depend on shell parameters.

Phase-contrast scanning transmission electron microscopy.

PubMed

Minoda, Hiroki; Tamai, Takayuki; Iijima, Hirofumi; Hosokawa, Fumio; Kondo, Yukihito

2015-06-01

This report introduces the first results obtained using phase-contrast scanning transmission electron microscopy (P-STEM). A carbon-film phase plate (PP) with a small center hole is placed in the condenser aperture plane so that a phase shift is introduced in the incident electron waves except those passing through the center hole. A cosine-type phase-contrast transfer function emerges when the phase-shifted scattered waves interfere with the non-phase-shifted unscattered waves, which passed through the center hole before incidence onto the specimen. The phase contrast resulting in P-STEM is optically identical to that in phase-contrast transmission electron microscopy that is used to provide high contrast for weak phase objects. Therefore, the use of PPs can enhance the phase contrast of the STEM images of specimens in principle. The phase shift resulting from the PP, whose thickness corresponds to a phase shift of π, has been confirmed using interference fringes displayed in the Ronchigram of a silicon single crystal specimen. The interference fringes were found to abruptly shift at the edge of the PP hole by π. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Condenser-free contrast methods for transmitted-light microscopy

PubMed Central

WEBB, K F

2015-01-01

Phase contrast microscopy allows the study of highly transparent yet detail-rich specimens by producing intensity contrast from phase objects within the sample. Presented here is a generalized phase contrast illumination schema in which condenser optics are entirely abrogated, yielding a condenser-free yet highly effective method of obtaining phase contrast in transmitted-light microscopy. A ring of light emitting diodes (LEDs) is positioned within the light-path such that observation of the objective back focal plane places the illuminating ring in appropriate conjunction with the phase ring. It is demonstrated that true Zernike phase contrast is obtained, whose geometry can be flexibly manipulated to provide an arbitrary working distance between illuminator and sample. Condenser-free phase contrast is demonstrated across a range of magnifications (4–100×), numerical apertures (0.13–1.65NA) and conventional phase positions. Also demonstrated is condenser-free darkfield microscopy as well as combinatorial contrast including Rheinberg illumination and simultaneous, colour-contrasted, brightfield, darkfield and Zernike phase contrast. By providing enhanced and arbitrary working space above the preparation, a range of concurrent imaging and electrophysiological techniques will be technically facilitated. Condenser-free phase contrast is demonstrated in conjunction with scanning ion conductance microscopy (SICM), using a notched ring to admit the scanned probe. The compact, versatile LED illumination schema will further lend itself to novel next-generation transmitted-light microscopy designs. The condenser-free illumination method, using rings of independent or radially-scanned emitters, may be exploited in future in other electromagnetic wavebands, including X-rays or the infrared. PMID:25226859

Explicit Filtering Based Low-Dose Differential Phase Reconstruction Algorithm with the Grating Interferometry.

PubMed

Jiang, Xiaolei; Zhang, Li; Zhang, Ran; Yin, Hongxia; Wang, Zhenchang

2015-01-01

X-ray grating interferometry offers a novel framework for the study of weakly absorbing samples. Three kinds of information, that is, the attenuation, differential phase contrast (DPC), and dark-field images, can be obtained after a single scanning, providing additional and complementary information to the conventional attenuation image. Phase shifts of X-rays are measured by the DPC method; hence, DPC-CT reconstructs refraction indexes rather than attenuation coefficients. In this work, we propose an explicit filtering based low-dose differential phase reconstruction algorithm, which enables reconstruction from reduced scanning without artifacts. The algorithm adopts a differential algebraic reconstruction technique (DART) with the explicit filtering based sparse regularization rather than the commonly used total variation (TV) method. Both the numerical simulation and the biological sample experiment demonstrate the feasibility of the proposed algorithm.

Explicit Filtering Based Low-Dose Differential Phase Reconstruction Algorithm with the Grating Interferometry

PubMed Central

Zhang, Li; Zhang, Ran; Yin, Hongxia; Wang, Zhenchang

2015-01-01

X-ray grating interferometry offers a novel framework for the study of weakly absorbing samples. Three kinds of information, that is, the attenuation, differential phase contrast (DPC), and dark-field images, can be obtained after a single scanning, providing additional and complementary information to the conventional attenuation image. Phase shifts of X-rays are measured by the DPC method; hence, DPC-CT reconstructs refraction indexes rather than attenuation coefficients. In this work, we propose an explicit filtering based low-dose differential phase reconstruction algorithm, which enables reconstruction from reduced scanning without artifacts. The algorithm adopts a differential algebraic reconstruction technique (DART) with the explicit filtering based sparse regularization rather than the commonly used total variation (TV) method. Both the numerical simulation and the biological sample experiment demonstrate the feasibility of the proposed algorithm. PMID:26089971

The contrasting response of Hadley circulation to different meridional structure of sea surface temperature in CMIP5

NASA Astrophysics Data System (ADS)

Feng, Juan; Li, Jianping; Zhu, Jianlei; Li, Yang; Li, Fei

2018-02-01

The response of the Hadley circulation (HC) to the sea surface temperature (SST) is determined by the meridional structure of SST and varies according to the changing nature of this meridional structure. The capability of the models from the phase 5 of the Coupled Model Intercomparison Project (CMIP5) is utilized to represent the contrast response of the HC to different meridional SST structures. To evaluate the responses, the variations of HC and SST were linearly decomposed into two components: the equatorially asymmetric (HEA for HC, and SEA for SST) and equatorially symmetric (HES for HC, and SES for SST) components. The result shows that the climatological features of HC and tropical SST (including the spatial structures and amplitude) are reasonably simulated in all the models. However, the response contrast of HC to different SST meridional structures shows uncertainties among models. This may be due to the fact that the long-term temporal variabilities of HEA, HES, and SEA are limited reproduced in the models, although the spatial structures of their long-term variabilities are relatively reasonably simulated. These results indicate that the performance of the CMIP5 models to simulate long-term temporal variability of different meridional SST structures and related HC variations plays a fundamental role in the successful reproduction of the response of HC to different meridional SST structures.

Particle dynamics and pattern formation in a rotating suspension of positively buoyant particles

NASA Astrophysics Data System (ADS)

Konidena, Sudarshan; Lee, Jonghoon; Reddy, K. Anki; Singh, Anugrah

2018-04-01

Numerical simulations of positively buoyant suspension in a horizontally rotating cylinder were performed to study the formation of radial and axial patterns. The order parameter for the low-frequency segregated phase and dispersed phase is similar to that predicted for the settling suspension by Lee and Ladd [J. Fluid Mech. 577, 183 (2007), 10.1017/S002211200700465X], which is the average angular velocity of the particles. The particle density profiles for axial bands in the buoyancy-dominated phase shows an amplitude equivalent to the diameter of the cylinder. Axial density profiles show sinusoidal behavior for the drag-dominant phase and oscillating sinusoidal behavior for the centrifugal-force-dominant phase. Results also indicate that the traveling bands are formed as a consequence of the inhomogeneous distribution of particles arising from a certain imbalance of drag, buoyancy, and centrifugal forces. In the centrifugal limit, particles move towards the center of the cylinder, aggregating to form a dense core of particles with its axis coinciding with that of the rotating cylinder, a behavior which is in contrast to the sedimenting particles. The particle distribution patterns obtained from the simulations are found to be in good agreement with the experiments of Kalyankar et al. [Phys. Fluids 20, 083301 (2008), 10.1063/1.2970156].

COMPUTATIONAL MODELING OF CIRCULATING FLUIDIZED BED REACTORS

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

Ibrahim, Essam A

2013-01-09

Details of numerical simulations of two-phase gas-solid turbulent flow in the riser section of Circulating Fluidized Bed Reactor (CFBR) using Computational Fluid Dynamics (CFD) technique are reported. Two CFBR riser configurations are considered and modeled. Each of these two riser models consist of inlet, exit, connecting elbows and a main pipe. Both riser configurations are cylindrical and have the same diameter but differ in their inlet lengths and main pipe height to enable investigation of riser geometrical scaling effects. In addition, two types of solid particles are exploited in the solid phase of the two-phase gas-solid riser flow simulations tomore » study the influence of solid loading ratio on flow patterns. The gaseous phase in the two-phase flow is represented by standard atmospheric air. The CFD-based FLUENT software is employed to obtain steady state and transient solutions for flow modulations in the riser. The physical dimensions, types and numbers of computation meshes, and solution methodology utilized in the present work are stated. Flow parameters, such as static and dynamic pressure, species velocity, and volume fractions are monitored and analyzed. The differences in the computational results between the two models, under steady and transient conditions, are compared, contrasted, and discussed.« less

Optimized phases for the acquisition of J-spectra in coupled spin systems for thermally and PHIP polarized molecules.

PubMed

Bussandri, S; Prina, I; Acosta, R H; Buljubasich, L

2018-04-01

We demonstrate that the relative phases in the refocusing pulses of multipulse sequences can compensate for pulse errors and off-resonant effects, which are commonly encountered in J-spectroscopy when CPMG is used for acquisition. The use of supercycles has been considered many times in the past, but always from the view point of time-domain NMR, that is, in an effort to lengthen the decay of the magnetization. Here we use simple spin-coupled systems, in which the quantum evolution of the system can be simulated and contrasted to experimental results. In order to explore fine details, we resort to partial J-spectroscopy, that is, to the acquisition of J-spectra of a defined multiplet, which is acquired with a suitable digital filter. We unambiguously show that when finite radiofrequency pulses are considered, the off-resonance effects on nearby multiplets affects the dynamics of the spins within the spectral window under acquisition. Moreover, the most robust phase cycling scheme for our setup consists of a 4-pulse cycle, with phases yyyy‾ or xxxx‾ for an excitation pulse with phase x. We show simulated and experimental results in both thermally polarized and PHIP hyperpolarized systems. Copyright © 2018 Elsevier Inc. All rights reserved.

Optimized phases for the acquisition of J-spectra in coupled spin systems for thermally and PHIP polarized molecules

NASA Astrophysics Data System (ADS)

Bussandri, S.; Prina, I.; Acosta, R. H.; Buljubasich, L.

2018-04-01

We demonstrate that the relative phases in the refocusing pulses of multipulse sequences can compensate for pulse errors and off-resonant effects, which are commonly encountered in J-spectroscopy when CPMG is used for acquisition. The use of supercycles has been considered many times in the past, but always from the view point of time-domain NMR, that is, in an effort to lengthen the decay of the magnetization. Here we use simple spin-coupled systems, in which the quantum evolution of the system can be simulated and contrasted to experimental results. In order to explore fine details, we resort to partial J-spectroscopy, that is, to the acquisition of J-spectra of a defined multiplet, which is acquired with a suitable digital filter. We unambiguously show that when finite radiofrequency pulses are considered, the off-resonance effects on nearby multiplets affects the dynamics of the spins within the spectral window under acquisition. Moreover, the most robust phase cycling scheme for our setup consists of a 4-pulse cycle, with phases yy yy ‾ or xx xx ‾ for an excitation pulse with phase x. We show simulated and experimental results in both thermally polarized and PHIP hyperpolarized systems.

Burial and thermal history simulation of the Abu Rudeis-Sidri oil field, Gulf of Suez-Egypt: A 1D basin modeling study

NASA Astrophysics Data System (ADS)

Awadalla, Ahmed; Hegab, Omar A.; Ahmed, Mohammed A.; Hassan, Saad

2018-02-01

An integrated 1D model on seven wells has been performed to simulate the multi-tectonic phases and multiple thermal regimes in the Abu Rudeis-Sidri oilfield. Concordance between measured and calculated present-day temperatures is achieved with present-day heat flows in the range of 42-55 mW/m2. Reconstruction of the thermal and burial histories provides information on the paleotemperature profiles, the timing of thermal activation as well as the effect of the Oligo-Miocene rifting phases and its associated magmatic activity. The burial histories show the pre-rift subsidence was progressive but modest, whereas the syn-rift was more rapid (contemporaneous with the main rifting phases and basin formation). Finally, the early post-rift thermal subsidence was slow to moderate in contrast to the late post-rift thermal subsidence which was moderate to rapid. The simulated paleo heat flow illustrates a steady state for the pre-rift phase and non-steady state (transient) for syn-rift and postrift phases. Three geothermal regimes are recognized, each of which is associated with a specific geological domain. 1) A lower geothermal regime reflects the impact of stable tectonics (pre-rift). 2) The higher temperature distribution reflects the syn-rift high depositional rate as well as the impact of stretching and thinning (rifting phases) of the lithosphere. 3) A local higher geothermal pulse owing to the magmatic activity during the Oligo-Miocene time (ARM-1 and Sidri-7 wells). Paleoheat flow values of 100mW/m2 (Oligo-Miocene rifting phase) increased to 120mW/m2 (Miocene rifting phase) and lesser magnitude of 80mW/m2 (Mio- Pliocene reactivation phase) have been specified. These affected the thermal regime and temperature distribution by causing perturbations in subsurface temperatures. A decline in the background value of 60mW/m2 owing to conductive cooling has been assigned. The blanketing effect caused by low thermal conductivity of the basin-fill sediments has been simulated as well.

Regularized iterative integration combined with non-linear diffusion filtering for phase-contrast x-ray computed tomography.

PubMed

Burger, Karin; Koehler, Thomas; Chabior, Michael; Allner, Sebastian; Marschner, Mathias; Fehringer, Andreas; Willner, Marian; Pfeiffer, Franz; Noël, Peter

2014-12-29

Phase-contrast x-ray computed tomography has a high potential to become clinically implemented because of its complementarity to conventional absorption-contrast.In this study, we investigate noise-reducing but resolution-preserving analytical reconstruction methods to improve differential phase-contrast imaging. We apply the non-linear Perona-Malik filter on phase-contrast data prior or post filtered backprojected reconstruction. Secondly, the Hilbert kernel is replaced by regularized iterative integration followed by ramp filtered backprojection as used for absorption-contrast imaging. Combining the Perona-Malik filter with this integration algorithm allows to successfully reveal relevant sample features, quantitatively confirmed by significantly increased structural similarity indices and contrast-to-noise ratios. With this concept, phase-contrast imaging can be performed at considerably lower dose.

Baryonic impact on the dark matter orbital properties of Milky Way-sized haloes

NASA Astrophysics Data System (ADS)

Zhu, Qirong; Hernquist, Lars; Marinacci, Federico; Springel, Volker; Li, Yuexing

2017-04-01

We study the orbital properties of dark matter haloes by combining a spectral method and cosmological simulations of Milky Way-sized Galaxies. We compare the dynamics and orbits of individual dark matter particles from both hydrodynamic and N-body simulations, and find that the fraction of box, tube and resonant orbits of the dark matter halo decreases significantly due to the effects of baryons. In particular, the central region of the dark matter halo in the hydrodynamic simulation is dominated by regular, short-axis tube orbits, in contrast to the chaotic, box and thin orbits dominant in the N-body run. This leads to a more spherical dark matter halo in the hydrodynamic run compared to a prolate one as commonly seen in the N-body simulations. Furthermore, by using a kernel-based density estimator, we compare the coarse-grained phase-space densities of dark matter haloes in both simulations and find that it is lower by ˜0.5 dex in the hydrodynamic run due to changes in the angular momentum distribution, which indicates that the baryonic process that affects the dark matter is irreversible. Our results imply that baryons play an important role in determining the shape, kinematics and phase-space density of dark matter haloes in galaxies.

Single particle analysis based on Zernike phase contrast transmission electron microscopy.

PubMed

Danev, Radostin; Nagayama, Kuniaki

2008-02-01

We present the first application of Zernike phase-contrast transmission electron microscopy to single-particle 3D reconstruction of a protein, using GroEL chaperonin as the test specimen. We evaluated the performance of the technique by comparing 3D models derived from Zernike phase contrast imaging, with models from conventional underfocus phase contrast imaging. The same resolution, about 12A, was achieved by both imaging methods. The reconstruction based on Zernike phase contrast data required about 30% fewer particles. The advantages and prospects of each technique are discussed.

Cosmology in one dimension: Vlasov dynamics.

PubMed

Manfredi, Giovanni; Rouet, Jean-Louis; Miller, Bruce; Shiozawa, Yui

2016-04-01

Numerical simulations of self-gravitating systems are generally based on N-body codes, which solve the equations of motion of a large number of interacting particles. This approach suffers from poor statistical sampling in regions of low density. In contrast, Vlasov codes, by meshing the entire phase space, can reach higher accuracy irrespective of the density. Here, we perform one-dimensional Vlasov simulations of a long-standing cosmological problem, namely, the fractal properties of an expanding Einstein-de Sitter universe in Newtonian gravity. The N-body results are confirmed for high-density regions and extended to regions of low matter density, where the N-body approach usually fails.

Quantitative Susceptibility Mapping of Human Brain Reflects Spatial Variation in Tissue Composition

PubMed Central

Li, Wei; Wu, Bing; Liu, Chunlei

2011-01-01

Image phase from gradient echo MRI provides a unique contrast that reflects brain tissue composition variations, such as iron and myelin distribution. Phase imaging is emerging as a powerful tool for the investigation of functional brain anatomy and disease diagnosis. However, the quantitative value of phase is compromised by its nonlocal and orientation dependent properties. There is an increasing need for reliable quantification of magnetic susceptibility, the intrinsic property of tissue. In this study, we developed a novel and accurate susceptibility mapping method that is also phase-wrap insensitive. The proposed susceptibility mapping method utilized two complementary equations: (1) the Fourier relationship of phase and magnetic susceptibility; and (2) the first-order partial derivative of the first equation in the spatial frequency domain. In numerical simulation, this method reconstructed the susceptibility map almost free of streaking artifact. Further, the iterative implementation of this method allowed for high quality reconstruction of susceptibility maps of human brain in vivo. The reconstructed susceptibility map provided excellent contrast of iron-rich deep nuclei and white matter bundles from surrounding tissues. Further, it also revealed anisotropic magnetic susceptibility in brain white matter. Hence, the proposed susceptibility mapping method may provide a powerful tool for the study of brain physiology and pathophysiology. Further elucidation of anisotropic magnetic susceptibility in vivo may allow us to gain more insight into the white matter microarchitectures. PMID:21224002

Simulation study on exchange interaction and unique magnetization near ferromagnetic morphotropic phase boundary.

PubMed

Wei, Songrui; Liao, Xiaoqi; Gao, Yipeng; Yang, Sen; Wang, Dong; Song, Xiaoping

2017-11-08

Extensive efforts have been made in searching enhanced functionalities near the so-called morphotropic phase boundaries (MPBs) in both ferroelectric and ferromagnetic materials. Due to the exchange anti-symmetry of the wave function of fermions, it is widely recognized that the exchange interaction plays a critical role in ferromagnetism. As a quantum effect, the exchange interaction is magnitudes larger than electric interaction, leading to a fundamental difference between ferroelectricity and ferromagnetism. In this paper, we establish an energetic model capturing the interplay among the anisotropy energy, magnetostatic energy and the exchange energy to investigate systematically the effects of the exchange energy on the behavior of the ferromagnetic MPB. For the first time, it is found that the exchange energy can narrow the width of MPB region in the composition temperature phase diagram for ferromagnetic MPB systems. As temperature increases, MPB region becomes wider because of the weakening of the exchange interaction. Our simulation results suggest that the exchange energy play a critical role on the unique behavior of ferromagnetic MPB, which is in contrast different from that of ferroelectric MPB.

Range expansion of heterogeneous populations.

PubMed

Reiter, Matthias; Rulands, Steffen; Frey, Erwin

2014-04-11

Risk spreading in bacterial populations is generally regarded as a strategy to maximize survival. Here, we study its role during range expansion of a genetically diverse population where growth and motility are two alternative traits. We find that during the initial expansion phase fast-growing cells do have a selective advantage. By contrast, asymptotically, generalists balancing motility and reproduction are evolutionarily most successful. These findings are rationalized by a set of coupled Fisher equations complemented by stochastic simulations.

Improving vision by pupil masking

PubMed Central

Bonaque-González, Sergio; Ríos-Rodríguez, Susana; López-Gil, Norberto

2016-01-01

We propose an alternative solution to improve visual quality by spatially modulating the amplitude of light passing into the eye (related to the eye's transmittance), in contrast to traditional correction of the wavefront phase (related to the local refractive power). Numerical simulations show that masking the aberrated areas at the pupil plane should enhance visual function, especially in highly aberrated eyes. This correction could be implemented in practice using customized contact or intraocular lenses. PMID:27446688

Analysis of a multi-wavelength multi-camera phase-shifting profilometric system for real-time operation

NASA Astrophysics Data System (ADS)

Stoykova, Elena; Gotchev, Atanas; Sainov, Ventseslav

2011-01-01

Real-time accomplishment of a phase-shifting profilometry through simultaneous projection and recording of fringe patterns requires a reliable phase retrieval procedure. In the present work we consider a four-wavelength multi-camera system with four sinusoidal phase gratings for pattern projection that implements a four-step algorithm. Successful operation of the system depends on overcoming two challenges which stem out from the inherent limitations of the phase-shifting algorithm, namely the demand for a sinusoidal fringe profile and the necessity to ensure equal background and contrast of fringes in the recorded fringe patterns. As a first task, we analyze the systematic errors due to the combined influence of the higher harmonics and multi-wavelength illumination in the Fresnel diffraction zone considering the case when the modulation parameters of the four gratings are different. As a second task we simulate the system performance to evaluate the degrading effect of the speckle noise and the spatially varying fringe modulation at non-uniform illumination on the overall accuracy of the profilometric measurement. We consider the case of non-correlated speckle realizations in the recorded fringe patterns due to four-wavelength illumination. Finally, we apply a phase retrieval procedure which includes normalization, background removal and denoising of the recorded fringe patterns to both simulated and measured data obtained for a dome surface.

When will low-contrast features be visible in a STEM X-ray spectrum image?

DOE PAGES

Parish, Chad M.

2015-04-01

When will a small or low-contrast feature, such as an embedded second-phase particle, be visible in a scanning transmission electron microscopy (STEM) X-ray map? This work illustrates a computationally inexpensive method to simulate X-ray maps and spectrum images (SIs), based upon the equations of X-ray generation and detection. To particularize the general procedure, an example of nanostructured ferritic alloy (NFA) containing nm-sized Y 2Ti 2O 7 embedded precipitates in ferritic stainless steel matrix is chosen. The proposed model produces physically appearing simulated SI data sets, which can either be reduced to X-ray dot maps or analyzed via multivariate statistical analysis.more » Comparison to NFA X-ray maps acquired using three different STEM instruments match the generated simulations quite well, despite the large number of simplifying assumptions used. A figure of merit of electron dose multiplied by X-ray collection solid angle is proposed to compare feature detectability from one data set (simulated or experimental) to another. The proposed method can scope experiments that are feasible under specific analysis conditions on a given microscope. As a result, future applications, such as spallation proton–neutron irradiations, core-shell nanoparticles, or dopants in polycrystalline photovoltaic solar cells, are proposed.« less

Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Schmidt, Lisa; Przibilla, Sabine; Rommel, Christina; Vollmer, Angelika; Ketelhut, Steffi; Schnekenburger, Jürgen; von Bally, Gert

2010-04-01

Digital holographic microscopy (DHM) provides label-free quantitative phase contrast with low demands on sample preparation. Nevertheless, for DHM measurements on fixed cells the mounting medium has to be considered while the phase contrast of living cells may be influenced by the used buffer solution. To quantify these effects, the maximum cell caused phase contrast and the visibility of the nucleoli were analyzed. A second aim of the study was to identify subcellular components in DHM phase contrast images. Therefore, comparative investigations using bright field imaging, DHM and fluorescence microscopy with 4',6- Diamidino-2-phenylindol (DAPI) staining were performed. DAPI-staining visualizes cell components containing DNA. The obtained results demonstrate exemplarily for two tumor cell lines that from DHM phase contrast images of fixed cells in phosphate buffer saline (PBS) cell thickness values are obtained which are comparable to living cells. Furthermore, it is shown that in many cases nucleus components can be identified only by DHM phase contrast.

Shedding light on the different behavior of ionic and nonionic surfactants in emulsion polymerization: from atomistic simulations to experimental observations.

PubMed

Magi Meconi, Giulia; Ballard, Nicholas; Asua, José M; Zangi, Ronen

2017-12-06

Although surfactants are known to play a vital role in polymerization reactions carried out in dispersed media, many aspects of their use are poorly understood, perhaps none more so than the vastly different action of ionic and nonionic surfactants in emulsion polymerization. In this work, we combine experimental measurements of emulsion polymerization of styrene with atomistic molecular dynamics simulations to better understand the behavior of surfactants at monomer/polymer-water interfaces. In a batch emulsion polymerization of styrene, the nonionic surfactant Disponil AFX 1080 leads to two nucleation periods, in contrast to the behavior observed for the ionic surfactant SDS. This can be explained by the absorption of the nonionic surfactant into the organic phase at the early stages of the polymerization reaction which is then released as the reaction progresses. Indeed, we find that the partition coefficient of the surfactant between the organic phase and water increases with the amount of monomer in the former, and preferential partitioning is detected to organic phases containing at least 55% styrene. Results from molecular dynamics simulations confirm that spontaneous dissolution of the non-ionic surfactant into a styrene-rich organic phase occurs above a critical concentration of the surfactant adsorbed at the interface. Above this critical concentration, a linear correlation between the amount of surfactant adsorbed at the interface and that absorbed inside the organic phase is observed. To facilitate this absorption into a completely hydrophobic medium, water molecules accompany the intruding surfactants. Similar simulations but with the ionic surfactant instead did not result in any absorption of the surfactant into a neat styrene phase, likely because of its strongly hydrophilic head group. The unusual partitioning behavior of nonionic surfactants explains a number of observable features of emulsion polymerization reactions which use nonionic surfactants and should help with future development of processes for improved control over polymerization.

Schlieren, Phase-Contrast, and Spectroscopy Diagnostics for the LBNL HIF Plasma Channel Experiment

NASA Astrophysics Data System (ADS)

Ponce, D. M.; Niemann, C.; Fessenden, T. J.; Leemans, W.; Vandersloot, K.; Dahlbacka, G.; Yu, S. S.; Sharp, W. M.; Tauschwitz, A.

1999-11-01

The LBNL Plasma Channel experiment has demonstrated stable 42-cm Z-pinch discharge plasma channels with peak currents in excess of 50 kA for a 7 torr nitrogen, 30 kV discharge. These channels offer the possibility of transporting heavy-ion beams for inertial fusion. We postulate that the stability of these channels resides in the existance of a neutral-gas density depresion created by a pre-pulse discharge before the main capacitor bank discharge is created. Here, we present the results and experimental diagnostics setup used for the study of the pre-pulse and main bank channels. Observation of both the plasma and neutral gas dynamics is achieved. Schlieren, Zernike's phase-contrast, and spectroscopic techniques are used. Preliminary Schlieren results show a gas shockwave moving radially at a rate of ≈ 10^6 mm/sec as a result of the fast and localized deposited energy during the evolution of the pre-pulse channel. This data will be used to validate simulation codes (BUCKY and CYCLOPS).

Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction.

PubMed

Müller, Knut; Krause, Florian F; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

2014-12-15

By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms.

Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction

NASA Astrophysics Data System (ADS)

Müller, Knut; Krause, Florian F.; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

2014-12-01

By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms.

Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction

PubMed Central

Müller, Knut; Krause, Florian F.; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

2014-01-01

By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms. PMID:25501385

Modelling sheet-flow sediment transport in wave-bottom boundary layers using discrete-element modelling.

PubMed

Calantoni, Joseph; Holland, K Todd; Drake, Thomas G

2004-09-15

Sediment transport in oscillatory boundary layers is a process that drives coastal geomorphological change. Most formulae for bed-load transport in nearshore regions subsume the smallest-scale physics of the phenomena by parametrizing interactions amongst particles. In contrast, we directly simulate granular physics in the wave-bottom boundary layer using a discrete-element model comprised of a three-dimensional particle phase coupled to a one-dimensional fluid phase via Newton's third law through forces of buoyancy, drag and added mass. The particulate sediment phase is modelled using discrete particles formed to approximate natural grains by overlapping two spheres. Both the size of each sphere and the degree of overlap can be varied for these composite particles to generate a range of non-spherical grains. Simulations of particles having a range of shapes showed that the critical angle--the angle at which a grain pile will fail when tilted slowly from rest--increases from approximately 26 degrees for spherical particles to nearly 39 degrees for highly non-spherical composite particles having a dumbbell shape. Simulations of oscillatory sheet flow were conducted using composite particles with an angle of repose of approximately 33 degrees and a Corey shape factor greater than about 0.8, similar to the properties of beach sand. The results from the sheet-flow simulations with composite particles agreed more closely with laboratory measurements than similar simulations conducted using spherical particles. The findings suggest that particle shape may be an important factor for determining bed-load flux, particularly for larger bed slopes.

Structural dependence of MEH-PPV chromism in solution.

PubMed

de Magalhães, Carlos E T; Savedra, Ranylson M L; Dias, Karina S; Ramos, Rodrigo; Siqueira, Melissa F

2017-03-01

The chromism observed in the MEH-PPV polymer in tetrahydrofuran (THF) solution is discussed as a function of the structural morphology of the backbone chains. To evaluate this phenomenon, we carried out simulations employing a hybrid methodology using molecular dynamics and quantum mechanical approaches. Our results support the hypothesis that the morphological order-disorder transition is related to the change from red to blue phase observed experimentally. The morphological disorder is associated with total or partial twisted arrangements in the polymer backbone, which induces an electronic conjugation length more confined to shorter segments. In addition, the main band of the MEH-PPV UV-Vis spectrum at the lower wavelength is related to the blue phase, in contrast to the red phase found for the more planar backbone chains.

No Collective Neutrino Flavor Conversions during the Supernova Accretion Phase

NASA Astrophysics Data System (ADS)

Chakraborty, Sovan; Fischer, Tobias; Mirizzi, Alessandro; Saviano, Ninetta; Tomàs, Ricard

2011-10-01

We perform a dedicated study of the supernova (SN) neutrino flavor evolution during the accretion phase, using results from recent neutrino radiation hydrodynamics simulations. In contrast to what was expected in the presence of only neutrino-neutrino interactions, we find that the multiangle effects associated with the dense ordinary matter suppress collective oscillations. The matter suppression implies that neutrino oscillations will start outside the neutrino decoupling region and therefore will have a negligible impact on the neutrino heating and the explosion dynamics. Furthermore, the possible detection of the next galactic SN neutrino signal from the accretion phase, based on the usual Mikheyev-Smirnov-Wolfenstein effect in the SN mantle and Earth matter effects, can reveal the neutrino mass hierarchy in the case that the mixing angle θ13 is not very small.

No collective neutrino flavor conversions during the supernova accretion phase.

PubMed

Chakraborty, Sovan; Fischer, Tobias; Mirizzi, Alessandro; Saviano, Ninetta; Tomàs, Ricard

2011-10-07

We perform a dedicated study of the supernova (SN) neutrino flavor evolution during the accretion phase, using results from recent neutrino radiation hydrodynamics simulations. In contrast to what was expected in the presence of only neutrino-neutrino interactions, we find that the multiangle effects associated with the dense ordinary matter suppress collective oscillations. The matter suppression implies that neutrino oscillations will start outside the neutrino decoupling region and therefore will have a negligible impact on the neutrino heating and the explosion dynamics. Furthermore, the possible detection of the next galactic SN neutrino signal from the accretion phase, based on the usual Mikheyev-Smirnov-Wolfenstein effect in the SN mantle and Earth matter effects, can reveal the neutrino mass hierarchy in the case that the mixing angle θ(13) is not very small.

Report of improved performance in Talbot–Lau phase-contrast computed tomography

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

Weber, Thomas, E-mail: thomas.weber@fau.de; Pelzer, Georg; Rieger, Jens

Purpose: Many expectations have been raised since the use of conventional x-ray tubes on grating-based x-ray phase-contrast imaging. Despite a reported increase in contrast-to-noise ratio (CNR) in many publications, there is doubt on whether phase-contrast computed tomography (CT) is advantageous in clinical CT scanners in vivo. The aim of this paper is to contribute to this discussion by analyzing the performance of a phase-contrast CT laboratory setup. Methods: A phase-contrast CT performance analysis was done. Projection images of a phantom were recorded, and image slices were reconstructed using standard filtered back projection methods. The resulting image slices were analyzed bymore » determining the CNRs in the attenuation and phase image. These results were compared to analytically calculated expectations according to the already published phase-contrast CT performance analysis by Raupach and Flohr [Med. Phys. 39, 4761–4774 (2012)]. There, a severe mistake was found leading to wrong predictions of the performance of phase-contrast CT. The error was corrected and with the new formulae, the experimentally obtained results matched the analytical calculations. Results: The squared ratios of the phase-contrast CNR and the attenuation CNR obtained in the authors’ experiment are five- to ten-fold higher than predicted by Raupach and Flohr [Med. Phys. 39, 4761–4774 (2012)]. The effective lateral spatial coherence length deduced outnumbers the already optimistic assumption of Raupach and Flohr [Med. Phys. 39, 4761–4774 (2012)] by a factor of 3. Conclusions: The authors’ results indicate that the assumptions made in former performance analyses are pessimistic. The break-even point, when phase-contrast CT outperforms attenuation CT, is within reach even with realistic, nonperfect gratings. Further improvements to state-of-the-art clinical CT scanners, like increasing the spatial resolution, could change the balance in favor of phase-contrast computed tomography even more. This could be done by, e.g., quantum-counting pixel detectors with four-fold smaller pixel pitches.« less

Contrast computation methods for interferometric measurement of sensor modulation transfer function

NASA Astrophysics Data System (ADS)

Battula, Tharun; Georgiev, Todor; Gille, Jennifer; Goma, Sergio

2018-01-01

Accurate measurement of image-sensor frequency response over a wide range of spatial frequencies is very important for analyzing pixel array characteristics, such as modulation transfer function (MTF), crosstalk, and active pixel shape. Such analysis is especially significant in computational photography for the purposes of deconvolution, multi-image superresolution, and improved light-field capture. We use a lensless interferometric setup that produces high-quality fringes for measuring MTF over a wide range of frequencies (here, 37 to 434 line pairs per mm). We discuss the theoretical framework, involving Michelson and Fourier contrast measurement of the MTF, addressing phase alignment problems using a moiré pattern. We solidify the definition of Fourier contrast mathematically and compare it to Michelson contrast. Our interferometric measurement method shows high detail in the MTF, especially at high frequencies (above Nyquist frequency). We are able to estimate active pixel size and pixel pitch from measurements. We compare both simulation and experimental MTF results to a lens-free slanted-edge implementation using commercial software.

Fresnel diffractograms from pure-phase wave fields under perfect spatio-temporal coherence: Non-linear/non-local aspects and far-field behavior.

PubMed

Trost, F; Hahn, S; Müller, Y; Gasilov, S; Hofmann, R; Baumbach, T

2017-12-18

Recently, the diffractogram, that is, the Fourier transform of the intensity contrast induced by Fresnel free-space propagation of a given (exit) wave field, was investigated non-perturbatively in the phase-scaling factor S (controlling the strength of phase variation) for the special case of a Gaussian phase of width [Formula: see text]. Surprisingly, an additional low-frequency zero σ *  = σ * (S, F) >0 emerges critically at small Fresnel number F (σ proportional to square of 2D spatial frequency). Here, we study the S-scaling behavior of the entire diffractogram. We identify a valley of maximum S-scaling linearity in the F - σ plane corresponding to a nearly universal physical frequency ξml = (0:143 ± 0.001)w -1/2 . Large values of F (near field) are shown to imply S-scaling linearity for low σ but nowhere else (overdamped non-oscillatory). In contrast, small F values (far field) entail distinct, sizable s-bands of good S-scaling linearity (damped oscillatory). These bands also occur in simulated diffractograms induced by a complex phase map (Lena). The transition from damped oscillatory to overdamped non-oscillatory diffractograms is shown to be a critical phenomenon for the Gaussian case. We also give evidence for the occurrence of this transition in an X-ray imaging experiment. Finally, we show that the extreme far-field limit generates a σ-universal diffractogram under certain requirements on the phase map: information on phase shape then is solely encoded in S-scaling behavior.

A Simple Configuration for Quantitative Phase Contrast Microscopy of Transmissible Samples

NASA Astrophysics Data System (ADS)

Sengupta, Chandan; Dasgupta, Koustav; Bhattacharya, K.

Phase microscopy attempts to visualize and quantify the phase distribution of samples which are otherwise invisible under microscope without the use of stains. The two principal approaches to phase microscopy are essentially those of Fourier plane modulation and interferometric techniques. Although the former, first proposed by Zernike, had been the harbinger of phase microscopy, it was the latter that allowed for quantitative evaluation of phase samples. However interferometric techniques are fraught with associated problems such as complicated setup involving mirrors and beam-splitters, the need for a matched objective in the reference arm and also the need for vibration isolation. The present work proposes a single element cube beam-splitter (CBS) interferometer combined with a microscope objective (MO) for interference microscopy. Because of the monolithic nature of the interferometer, the system is almost insensitive to vibrations and relatively simple to align. It will be shown that phase shifting properties may also be introduced by suitable and proper use of polarizing devices. Initial results showing the quantitative three dimensional phase profiles of simulated and actual biological specimens are presented.

Liquid–liquid phase transition in hydrogen by coupled electron–ion Monte Carlo simulations

DOE PAGES

Pierleoni, Carlo; Morales, Miguel A.; Rillo, Giovanni; ...

2016-04-20

The phase diagram of high-pressure hydrogen is of great interest for fundamental research, planetary physics, and energy applications. A first-order phase transition in the fluid phase between a molecular insulating fluid and a monoatomic metallic fluid has been predicted. The existence and precise location of the transition line is relevant for planetary models. Recent experiments reported contrasting results about the location of the transition. Theoretical results based on density functional theory are also very scattered. We report highly accurate coupled electron-ion Monte Carlo calculations of this transition, finding results that lie between the two experimental predictions, close to that measuredmore » in diamond anvil cell experiments but at 25-30 GPa higher pressure. Here, the transition along an isotherm is signaled by a discontinuity in the specific volume, a sudden dissociation of the molecules, a jump in electrical conductivity, and loss of electron localization.« less

Winner-take-all in a phase oscillator system with adaptation.

PubMed

Burylko, Oleksandr; Kazanovich, Yakov; Borisyuk, Roman

2018-01-11

We consider a system of generalized phase oscillators with a central element and radial connections. In contrast to conventional phase oscillators of the Kuramoto type, the dynamic variables in our system include not only the phase of each oscillator but also the natural frequency of the central oscillator, and the connection strengths from the peripheral oscillators to the central oscillator. With appropriate parameter values the system demonstrates winner-take-all behavior in terms of the competition between peripheral oscillators for the synchronization with the central oscillator. Conditions for the winner-take-all regime are derived for stationary and non-stationary types of system dynamics. Bifurcation analysis of the transition from stationary to non-stationary winner-take-all dynamics is presented. A new bifurcation type called a Saddle Node on Invariant Torus (SNIT) bifurcation was observed and is described in detail. Computer simulations of the system allow an optimal choice of parameters for winner-take-all implementation.

Equilibrium evolution in oscillating-field current-drive experiments

NASA Astrophysics Data System (ADS)

McCollam, K. J.; Anderson, J. K.; Blair, A. P.; Craig, D.; Den Hartog, D. J.; Ebrahimi, F.; O'Connell, R.; Reusch, J. A.; Sarff, J. S.; Stephens, H. D.; Stone, D. R.; Brower, D. L.; Deng, B. H.; Ding, W. X.

2010-08-01

Oscillating-field current drive (OFCD) is a proposed method of steady-state toroidal plasma sustainment in which ac poloidal and toroidal loop voltages are applied to produce a dc plasma current. OFCD is added to standard, inductively sustained reversed-field pinch plasmas in the Madison Symmetric Torus [R. N. Dexter et al., Fusion Technol. 19, 131 (1991)]. Equilibrium profiles and fluctuations during a single cycle are measured and analyzed for different relative phases between the two OFCD voltages and for OFCD off. For OFCD phases leading to the most added plasma current, the measured energy confinement is slightly better than that for OFCD off. By contrast, the phase of the maximum OFCD helicity-injection rate also has the maximum decay rate, which is ascribed to transport losses during discrete magnetic-fluctuation events induced by OFCD. Resistive-magnetohydrodynamic simulations of the experiments reproduce the observed phase dependence of the added current.

Leaching of cadmium and tellurium from cadmium telluride (CdTe) thin-film solar panels under simulated landfill conditions.

PubMed

Ramos-Ruiz, Adriana; Wilkening, Jean V; Field, James A; Sierra-Alvarez, Reyes

2017-08-15

A crushed non-encapsulated CdTe thin-film solar cell was subjected to two standardized batch leaching tests (i.e., Toxicity Characteristic Leaching Procedure (TCLP) and California Waste Extraction Test (WET)) and to a continuous-flow column test to assess cadmium (Cd) and tellurium (Te) dissolution under conditions simulating the acidic- and the methanogenic phases of municipal solid waste landfills. Low levels of Cd and Te were solubilized in both batch leaching tests (<8.2% and <3.6% of added Cd and Te, respectively). On the other hand, over the course of 30days, 73% of the Cd and 21% of the Te were released to the synthetic leachate of a continuous-flow column simulating the acidic landfill phase. The dissolved Cd concentration was 3.24-fold higher than the TCLP limit (1mgL -1 ), and 650-fold higher than the maximum contaminant level established by the US-EPA for this metal in drinking water (0.005mgL -1 ). In contrast, the release of Cd and Te to the effluent of the continuous-flow column simulating the methanogenic phase of a landfill was negligible. The remarkable difference in the leaching behavior of CdTe in the columns is related to different aqueous pH and redox conditions promoted by the microbial communities in the columns, and is in agreement with thermodynamic predictions. Copyright © 2017 Elsevier B.V. All rights reserved.

In-Line Phase-Contrast X-ray Imaging and Tomography for Materials Science

PubMed Central

Mayo, Sheridan C.; Stevenson, Andrew W.; Wilkins, Stephen W.

2012-01-01

X-ray phase-contrast imaging and tomography make use of the refraction of X-rays by the sample in image formation. This provides considerable additional information in the image compared to conventional X-ray imaging methods, which rely solely on X-ray absorption by the sample. Phase-contrast imaging highlights edges and internal boundaries of a sample and is thus complementary to absorption contrast, which is more sensitive to the bulk of the sample. Phase-contrast can also be used to image low-density materials, which do not absorb X-rays sufficiently to form a conventional X-ray image. In the context of materials science, X-ray phase-contrast imaging and tomography have particular value in the 2D and 3D characterization of low-density materials, the detection of cracks and voids and the analysis of composites and multiphase materials where the different components have similar X-ray attenuation coefficients. Here we review the use of phase-contrast imaging and tomography for a wide variety of materials science characterization problems using both synchrotron and laboratory sources and further demonstrate the particular benefits of phase contrast in the laboratory setting with a series of case studies. PMID:28817018

In-Line Phase-Contrast X-ray Imaging and Tomography for Materials Science.

PubMed

Mayo, Sheridan C; Stevenson, Andrew W; Wilkins, Stephen W

2012-05-24

X-ray phase-contrast imaging and tomography make use of the refraction of X-rays by the sample in image formation. This provides considerable additional information in the image compared to conventional X-ray imaging methods, which rely solely on X-ray absorption by the sample. Phase-contrast imaging highlights edges and internal boundaries of a sample and is thus complementary to absorption contrast, which is more sensitive to the bulk of the sample. Phase-contrast can also be used to image low-density materials, which do not absorb X-rays sufficiently to form a conventional X-ray image. In the context of materials science, X-ray phase-contrast imaging and tomography have particular value in the 2D and 3D characterization of low-density materials, the detection of cracks and voids and the analysis of composites and multiphase materials where the different components have similar X-ray attenuation coefficients. Here we review the use of phase-contrast imaging and tomography for a wide variety of materials science characterization problems using both synchrotron and laboratory sources and further demonstrate the particular benefits of phase contrast in the laboratory setting with a series of case studies.

Computational studies of thermal and quantum phase transitions approached through non-equilibrium quenching

NASA Astrophysics Data System (ADS)

Liu, Cheng-Wei

Phase transitions and their associated critical phenomena are of fundamental importance and play a crucial role in the development of statistical physics for both classical and quantum systems. Phase transitions embody diverse aspects of physics and also have numerous applications outside physics, e.g., in chemistry, biology, and combinatorial optimization problems in computer science. Many problems can be reduced to a system consisting of a large number of interacting agents, which under some circumstances (e.g., changes of external parameters) exhibit collective behavior; this type of scenario also underlies phase transitions. The theoretical understanding of equilibrium phase transitions was put on a solid footing with the establishment of the renormalization group. In contrast, non-equilibrium phase transition are relatively less understood and currently a very active research topic. One important milestone here is the Kibble-Zurek (KZ) mechanism, which provides a useful framework for describing a system with a transition point approached through a non-equilibrium quench process. I developed two efficient Monte Carlo techniques for studying phase transitions, one is for classical phase transition and the other is for quantum phase transitions, both are under the framework of KZ scaling. For classical phase transition, I develop a non-equilibrium quench (NEQ) simulation that can completely avoid the critical slowing down problem. For quantum phase transitions, I develop a new algorithm, named quasi-adiabatic quantum Monte Carlo (QAQMC) algorithm for studying quantum quenches. I demonstrate the utility of QAQMC quantum Ising model and obtain high-precision results at the transition point, in particular showing generalized dynamic scaling in the quantum system. To further extend the methods, I study more complex systems such as spin-glasses and random graphs. The techniques allow us to investigate the problems efficiently. From the classical perspective, using the NEQ approach I verify the universality class of the 3D Ising spin-glasses. I also investigate the random 3-regular graphs in terms of both classical and quantum phase transitions. I demonstrate that under this simulation scheme, one can extract information associated with the classical and quantum spin-glass transitions without any knowledge prior to the simulation.

Prospective randomized comparison of standard didactic lecture versus high-fidelity simulation for radiology resident contrast reaction management training.

PubMed

Wang, Carolyn L; Schopp, Jennifer G; Petscavage, Jonelle M; Paladin, Angelisa M; Richardson, Michael L; Bush, William H

2011-06-01

The objective of our study was to assess whether high-fidelity simulation-based training is more effective than traditional didactic lecture to train radiology residents in the management of contrast reactions. This was a prospective study of 44 radiology residents randomized into a simulation group versus a lecture group. All residents attended a contrast reaction didactic lecture. Four months later, baseline knowledge was assessed with a written test, which we refer to as the "pretest." After the pretest, the 21 residents in the lecture group attended a repeat didactic lecture and the 23 residents in the simulation group underwent high-fidelity simulation-based training with five contrast reaction scenarios. Next, all residents took a second written test, which we refer to as the "posttest." Two months after the posttest, both groups took a third written test, which we refer to as the "delayed posttest," and underwent performance testing with a high-fidelity severe contrast reaction scenario graded on predefined critical actions. There was no statistically significant difference between the simulation and lecture group pretest, immediate posttest, or delayed posttest scores. The simulation group performed better than the lecture group on the severe contrast reaction simulation scenario (p = 0.001). The simulation group reported improved comfort in identifying and managing contrast reactions and administering medications after the simulation training (p ≤ 0.04) and was more comfortable than the control group (p = 0.03), which reported no change in comfort level after the repeat didactic lecture. When compared with didactic lecture, high-fidelity simulation-based training of contrast reaction management shows equal results on written test scores but improved performance during a high-fidelity severe contrast reaction simulation scenario.

Highly noise-tolerant hybrid algorithm for phase retrieval from a single-shot spatial carrier fringe pattern

NASA Astrophysics Data System (ADS)

Dong, Zhichao; Cheng, Haobo

2018-01-01

A highly noise-tolerant hybrid algorithm (NTHA) is proposed in this study for phase retrieval from a single-shot spatial carrier fringe pattern (SCFP), which effectively combines the merits of spatial carrier phase shift method and two dimensional continuous wavelet transform (2D-CWT). NTHA firstly extracts three phase-shifted fringe patterns from the SCFP with one pixel malposition; then calculates phase gradients by subtracting the reference phase from the other two target phases, which are retrieved respectively from three phase-shifted fringe patterns by 2D-CWT; finally, reconstructs the phase map by a least square gradient integration method. Its typical characters include but not limited to: (1) doesn't require the spatial carrier to be constant; (2) the subtraction mitigates edge errors of 2D-CWT; (3) highly noise-tolerant, because not only 2D-CWT is noise-insensitive, but also the noise in the fringe pattern doesn't directly take part in the phase reconstruction as in previous hybrid algorithm. Its feasibility and performances are validated extensively by simulations and contrastive experiments to temporal phase shift method, Fourier transform and 2D-CWT methods.

Applications of phase-contrast x-ray imaging to medicine using an x-ray interferometer

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Yoneyama, Akio; Takeda, Tohoru; Itai, Yuji; Tu, Jinhong; Hirano, Keiichi

1999-10-01

We are investigating possible medical applications of phase- contrast X-ray imaging using an X-ray interferometer. This paper introduces the strategy of the research project and the present status. The main subject is to broaden the observation area to enable in vivo observation. For this purpose, large X-ray interferometers were developed, and 2.5 cm X 1.5 cm interference patterns were generated using synchrotron X-rays. An improvement of the spatial resolution is also included in the project, and an X-ray interferometer designed for high-resolution phase-contrast X-ray imaging was fabricated and tested. In parallel with the instrumental developments, various soft tissues are observed by phase- contrast X-ray CT to find correspondence between the generated contrast and our histological knowledge. The observation done so far suggests that cancerous tissues are differentiated from normal tissues and that blood can produce phase contrast. Furthermore, this project includes exploring materials that modulate phase contrast for selective imaging.

Strain-induced alignment and phase behavior of blue phase liquid crystals confined to thin films.

PubMed

Bukusoglu, Emre; Martinez-Gonzalez, Jose A; Wang, Xiaoguang; Zhou, Ye; de Pablo, Juan J; Abbott, Nicholas L

2017-12-06

We report on the influence of surface confinement on the phase behavior and strain-induced alignment of thin films of blue phase liquid crystals (BPs). Confining surfaces comprised of bare glass, dimethyloctadecyl [3-(trimethoxysilyl)propyl] ammonium chloride (DMOAP)-functionalized glass, or polyvinyl alcohol (PVA)-coated glass were used with or without mechanically rubbing to influence the azimuthal anchoring of the BPs. These experiments reveal that confinement can change the phase behavior of the BP films. For example, in experiments performed with rubbed-PVA surfaces, we measured the elastic strain of the BPs to change the isotropic-BPII phase boundary, suppressing formation of BPII for film thicknesses incommensurate with the BPII lattice. In addition, we observed strain-induced alignment of the BPs to exhibit a complex dependence on both the surface chemistry and azimuthal alignment of the BPs. For example, when using bare glass surfaces causing azimuthally degenerate and planar anchoring, BPI oriented with (110) planes of the unit cell parallel to the contacting surfaces for thicknesses below 3 μm but transitioned to an orientation with (200) planes aligned parallel to the contacting surfaces for thicknesses above 4 μm. In contrast, BPI aligned with (110) planes parallel to confining surfaces for all other thicknesses and surface treatments, including bare glass with uniform azimuthal alignment. Complementary simulations based on minimization of the total free energy (Landau-de Gennes formalism) confirmed a thickness-dependent reorientation due to strain of BPI unit cells within a window of surface anchoring energies and in the absence of uniform azimuthal alignment. In contrast to BPI, BPII did not exhibit thickness-dependent orientations but did exhibit orientations that were dependent on the surface chemistry, a result that was also captured in simulations by varying the anchoring energies. Overall, the results in this paper reveal that the orientations assumed by BPs in thin films reflect a complex interplay of surface interactions and elastic energies associated with strain of the BP lattice. The results also provide new principles and methods to control the structure and properties of BP thin films, which may find use in BP-templated material synthesis, and BP-based optical and electronic devices.

Contrast-to-noise ratio optimization for a prototype phase-contrast computed tomography scanner.

PubMed

Müller, Mark; Yaroshenko, Andre; Velroyen, Astrid; Bech, Martin; Tapfer, Arne; Pauwels, Bart; Bruyndonckx, Peter; Sasov, Alexander; Pfeiffer, Franz

2015-12-01

In the field of biomedical X-ray imaging, novel techniques, such as phase-contrast and dark-field imaging, have the potential to enhance the contrast and provide complementary structural information about a specimen. In this paper, a first prototype of a preclinical X-ray phase-contrast CT scanner based on a Talbot-Lau interferometer is characterized. We present a study of the contrast-to-noise ratios for attenuation and phase-contrast images acquired with the prototype scanner. The shown results are based on a series of projection images and tomographic data sets of a plastic phantom in phase and attenuation-contrast recorded with varying acquisition settings. Subsequently, the signal and noise distribution of different regions in the phantom were determined. We present a novel method for estimation of contrast-to-noise ratios for projection images based on the cylindrical geometry of the phantom. Analytical functions, representing the expected signal in phase and attenuation-contrast for a circular object, are fitted to individual line profiles of the projection data. The free parameter of the fit function is used to estimate the contrast and the goodness of the fit is determined to assess the noise in the respective signal. The results depict the dependence of the contrast-to-noise ratios on the applied source voltages, the number of steps of the phase stepping routine, and the exposure times for an individual step. Moreover, the influence of the number of projection angles on the image quality of CT slices is investigated. Finally, the implications for future imaging purposes with the scanner are discussed.

Free-energy-based lattice Boltzmann model for the simulation of multiphase flows with density contrast.

PubMed

Shao, J Y; Shu, C; Huang, H B; Chew, Y T

2014-03-01

A free-energy-based phase-field lattice Boltzmann method is proposed in this work to simulate multiphase flows with density contrast. The present method is to improve the Zheng-Shu-Chew (ZSC) model [Zheng, Shu, and Chew, J. Comput. Phys. 218, 353 (2006)] for correct consideration of density contrast in the momentum equation. The original ZSC model uses the particle distribution function in the lattice Boltzmann equation (LBE) for the mean density and momentum, which cannot properly consider the effect of local density variation in the momentum equation. To correctly consider it, the particle distribution function in the LBE must be for the local density and momentum. However, when the LBE of such distribution function is solved, it will encounter a severe numerical instability. To overcome this difficulty, a transformation, which is similar to the one used in the Lee-Lin (LL) model [Lee and Lin, J. Comput. Phys. 206, 16 (2005)] is introduced in this work to change the particle distribution function for the local density and momentum into that for the mean density and momentum. As a result, the present model still uses the particle distribution function for the mean density and momentum, and in the meantime, considers the effect of local density variation in the LBE as a forcing term. Numerical examples demonstrate that both the present model and the LL model can correctly simulate multiphase flows with density contrast, and the present model has an obvious improvement over the ZSC model in terms of solution accuracy. In terms of computational time, the present model is less efficient than the ZSC model, but is much more efficient than the LL model.

Cross-phase modulation spectral shifting: nonlinear phase contrast in a pump-probe microscope

PubMed Central

Wilson, Jesse W.; Samineni, Prathyush; Warren, Warren S.; Fischer, Martin C.

2012-01-01

Microscopy with nonlinear phase contrast is achieved by a simple modification to a nonlinear pump-probe microscope. The technique measures cross-phase modulation by detecting a pump-induced spectral shift in the probe pulse. Images with nonlinear phase contrast are acquired both in transparent and absorptive media. In paraffin-embedded biopsy sections, cross-phase modulation complements the chemically-specific pump-probe images with structural context. PMID:22567580

Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC).

PubMed

Phillips, Zachary F; Chen, Michael; Waller, Laura

2017-01-01

We present a new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. Our system consists of a commercial brightfield microscope with one hardware modification-an inexpensive 3D printed condenser insert. The method, color-multiplexed Differential Phase Contrast (cDPC), is a single-shot variant of Differential Phase Contrast (DPC), which recovers the phase of a sample from images with asymmetric illumination. We employ partially coherent illumination to achieve resolution corresponding to 2× the objective NA. Quantitative phase can then be used to synthesize DIC and phase contrast images or extract shape and density. We demonstrate amplitude and phase recovery at camera-limited frame rates (50 fps) for various in vitro cell samples and c. elegans in a micro-fluidic channel.

Geometry-constraint-scan imaging for in-line phase contrast micro-CT.

PubMed

Fu, Jian; Yu, Guangyuan; Fan, Dekai

2014-01-01

X-ray phase contrast computed tomography (CT) uses the phase shift that x-rays undergo when passing through matter, rather than their attenuation, as the imaging signal and may provide better image quality in soft-tissue and biomedical materials with low atomic number. Here a geometry-constraint-scan imaging technique for in-line phase contrast micro-CT is reported. It consists of two circular-trajectory scans with x-ray detector at different positions, the phase projection extraction method with the Fresnel free-propagation theory and the filter back-projection reconstruction algorithm. This method removes the contact-detector scan and the pure phase object assumption in classical in-line phase contrast Micro-CT. Consequently it relaxes the experimental conditions and improves the image contrast. This work comprises a numerical study of this technique and its experimental verification using a biomedical composite dataset measured at an x-ray tube source Micro-CT setup. The numerical and experimental results demonstrate the validity of the presented method. It will be of interest for a wide range of in-line phase contrast Micro-CT applications in biology and medicine.

Ponderomotive phase plate for transmission electron microscopes

DOEpatents

Reed, Bryan W [Livermore, CA

2012-07-10

A ponderomotive phase plate system and method for controllably producing highly tunable phase contrast transfer functions in a transmission electron microscope (TEM) for high resolution and biological phase contrast imaging. The system and method includes a laser source and a beam transport system to produce a focused laser crossover as a phase plate, so that a ponderomotive potential of the focused laser crossover produces a scattering-angle-dependent phase shift in the electrons of the post-sample electron beam corresponding to a desired phase contrast transfer function.

X-ray computed tomography of wood-adhesive bondlines: Attenuation and phase-contrast effects

DOE PAGES

Paris, Jesse L.; Kamke, Frederick A.; Xiao, Xianghui

2015-07-29

Microscale X-ray computed tomography (XCT) is discussed as a technique for identifying 3D adhesive distribution in wood-adhesive bondlines. Visualization and material segmentation of the adhesives from the surrounding cellular structures require sufficient gray-scale contrast in the reconstructed XCT data. Commercial wood-adhesive polymers have similar chemical characteristics and density to wood cell wall polymers and therefore do not provide good XCT attenuation contrast in their native form. Here, three different adhesive types, namely phenol formaldehyde, polymeric diphenylmethane diisocyanate, and a hybrid polyvinyl acetate, are tagged with iodine such that they yield sufficient X-ray attenuation contrast. However, phase-contrast effects at material edgesmore » complicate image quality and segmentation in XCT data reconstructed with conventional filtered backprojection absorption contrast algorithms. A quantitative phase retrieval algorithm, which isolates and removes the phase-contrast effect, was demonstrated. The paper discusses and illustrates the balance between material X-ray attenuation and phase-contrast effects in all quantitative XCT analyses of wood-adhesive bondlines.« less

X-ray computed tomography of wood-adhesive bondlines: Attenuation and phase-contrast effects

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

Paris, Jesse L.; Kamke, Frederick A.; Xiao, Xianghui

Microscale X-ray computed tomography (XCT) is discussed as a technique for identifying 3D adhesive distribution in wood-adhesive bondlines. Visualization and material segmentation of the adhesives from the surrounding cellular structures require sufficient gray-scale contrast in the reconstructed XCT data. Commercial wood-adhesive polymers have similar chemical characteristics and density to wood cell wall polymers and therefore do not provide good XCT attenuation contrast in their native form. Here, three different adhesive types, namely phenol formaldehyde, polymeric diphenylmethane diisocyanate, and a hybrid polyvinyl acetate, are tagged with iodine such that they yield sufficient X-ray attenuation contrast. However, phase-contrast effects at material edgesmore » complicate image quality and segmentation in XCT data reconstructed with conventional filtered backprojection absorption contrast algorithms. A quantitative phase retrieval algorithm, which isolates and removes the phase-contrast effect, was demonstrated. The paper discusses and illustrates the balance between material X-ray attenuation and phase-contrast effects in all quantitative XCT analyses of wood-adhesive bondlines.« less

In situ X-Ray Diffraction of Shock-Compressed Fused Silica

NASA Astrophysics Data System (ADS)

Tracy, Sally June; Turneaure, Stefan J.; Duffy, Thomas S.

2018-03-01

Because of its widespread applications in materials science and geophysics, SiO2 has been extensively examined under shock compression. Both quartz and fused silica transform through a so-called "mixed-phase region" to a dense, low compressibility high-pressure phase. For decades, the nature of this phase has been a subject of debate. Proposed structures include crystalline stishovite, another high-pressure crystalline phase, or a dense amorphous phase. Here we use plate-impact experiments and pulsed synchrotron x-ray diffraction to examine the structure of fused silica shock compressed to 63 GPa. In contrast to recent laser-driven compression experiments, we find that fused silica adopts a dense amorphous structure at 34 GPa and below. When compressed above 34 GPa, fused silica transforms to untextured polycrystalline stishovite. Our results can explain previously ambiguous features of the shock-compression behavior of fused silica and are consistent with recent molecular dynamics simulations. Stishovite grain sizes are estimated to be ˜5 - 30 nm for compression over a few hundred nanosecond time scale.

Biological applications of phase-contrast electron microscopy.

PubMed

Nagayama, Kuniaki

2014-01-01

Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.

X-ray micro-tomography for investigations of brain tissues on cellular level

NASA Astrophysics Data System (ADS)

Khimchenko, Anna; Schulz, Georg; Deyhle, Hans; Thalmann, Peter; Zanette, Irene; Zdora, Marie-Christine; Bikis, Christos; Hipp, Alexander; Hieber, Simone E.; Schweighauser, Gabriel; Hench, Jürgen; Müller, Bert

2016-10-01

X-ray imaging in absorption contrast mode is well established for hard tissue visualization. However, performance for lower density materials is limited due to a reduced contrast. Our aim is three-dimensional (3D) characterization of micro-morphology of human brain tissues down to (sub-)cellular resolution within a laboratory environment. Using the laboratory-based microtomography (μCT) system nanotom m (GE Sensing and Inspection Technologies GmbH, Wunstorf, Germany) and synchrotron radiation at the Diamond-Manchester Imaging Branchline I13-2 (Diamond Light Source, Didcot, UK), we have acquired 3D data with a resolution down to 0.45 μm for visualization of a human cerebellum specimen down to cellular level. We have shown that all selected modalities, namely laboratory-based absorption contrast micro-tomography (LBμCT), synchrotron radiation based in-line single distance phase contrast tomography (SDPR) and synchrotron radiation based single-grating interferometry (GI), can reach cellular resolution for tissue samples with a size in the mm-range. The results are discussed qualitatively in comparison to optical microscopy of haematoxylin and eosin (HE) stained sections. As phase contrast yields to a better data quality for soft tissues and in order to overcome restrictions of limited beamline access for phase contrast measurements, we have equipped the μCT system nanotom m with a double-grating phase contrast set-up. Preliminary experimental results of a knee sample consisting of a bony part and a cartilage demonstrate that phase contrast data exhibits better quality compared to absorption contrast. Currently, the set-up is under adjustment. It is expected that cellular resolution would also be achieved. The questions arise (1) what would be the quality gain of laboratory-based phase contrast in comparison to laboratory-based absorption contrast tomography and (2) could laboratory-based phase contrast data provide comparable results to synchrotron radiation based phase contrast data.

Multilayer adsorption of C2H4 and CF4 on graphite: Grand Canonical Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Abdelatif, H.; Drir, M.

2016-11-01

We study the phase transitions in adsorbed multilayers by Grand Canonical Monte Carlo simulations (GCMC) of the lattice-gas model. The focus will be on ethylene (C2H4) and tetrafluoromethane (CF4) on a homogeneous graphite surface. Earlier simulations of these systems investigated structural properties, dynamical behaviors of adsorbed films and thermodynamic quantities such as isosteric heat. The main purpose of this study is to consider the adsorbed multilayers by the evaluation of the layering behavior, the wetting phenomena and the critical temperatures. The isotherms obtained for temperature from 50 K to 170 K reproduce a number of interesting features observed experimentally: (i) we observe an important number of layers in contrast with previous simulations, (ii) a finite number of layers at saturated pressure for low temperatures are found, (iii) the isotherms present vertical steps typical of layer-by-layer growth, at higher temperatures these distinct layers tend to disappear signifying that the film thickness increases continuously, (iv) a thin film to thick film transition near the triple point temperature is noticed. In addition to this qualitative description, quantitative information are determined including temperatures and relative pressures of layers formation, layer-critical-point temperatures and phase diagrams. Comparing the two systems, ethylene/graphite and tetrafluoromethane/graphite, we observe a qualitatively similar behavior.

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

NASA Astrophysics Data System (ADS)

Habershon, Scott; Manolopoulos, David E.

2009-12-01

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

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

PubMed

Habershon, Scott; Manolopoulos, David E

2009-12-28

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

A study of MRI gradient echo signals from discrete magnetic particles with considerations of several parameters in simulations.

PubMed

Kokeny, Paul; Cheng, Yu-Chung N; Xie, He

2018-05-01

Modeling MRI signal behaviors in the presence of discrete magnetic particles is important, as magnetic particles appear in nanoparticle labeled cells, contrast agents, and other biological forms of iron. Currently, many models that take into account the discrete particle nature in a system have been used to predict magnitude signal decays in the form of R2* or R2' from one single voxel. Little work has been done for predicting phase signals. In addition, most calculations of phase signals rely on the assumption that a system containing discrete particles behaves as a continuous medium. In this work, numerical simulations are used to investigate MRI magnitude and phase signals from discrete particles, without diffusion effects. Factors such as particle size, number density, susceptibility, volume fraction, particle arrangements for their randomness, and field of view have been considered in simulations. The results are compared to either a ground truth model, theoretical work based on continuous mediums, or previous literature. Suitable parameters used to model particles in several voxels that lead to acceptable magnetic field distributions around particle surfaces and accurate MR signals are identified. The phase values as a function of echo time from a central voxel filled by particles can be significantly different from those of a continuous cubic medium. However, a completely random distribution of particles can lead to an R2' value which agrees with the prediction from the static dephasing theory. A sphere with a radius of at least 4 grid points used in simulations is found to be acceptable to generate MR signals equivalent from a larger sphere. Increasing number of particles with a fixed volume fraction in simulations reduces the resulting variance in the phase behavior, and converges to almost the same phase value for different particle numbers at each echo time. The variance of phase values is also reduced when increasing the number of particles in a fixed voxel. These results indicate that MRI signals from voxels containing discrete particles, even with a sufficient number of particles per voxel, cannot be properly modeled by a continuous medium with an equivalent susceptibility value in the voxel. Copyright © 2017 Elsevier Inc. All rights reserved.

Physiologic Simulation of the Fontan Surgery with Variable Wall Properties and Respiration

NASA Astrophysics Data System (ADS)

Long, Christopher; Bazilevs, Yuri; Feinstein, Jeffrey; Marsden, Alison

2010-11-01

Children born with single ventricle heart defects typically undergo a surgical procedure known as a total cavopulmonary connection (TCPC). The goal of this work is to perform hemodynamic simulations accounting for motion of the arterial walls in the TCPC. We perform fluid structure interactions (FSI) simulations using an Arbitrary Lagrangian Eulerian (ALE) finite element framework into a patient-specific model of the TCPC. The patient's post-op anatomy is reconstructed from MRI data. Respiration rate, heart rate, and venous pressures are obtained from catheterization data, and flowrates are obtained from phase contrast MRI data and are used together with a respiratory model. Lumped parameter (RCR) boundary conditions are used at the outlets. This study is the first to introduce variable elastic properties for the different areas of the TCPC, including a Gore-Tex conduit. Quantities such as wall shear stresses and pressures at critical junctions are extracted from the simulation and are compared with pressure tracings from clinical data as well as with rigid wall simulations.

Arctic Mixed-phase Clouds Simulated by a Cloud-Resolving Model: Comparison with ARM Observations and Sensitivity to Microphysics Parameterizations

NASA Technical Reports Server (NTRS)

Xu, Kuan-Man; Luo, Yali; Morrison, Hugh; Mcfarquhar, G.M.

2008-01-01

Single-layer mixed-phase stratiform (MPS) Arctic clouds, which formed under conditions of large surface heat flux combined with general subsidence during a subperiod of the Atmospheric Radiation Measurement (ARM) Program Mixed-Phase Arctic Cloud Experiment (M-PACE), are simulated with a cloud resolving model (CRM). The CRM is implemented with either an advanced two-moment (M05) or a commonly used one-moment (L83) bulk microphysics scheme and a state-of-the-art radiative transfer scheme. The CONTROL simulation, that uses the M05 scheme and observed aerosol size distribution and ice nulei (IN) number concentration, reproduces the magnitudes and vertical structures of cloud liquid water content (LWC), total ice water content (IWC), number concentration and effective radius of cloud droplets as suggested by the M-PACE observations. It underestimates ice crystal number concentrations by an order of magnitude and overestimates effective radius of ice crystals by a factor of 2-3. The OneM experiment, that uses the L83 scheme, produces values of liquid water path (LWP) and ice plus snow water path (ISWP) that were about 30% and 4 times, respectively, of those produced by the CONTROL. Its vertical profile of IWC exhibits a bimodal distribution in contrast to the constant distribution of IWC produced in the CONTROL and observations.

Simulations of skin barrier function: free energies of hydrophobic and hydrophilic transmembrane pores in ceramide bilayers.

PubMed

Notman, Rebecca; Anwar, Jamshed; Briels, W J; Noro, Massimo G; den Otter, Wouter K

2008-11-15

Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening.

Simulations of Skin Barrier Function: Free Energies of Hydrophobic and Hydrophilic Transmembrane Pores in Ceramide Bilayers

PubMed Central

Notman, Rebecca; Anwar, Jamshed; Briels, W. J.; Noro, Massimo G.; den Otter, Wouter K.

2008-01-01

Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening. PMID:18708461

Complexation Enhancement Drives Water-to-Oil Ion Transport: A Simulation Study

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

Qiao, Baofu; Ferru, Geoffroy; Ellis, Ross J.

We address the structures and energetics of ion solvation in aqueous and organic solutions to understand liquid-liquid ion transport. Atomistic molecular dynamics (MD) simulations with polarizable force field are performed to study the coordination transformations driving lanthanide (Ln(III)) and nitrate ion transport between aqueous and an alkylamide-oil solution. An enhancement of the coordination behavior in the organic phase is achieved in contrast with the aqueous solution. In particular, the coordination number of Ce3+ increases from 8.9 in the aqueous to 9.9 in the organic solutions (from 8 in the aqueous to 8.8 in the organic systems for Yb3+). Moreover, themore » local coordination environ ment changes dramatically. Potential of mean force calculations show that the Ln(III)-ligand coordination interaction strengths follow the order of Ln(III-)nitrate> Ln(III)-water>Ln(III)-DMDBTDMA. They increase 2-fold in the lipophilic environment in comparison to the aqueous phase, and we attribute this to the shedding of the outer solvation shell. Our findings highlight the importance of outer sphere interactions on the competitive solvation energetics that cause ions to migrate between immiscible phases; an essential ingredient for advancing important applications such as rare earth metal separations. Some open questions in simulating the coordination behavior of heavy metals are also addressed.« less

Atomistic Simulations of Detonation Instabilities in Condensed Phase Systems

NASA Astrophysics Data System (ADS)

Kober, Edward; Heim, Andrew; Germann, Timothy; Jensen, Niels

2007-06-01

We report the results of simulations of condensed phase detonation phenomena using a model diatomic system: 2AB -> A2 + B2. The initial set of parameters for this system corresponded to the Model 0 set of C. White et al, which exhibits a steady, Chapman-Jouget (CJ) detonation structure with a reaction zone length of 30-100 å. This has a highly compressed CJ state (V/V0˜0.5) that does not consist of discrete molecular species. The potential form was modified so that a more molecular CJ state resulted, consistent with the models for conventional organic explosives. The new system has a less dense CJ state (V/V0˜0.8), and the reaction zone was substantially extended. The reaction rate fits Arrhenius-type kinetics with an activation energy of ˜2 eV, with a minor density dependence. In contrast, the original Model 0 system had a lower activation energy (˜1 eV) with a stronger density dependence. The new system exhibits quite marked two dimensional instability structures with well-defined wavelengths similar to what has been observed for gas-phase detonations and for nitromethane. Depending on the exothermicity and the width of the periodic simulations, these instabilities can result in either detonation failure or quasi-steady propagation. The observed propagation velocities are several per cent higher than CJ values derived from thermodynamic analyses.

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

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

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

DOE PAGES

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.; ...

2017-10-25

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

Measurement of pulsatile motion with millisecond resolution by MRI.

PubMed

Souchon, Rémi; Gennisson, Jean-Luc; Tanter, Mickael; Salomir, Rares; Chapelon, Jean-Yves; Rouvière, Olivier

2012-06-01

We investigated a technique based on phase-contrast cine MRI combined with deconvolution of the phase shift waveforms to measure rapidly varying pulsatile motion waveforms. The technique does not require steady-state displacement during motion encoding. Simulations and experiments were performed in porcine liver samples in view of a specific application, namely the observation of transient displacements induced by acoustic radiation force. Simulations illustrate the advantages and shortcomings of the methods. For experimental validation, the waveforms were acquired with an ultrafast ultrasound scanner (Supersonic Imagine Aixplorer), and the rates of decay of the waveforms (relaxation time) were compared. With bipolar motion-encoding gradient of 8.4 ms, the method was able to measure displacement waveforms with a temporal resolution of 1 ms over a time course of 40 ms. Reasonable agreement was found between the rate of decay of the waveforms measured in ultrasound (2.8 ms) and in MRI (2.7-3.3 ms). Copyright © 2011 Wiley-Liss, Inc.

Kernel-Phase Interferometry for Super-Resolution Detection of Faint Companions

NASA Astrophysics Data System (ADS)

Factor, Samuel M.; Kraus, Adam L.

2017-01-01

Direct detection of close in companions (exoplanets or binary systems) is notoriously difficult. While coronagraphs and point spread function (PSF) subtraction can be used to reduce contrast and dig out signals of companions under the PSF, there are still significant limitations in separation and contrast. Non-redundant aperture masking (NRM) interferometry can be used to detect companions well inside the PSF of a diffraction limited image, though the mask discards ˜95% of the light gathered by the telescope and thus the technique is severely flux limited. Kernel-phase analysis applies interferometric techniques similar to NRM to a diffraction limited image utilizing the full aperture. Instead of non-redundant closure-phases, kernel-phases are constructed from a grid of points on the full aperture, simulating a redundant interferometer. I have developed my own faint companion detection pipeline which utilizes an Bayesian analysis of kernel-phases. I have used this pipeline to search for new companions in archival images from HST/NICMOS in order to constrain planet and binary formation models at separations inaccessible to previous techniques. Using this method, it is possible to detect a companion well within the classical λ/D Rayleigh diffraction limit using a fraction of the telescope time as NRM. This technique can easily be applied to archival data as no mask is needed and will thus make the detection of close in companions cheap and simple as no additional observations are needed. Since the James Webb Space Telescope (JWST) will be able to perform NRM observations, further development and characterization of kernel-phase analysis will allow efficient use of highly competitive JWST telescope time.

Kernel-Phase Interferometry for Super-Resolution Detection of Faint Companions

NASA Astrophysics Data System (ADS)

Factor, Samuel

2016-10-01

Direct detection of close in companions (binary systems or exoplanets) is notoriously difficult. While chronagraphs and point spread function (PSF) subtraction can be used to reduce contrast and dig out signals of companions under the PSF, there are still significant limitations in separation and contrast. While non-redundant aperture masking (NRM) interferometry can be used to detect companions well inside the PSF of a diffraction limited image, the mask discards 95% of the light gathered by the telescope and thus the technique is severely flux limited. Kernel-phase analysis applies interferometric techniques similar to NRM though utilizing the full aperture. Instead of closure-phases, kernel-phases are constructed from a grid of points on the full aperture, simulating a redundant interferometer. I propose to develop my own faint companion detection pipeline which utilizes an MCMC analysis of kernel-phases. I will search for new companions in archival images from NIC1 and ACS/HRC in order to constrain binary and planet formation models at separations inaccessible to previous techniques. Using this method, it is possible to detect a companion well within the classical l/D Rayleigh diffraction limit using a fraction of the telescope time as NRM. This technique can easily be applied to archival data as no mask is needed and will thus make the detection of close in companions cheap and simple as no additional observations are needed. Since the James Webb Space Telescope (JWST) will be able to perform NRM observations, further development and characterization of kernel-phase analysis will allow efficient use of highly competitive JWST telescope time.

Post-coronagraphic tip-tilt sensing for vortex phase masks: The QACITS technique

NASA Astrophysics Data System (ADS)

Huby, E.; Baudoz, P.; Mawet, D.; Absil, O.

2015-12-01

Context. Small inner working angle coronagraphs, such as the vortex phase mask, are essential to exploit the full potential of ground-based telescopes in the context of exoplanet detection and characterization. However, the drawback of this attractive feature is a high sensitivity to pointing errors, which degrades the performance of the coronagraph. Aims: We propose a tip-tilt retrieval technique based on the analysis of the final coronagraphic image, hereafter called Quadrant Analysis of Coronagraphic Images for Tip-tilt Sensing (QACITS). Methods: Under the assumption of small phase aberrations, we show that the behavior of the vortex phase mask can be simply described from the entrance pupil to the Lyot stop plane with Zernike polynomials. This convenient formalism is used to establish the theoretical basis of the QACITS technique. We performed simulations to demonstrate the validity and limits of the technique, including the case of a centrally obstructed pupil. Results: The QACITS technique principle is validated with experimental results in the case of an unobstructed circular aperture, as well as simulations in presence of a central obstruction. The typical configuration of the Keck telescope (24% central obstruction) has been simulated with additional high order aberrations. In these conditions, our simulations show that the QACITS technique is still adapted to centrally obstructed pupils and performs tip-tilt retrieval with a precision of 5 × 10-2λ/D when wavefront errors amount to λ/ 14 rms and 10-2λ/D for λ/ 70 rms errors (with λ the wavelength and D the pupil diameter). Conclusions: We have developed and demonstrated a tip-tilt sensing technique for vortex coronagraphs. The implementation of the QACITS technique is based on the analysis of the scientific image and does not require any modification of the original setup. Current facilities equipped with a vortex phase mask can thus directly benefit from this technique to improve the contrast performance close to the axis.

Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC)

PubMed Central

2017-01-01

We present a new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. Our system consists of a commercial brightfield microscope with one hardware modification—an inexpensive 3D printed condenser insert. The method, color-multiplexed Differential Phase Contrast (cDPC), is a single-shot variant of Differential Phase Contrast (DPC), which recovers the phase of a sample from images with asymmetric illumination. We employ partially coherent illumination to achieve resolution corresponding to 2× the objective NA. Quantitative phase can then be used to synthesize DIC and phase contrast images or extract shape and density. We demonstrate amplitude and phase recovery at camera-limited frame rates (50 fps) for various in vitro cell samples and c. elegans in a micro-fluidic channel. PMID:28152023

Contrast-enhanced imaging of SPIO-labeled platelets using magnetomotive ultrasound

PubMed Central

Pope, Ava G.; Wu, Gongting; McWhorter, Frances Y.; Merricks, Elizabeth C.; Nichols, Timothy C.; Czernuszewicz, Tomasz J.; Gallippi, Caterina M.; Oldenburg, Amy L.

2013-01-01

The ability to image platelets in vivo can provide insight into blood clotting processes and coagulopathies, and aid in identifying sites of vascular endothelial damage related to trauma or cardiovascular disease. Toward this end, we have developed a magnetomotive ultrasound (MMUS) system that provides contrast-enhanced imaging of superparamagnetic iron oxide (SPIO) labeled platelets via magnetically-induced vibration. Platelets are a promising platform for functional imaging contrast because they readily take up SPIOs and are easily harvested from blood. Here we report a novel MMUS system that accommodates an arbitrarily thick sample while maintaining portability. We employed a frequency- and phase-locked motion detection algorithm based on bandpass filtering of the differential RF phase, which allows for the detection of sub-resolution vibration amplitudes on the order of several nanometers. We then demonstrated MMUS in homogenous tissue phantoms at SPIO concentrations as low as 0.09 mg/ml Fe (p < 0.0001, n = 6, t-test). Finally, we showed that our system is capable of 3-dimensional imaging of a 185 μL simulated clot containing SPIO-platelets. This highlights the potential utility for non-invasive imaging of platelet-rich clots, which would constitute a fundamental advance in technology for the study of hemostasis and detection of clinically relevant thrombi. PMID:24077004

Contrast-enhanced imaging of SPIO-labeled platelets using magnetomotive ultrasound

NASA Astrophysics Data System (ADS)

Pope, Ava G.; Wu, Gongting; McWhorter, Frances Y.; Merricks, Elizabeth P.; Nichols, Timothy C.; Czernuszewicz, Tomasz J.; Gallippi, Caterina M.; Oldenburg, Amy L.

2013-10-01

The ability to image platelets in vivo can provide insight into blood clotting processes and coagulopathies, and aid in identifying sites of vascular endothelial damage related to trauma or cardiovascular disease. Toward this end, we have developed a magnetomotive ultrasound (MMUS) system that provides contrast-enhanced imaging of superparamagnetic iron oxide (SPIO) labeled platelets via magnetically-induced vibration. Platelets are a promising platform for functional imaging contrast because they readily take up SPIOs and are easily harvested from blood. Here we report a novel MMUS system that accommodates an arbitrarily thick sample while maintaining portability. We employed a frequency- and phase-locked motion detection algorithm based on bandpass filtering of the differential RF phase, which allows for the detection of sub-resolution vibration amplitudes on the order of several nanometers. We then demonstrated MMUS in homogenous tissue phantoms at SPIO concentrations as low as 0.09 mg ml-1 Fe (p < 0.0001, n = 6, t-test). Finally, we showed that our system is capable of three-dimensional imaging of a 185 µL simulated clot containing SPIO-platelets. This highlights the potential utility for non-invasive imaging of platelet-rich clots, which would constitute a fundamental advance in technology for the study of hemostasis and detection of clinically relevant thrombi.

Contrast-enhanced imaging of SPIO-labeled platelets using magnetomotive ultrasound.

PubMed

Pope, Ava G; Wu, Gongting; McWhorter, Frances Y; Merricks, Elizabeth P; Nichols, Timothy C; Czernuszewicz, Tomasz J; Gallippi, Caterina M; Oldenburg, Amy L

2013-10-21

The ability to image platelets in vivo can provide insight into blood clotting processes and coagulopathies, and aid in identifying sites of vascular endothelial damage related to trauma or cardiovascular disease. Toward this end, we have developed a magnetomotive ultrasound (MMUS) system that provides contrast-enhanced imaging of superparamagnetic iron oxide (SPIO) labeled platelets via magnetically-induced vibration. Platelets are a promising platform for functional imaging contrast because they readily take up SPIOs and are easily harvested from blood. Here we report a novel MMUS system that accommodates an arbitrarily thick sample while maintaining portability. We employed a frequency- and phase-locked motion detection algorithm based on bandpass filtering of the differential RF phase, which allows for the detection of sub-resolution vibration amplitudes on the order of several nanometers. We then demonstrated MMUS in homogenous tissue phantoms at SPIO concentrations as low as 0.09 mg ml(-1) Fe (p < 0.0001, n = 6, t-test). Finally, we showed that our system is capable of three-dimensional imaging of a 185 µL simulated clot containing SPIO-platelets. This highlights the potential utility for non-invasive imaging of platelet-rich clots, which would constitute a fundamental advance in technology for the study of hemostasis and detection of clinically relevant thrombi.

How effective is advertising in duopoly markets?

NASA Astrophysics Data System (ADS)

Sznajd-Weron, K.; Weron, R.

2003-06-01

A simple Ising spin model which can describe the mechanism of advertising in a duopoly market is proposed. In contrast to other agent-based models, the influence does not flow inward from the surrounding neighbors to the center site, but spreads outward from the center to the neighbors. The model thus describes the spread of opinions among customers. It is shown via standard Monte Carlo simulations that very simple rules and inclusion of an external field-an advertising campaign-lead to phase transitions.

Phase-contrast x-ray computed tomography for observing biological specimens and organic materials

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji

1995-02-01

A novel three-dimensional x-ray imaging method has been developed by combining a phase-contrast x-ray imaging technique with x-ray computed tomography. This phase-contrast x-ray computed tomography (PCX-CT) provides sectional images of organic specimens that would produce absorption-contrast x-ray CT images with little contrast. Comparing PCX-CT images of rat cerebellum and cancerous rabbit liver specimens with corresponding absorption-contrast CT images shows that PCX-CT is much more sensitive to the internal structure of organic specimens.

4D phase contrast flow imaging for in-stent flow visualization and assessment of stent patency in peripheral vascular stents--a phantom study.

PubMed

Bunck, Alexander C; Jüttner, Alena; Kröger, Jan Robert; Burg, Matthias C; Kugel, Harald; Niederstadt, Thomas; Tiemann, Klaus; Schnackenburg, Bernhard; Crelier, Gerard R; Heindel, Walter; Maintz, David

2012-09-01

4D phase contrast flow imaging is increasingly used to study the hemodynamics in various vascular territories and pathologies. The aim of this study was to assess the feasibility and validity of MRI based 4D phase contrast flow imaging for the evaluation of in-stent blood flow in 17 commonly used peripheral stents. 17 different peripheral stents were implanted into a MR compatible flow phantom. In-stent visibility, maximal velocity and flow visualization were assessed and estimates of in-stent patency obtained from 4D phase contrast flow data sets were compared to a conventional 3D contrast-enhanced magnetic resonance angiography (CE-MRA) as well as 2D PC flow measurements. In all but 3 of the tested stents time-resolved 3D particle traces could be visualized inside the stent lumen. Quality of 4D flow visualization and CE-MRA images depended on stent type and stent orientation relative to the magnetic field. Compared to the visible lumen area determined by 3D CE-MRA, estimates of lumen patency derived from 4D flow measurements were significantly higher and less dependent on stent type. A higher number of stents could be assessed for in-stent patency by 4D phase contrast flow imaging (n=14) than by 2D phase contrast flow imaging (n=10). 4D phase contrast flow imaging in peripheral vascular stents is feasible and appears advantageous over conventional 3D contrast-enhanced MR angiography and 2D phase contrast flow imaging. It allows for in-stent flow visualization and flow quantification with varying quality depending on stent type. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Hard x-ray phase contrastmicroscopy - techniques and applications

NASA Astrophysics Data System (ADS)

Holzner, Christian

In 1918, Einstein provided the first description of the nature of the refractive index for X-rays, showing that phase contrast effects are significant. A century later, most x-ray microscopy and nearly all medical imaging remains based on absorption contrast, even though phase contrast offers orders of magnitude improvements in contrast and reduced radiation exposure at multi-keV x-ray energies. The work presented is concerned with developing practical and quantitative methods of phase contrast for x-ray microscopy. A theoretical framework for imaging in phase contrast is put forward; this is used to obtain quantitative images in a scanning microscope using a segmented detector, and to correct for artifacts in a commercial phase contrast x-ray nano-tomography system. The principle of reciprocity between scanning and full-field microscopes is then used to arrive at a novel solution: Zernike contrast in a scanning microscope. These approaches are compared on a theoretical and experimental basis in direct connection with applications using multi-keV x-ray microscopes at the Advanced Photon Source at Argonne National Laboratory. Phase contrast provides the best means to image mass and ultrastructure of light elements that mainly constitute biological matter, while stimulated x-ray fluorescence provides high sensitivity for studies of the distribution of heavier trace elements, such as metals. These approaches are combined in a complementary way to yield quantitative maps of elemental concentration from 2D images, with elements placed in their ultrastructural context. The combination of x-ray fluorescence and phase contrast poses an ideal match for routine, high resolution tomographic imaging of biological samples in the future. The presented techniques and demonstration experiments will help pave the way for this development.

Dynamical phase transitions in generalized Kuramoto model with distributed Sakaguchi phase

NASA Astrophysics Data System (ADS)

Banerjee, Amitava

2017-11-01

In this numerical work, we have systematically studied the dynamical phase transitions in the Kuramoto-Sakaguchi model of synchronizing phase oscillators controlled by disorder in the Sakaguchi phases. We derive the numerical steady state phase diagrams for quenched and annealed kinds of disorder in the Sakaguchi parameters, using the conventional order parameter and other such statistical quantities as strength of incoherence and discontinuity measures. We have also considered the correlation profile of the local order parameter fluctuations in the various phases identified. The phase diagrams for quenched disorder are qualitatively much different from those in the global coupling regime. The order of various transitions is confirmed by a study of the distribution of the order parameter and its fourth order Binder’s cumulant across the transition for an ensemble of initial distribution of phases. For the annealed type of disorder, in contrast to the case with quenched disorder, the system is almost insensitive to the amount of disorder. We also elucidate the role of chimeralike states in the synchronizing transition of the system, and study the effect of disorder on these states. Finally, we seek justification of our results from simulations guided by the Ott-Antonsen ansatz.

Origins of phase contrast in the atomic force microscope in liquids

PubMed Central

Melcher, John; Carrasco, Carolina; Xu, Xin; Carrascosa, José L.; Gómez-Herrero, Julio; José de Pablo, Pedro; Raman, Arvind

2009-01-01

We study the physical origins of phase contrast in dynamic atomic force microscopy (dAFM) in liquids where low-stiffness microcantilever probes are often used for nanoscale imaging of soft biological samples with gentle forces. Under these conditions, we show that the phase contrast derives primarily from a unique energy flow channel that opens up in liquids due to the momentary excitation of higher eigenmodes. Contrary to the common assumption, phase-contrast images in liquids using soft microcantilevers are often maps of short-range conservative interactions, such as local elastic response, rather than tip-sample dissipation. The theory is used to demonstrate variations in local elasticity of purple membrane and bacteriophage ϕ29 virions in buffer solutions using the phase-contrast images. PMID:19666560

Phase contrast imaging of cochlear soft tissue.

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

Smith, S.; Hwang, M.; Rau, C.

A noninvasive technique to image soft tissue could expedite diagnosis and disease management in the auditory system. We propose inline phase contrast imaging with hard X-rays as a novel method that overcomes the limitations of conventional absorption radiography for imaging soft tissue. In this study, phase contrast imaging of mouse cochleae was performed at the Argonne National Laboratory Advanced Photon Source. The phase contrast tomographic reconstructions show soft tissue structures of the cochlea, including the inner pillar cells, the inner spiral sulcus, the tectorial membrane, the basilar membrane, and the Reissner's membrane. The results suggest that phase contrast X-ray imagingmore » and tomographic techniques hold promise to noninvasively image cochlear structures at an unprecedented cellular level.« less

Origins of phase contrast in the atomic force microscope in liquids.

PubMed

Melcher, John; Carrasco, Carolina; Xu, Xin; Carrascosa, José L; Gómez-Herrero, Julio; José de Pablo, Pedro; Raman, Arvind

2009-08-18

We study the physical origins of phase contrast in dynamic atomic force microscopy (dAFM) in liquids where low-stiffness microcantilever probes are often used for nanoscale imaging of soft biological samples with gentle forces. Under these conditions, we show that the phase contrast derives primarily from a unique energy flow channel that opens up in liquids due to the momentary excitation of higher eigenmodes. Contrary to the common assumption, phase-contrast images in liquids using soft microcantilevers are often maps of short-range conservative interactions, such as local elastic response, rather than tip-sample dissipation. The theory is used to demonstrate variations in local elasticity of purple membrane and bacteriophage 29 virions in buffer solutions using the phase-contrast images.

Complex-valued time-series correlation increases sensitivity in FMRI analysis.

PubMed

Kociuba, Mary C; Rowe, Daniel B

2016-07-01

To develop a linear matrix representation of correlation between complex-valued (CV) time-series in the temporal Fourier frequency domain, and demonstrate its increased sensitivity over correlation between magnitude-only (MO) time-series in functional MRI (fMRI) analysis. The standard in fMRI is to discard the phase before the statistical analysis of the data, despite evidence of task related change in the phase time-series. With a real-valued isomorphism representation of Fourier reconstruction, correlation is computed in the temporal frequency domain with CV time-series data, rather than with the standard of MO data. A MATLAB simulation compares the Fisher-z transform of MO and CV correlations for varying degrees of task related magnitude and phase amplitude change in the time-series. The increased sensitivity of the complex-valued Fourier representation of correlation is also demonstrated with experimental human data. Since the correlation description in the temporal frequency domain is represented as a summation of second order temporal frequencies, the correlation is easily divided into experimentally relevant frequency bands for each voxel's temporal frequency spectrum. The MO and CV correlations for the experimental human data are analyzed for four voxels of interest (VOIs) to show the framework with high and low contrast-to-noise ratios in the motor cortex and the supplementary motor cortex. The simulation demonstrates the increased strength of CV correlations over MO correlations for low magnitude contrast-to-noise time-series. In the experimental human data, the MO correlation maps are noisier than the CV maps, and it is more difficult to distinguish the motor cortex in the MO correlation maps after spatial processing. Including both magnitude and phase in the spatial correlation computations more accurately defines the correlated left and right motor cortices. Sensitivity in correlation analysis is important to preserve the signal of interest in fMRI data sets with high noise variance, and avoid excessive processing induced correlation. Copyright © 2016 Elsevier Inc. All rights reserved.

Numerical simulation of drop impact on a thin film: the origin of the droplets in the splashing regime

NASA Astrophysics Data System (ADS)

Xie, Zhihua; Che, Zhizhao; Ismail, Renad; Pain, Chris; Matar, Omar

2015-11-01

Drop impact on a liquid layer is a feature of numerous multiphase flow problems, and has been the subject of numerous theoretical, experimental and numerical investigations. In the splashing regime, however, little attention has been focused on the origin of the droplets that are formed during the splashing process. The objective of this study is to investigate this issue numerically in order to improve our understanding of the mechanisms underlying splashing as a function of the relevant system parameters. In contrast to the conventional two-phase flow approach, commonly used to simulate splashing, here, a three-dimensional, three-phase flow model, with adaptive, unstructured meshing, is employed to study the liquid (droplet) - gas (surrounding air) - liquid (thin film) system. In the cases to be presented, both liquid phases have the same fluid property, although, clearly, our method can be used in the more general case of two different liquids. Numerical results of droplet impact on a thin film are analysed to determine whether the origin of the droplets following impact corresponds to the mother drop, or the thin film, or both. EPSRC Programme Grant, MEMPHIS, EP/K0039761/1.

OPTIMIZING THROUGH CO-EVOLUTIONARY AVALANCHES

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

S. BOETTCHER; A. PERCUS

2000-08-01

We explore a new general-purpose heuristic for finding high-quality solutions to hard optimization problems. The method, called extremal optimization, is inspired by ''self-organized critically,'' a concept introduced to describe emergent complexity in many physical systems. In contrast to Genetic Algorithms which operate on an entire ''gene-pool'' of possible solutions, extremal optimization successively replaces extremely undesirable elements of a sub-optimal solution with new, random ones. Large fluctuations, called ''avalanches,'' ensue that efficiently explore many local optima. Drawing upon models used to simulate far-from-equilibrium dynamics, extremal optimization complements approximation methods inspired by equilibrium statistical physics, such as simulated annealing. With only onemore » adjustable parameter, its performance has proved competitive with more elaborate methods, especially near phase transitions. Those phase transitions are found in the parameter space of most optimization problems, and have recently been conjectured to be the origin of some of the hardest instances in computational complexity. We will demonstrate how extremal optimization can be implemented for a variety of combinatorial optimization problems. We believe that extremal optimization will be a useful tool in the investigation of phase transitions in combinatorial optimization problems, hence valuable in elucidating the origin of computational complexity.« less

Study of the functional hyperconnectivity between couples of pilots during flight simulation: an EEG hyperscanning study.

PubMed

Astolfi, L; Toppi, J; Borghini, G; Vecchiato, G; Isabella, R; De Vico Fallani, F; Cincotti, F; Salinari, S; Mattia, D; He, B; Caltagirone, C; Babiloni, F

2011-01-01

Brain Hyperscanning, i.e. the simultaneous recording of the cerebral activity of different human subjects involved in interaction tasks, is a very recent field of Neuroscience aiming at understanding the cerebral processes generating and generated by social interactions. This approach allows the observation and modeling of the neural signature specifically dependent on the interaction between subjects, and, even more interestingly, of the functional links existing between the activities in the brains of the subjects interacting together. In this EEG hyperscanning study we explored the functional hyperconnectivity between the activity in different scalp sites of couples of Civil Aviation Pilots during different phases of a flight reproduced in a flight simulator. Results shown a dense network of connections between the two brains in the takeoff and landing phases, when the cooperation between them is maximal, in contrast with phases during which the activity of the two pilots was independent, when no or quite few links were shown. These results confirms that the study of the brain connectivity between the activity simultaneously acquired in human brains during interaction tasks can provide important information about the neural basis of the "spirit of the group".

Formation of nanotwin networks during high-temperature crystallization of amorphous germanium

DOE PAGES

Sandoval, Luis; Reina, Celia; Marian, Jaime

2015-11-26

Germanium is an extremely important material used for numerous functional applications in many fields of nanotechnology. In this paper, we study the crystallization of amorphous Ge using atomistic simulations of critical nano-metric nuclei at high temperatures. We find that crystallization occurs by the recurrent transfer of atoms via a diffusive process from the amorphous phase into suitably-oriented crystalline layers. We accompany our simulations with a comprehensive thermodynamic and kinetic analysis of the growth process, which explains the energy balance and the interfacial growth velocities governing grain growth. For the <111> crystallographic orientation, we find a degenerate atomic rearrangement process, withmore » two zero-energy modes corresponding to a perfect crystalline structure and the formation of a Σ3 twin boundary. Continued growth in this direction results in the development a twin network, in contrast with all other growth orientations, where the crystal grows defect-free. This particular mechanism of crystallization from amorphous phases is also observed during solid-phase epitaxial growth of <111> semiconductor crystals, where growth is restrained to one dimension. Lastly, we calculate the equivalent X-ray diffraction pattern of the obtained nanotwin networks, providing grounds for experimental validation.« less

Combining local search with co-evolution in a remarkably simple way

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

Boettcher, S.; Percus, A.

2000-05-01

The authors explore a new general-purpose heuristic for finding high-quality solutions to hard optimization problem. The method, called extremal optimization, is inspired by self-organized criticality, a concept introduced to describe emergent complexity in physical systems. In contrast to genetic algorithms, which operate on an entire gene-pool of possible solutions, extremal optimization successively replaces extremely undesirable elements of a single sub-optimal solution with new, random ones. Large fluctuations, or avalanches, ensue that efficiently explore many local optima. Drawing upon models used to simulate far-from-equilibrium dynamics, extremal optimization complements heuristics inspired by equilibrium statistical physics, such as simulated annealing. With only onemore » adjustable parameter, its performance has proved competitive with more elaborate methods, especially near phase transitions. Phase transitions are found in many combinatorial optimization problems, and have been conjectured to occur in the region of parameter space containing the hardest instances. We demonstrate how extremal optimization can be implemented for a variety of hard optimization problems. We believe that this will be a useful tool in the investigation of phase transitions in combinatorial optimization, thereby helping to elucidate the origin of computational complexity.« less

Formation of Nanotwin Networks during High-Temperature Crystallization of Amorphous Germanium

PubMed Central

Sandoval, Luis; Reina, Celia; Marian, Jaime

2015-01-01

Germanium is an extremely important material used for numerous functional applications in many fields of nanotechnology. In this paper, we study the crystallization of amorphous Ge using atomistic simulations of critical nano-metric nuclei at high temperatures. We find that crystallization occurs by the recurrent transfer of atoms via a diffusive process from the amorphous phase into suitably-oriented crystalline layers. We accompany our simulations with a comprehensive thermodynamic and kinetic analysis of the growth process, which explains the energy balance and the interfacial growth velocities governing grain growth. For the 〈111〉 crystallographic orientation, we find a degenerate atomic rearrangement process, with two zero-energy modes corresponding to a perfect crystalline structure and the formation of a Σ3 twin boundary. Continued growth in this direction results in the development a twin network, in contrast with all other growth orientations, where the crystal grows defect-free. This particular mechanism of crystallization from amorphous phases is also observed during solid-phase epitaxial growth of 〈111〉 semiconductor crystals, where growth is restrained to one dimension. We calculate the equivalent X-ray diffraction pattern of the obtained nanotwin networks, providing grounds for experimental validation. PMID:26607496

Mirror instability near the threshold: Hybrid simulations

NASA Astrophysics Data System (ADS)

Hellinger, P.; Trávníček, P.; Passot, T.; Sulem, P.; Kuznetsov, E. A.; Califano, F.

2007-12-01

Nonlinear behavior of the mirror instability near the threshold is investigated using 1-D hybrid simulations. The simulations demonstrate the presence of an early phase where quasi-linear effects dominate [ Shapiro and Shevchenko, 1964]. The quasi-linear diffusion is however not the main saturation mechanism. A second phase is observed where the mirror mode is linearly stable (the stability is evaluated using the instantaneous ion distribution function) but where the instability nevertheless continues to develop, leading to nonlinear coherent structures in the form of magnetic humps. This regime is well modeled by a nonlinear equation for the magnetic field evolution, derived from a reductive perturbative expansion of the Vlasov-Maxwell equations [ Kuznetsov et al., 2007] with a phenomenological term which represents local variations of the ion Larmor radius. In contrast with previous models where saturation is due to the cooling of a population of trapped particles, the resulting equation correctly reproduces the development of magnetic humps from an initial noise. References Kuznetsov, E., T. Passot and P. L. Sulem (2007), Dynamical model for nonlinear mirror modes near threshold, Phys. Rev. Lett., 98, 235003. Shapiro, V. D., and V. I. Shevchenko (1964), Sov. JETP, 18, 1109.

Testbed Demonstration of Low Order Wavefront Sensing and Control Technology for WFIRST Coronagraph

NASA Astrophysics Data System (ADS)

Shi, Fang; Balasubramanian, K.; Cady, E.; Kern, B.; Lam, R.; Mandic, M.; Patterson, K.; Poberezhskiy, I.; Shields, J.; Seo, J.; Tang, H.; Truong, T.; Wilson, D.

2017-01-01

NASA’s WFIRST-AFTA Coronagraph will be capable of directly imaging and spectrally characterizing giant exoplanets similar to Neptune and Jupiter, and possibly even super-Earths, around nearby stars. To maintain the required coronagraph performance in a realistic space environment, a Low Order Wavefront Sensing and Control (LOWFS/C) subsystem is necessary. The LOWFS/C will use the rejected stellar light to sense and suppress the telescope pointing drift and jitter as well as low order wavefront errors due to the changes in thermal loading of the telescope and the rest of the observatory. The LOWFS/C uses a Zernike phase contrast wavefront sensor with the phase shifting disk combined with the stellar light rejecting occulting mask, a key concept to minimize the non-common path error. Developed as a part of the Dynamic High Contrast Imaging Testbed (DHCIT), the LOWFS/C subsystem also consists of an Optical Telescope Assembly Simulator (OTA-S) to generate the realistic line-of-sight (LoS) drift and jitter as well as low order wavefront error from WFIRST-AFTA telescope’s vibration and thermal drift. The entire LOWFS/C subsystem have been integrated, calibrated, and tested in the Dynamic High Contrast Imaging Testbed. In this presentation we will show the results of LOWFS/C performance during the dynamic coronagraph tests in which we have demonstrated that LOWFS/C is able to maintain the coronagraph contrast with the presence of WFIRST like line-of-sight drift and jitter as well as low order wavefront drifts.

In-line phase contrast micro-CT reconstruction for biomedical specimens.

PubMed

Fu, Jian; Tan, Renbo

2014-01-01

X-ray phase contrast micro computed tomography (micro-CT) can non-destructively provide the internal structure information of soft tissues and low atomic number materials. It has become an invaluable analysis tool for biomedical specimens. Here an in-line phase contrast micro-CT reconstruction technique is reported, which consists of a projection extraction method and the conventional filter back-projection (FBP) reconstruction algorithm. The projection extraction is implemented by applying the Fourier transform to the forward projections of in-line phase contrast micro-CT. This work comprises a numerical study of the method and its experimental verification using a biomedical specimen dataset measured at an X-ray tube source micro-CT setup. The numerical and experimental results demonstrate that the presented technique can improve the imaging contrast of biomedical specimens. It will be of interest for a wide range of in-line phase contrast micro-CT applications in medicine and biology.

The optical lens coupled X-ray in-line phase contrast imaging system for the characterization of low Z materials

NASA Astrophysics Data System (ADS)

Wang, Kai; Lin, Wei; Dai, Fei; Li, Jun; Qi, Xiaobo; Lei, Haile; Liu, Yuanqiong

2018-05-01

Due to the high spatial resolution and contrast, the optical lens coupled X-ray in-line phase contrast imaging system with the secondary optical magnification is more suitable for the characterization of the low Z materials. The influence of the source to object distance and the object to scintillator distance on the image resolution and contrast is studied experimentally. A phase correlation algorithm is used for the image mosaic of a serial of X-ray phase contrast images acquired with high resolution, the resulting resolution is less than 1.0 μm, and the whole field of view is larger than 1.4 mm. Finally, the geometric morphology and the inner structure of various weakly absorbing samples and the evaporation of water in the plastic micro-shell are in situ characterized by the optical lens coupled X-ray in-line phase contrast imaging system.

Estimating disease prevalence in two-phase studies.

PubMed

Alonzo, Todd A; Pepe, Margaret Sullivan; Lumley, Thomas

2003-04-01

Disease prevalence is ideally estimated using a 'gold standard' to ascertain true disease status on all subjects in a population of interest. In practice, however, the gold standard may be too costly or invasive to be applied to all subjects, in which case a two-phase design is often employed. Phase 1 data consisting of inexpensive and non-invasive screening tests on all study subjects are used to determine the subjects that receive the gold standard in the second phase. Naive estimates of prevalence in two-phase studies can be biased (verification bias). Imputation and re-weighting estimators are often used to avoid this bias. We contrast the forms and attributes of the various prevalence estimators. Distribution theory and simulation studies are used to investigate their bias and efficiency. We conclude that the semiparametric efficient approach is the preferred method for prevalence estimation in two-phase studies. It is more robust and comparable in its efficiency to imputation and other re-weighting estimators. It is also easy to implement. We use this approach to examine the prevalence of depression in adolescents with data from the Great Smoky Mountain Study.

Intercomparison of Large-Eddy Simulations of Arctic Mixed-Phase Clouds: Importance of Ice Size Distribution Assumptions

NASA Technical Reports Server (NTRS)

Ovchinnikov, Mikhail; Ackerman, Andrew S.; Avramov, Alexander; Cheng, Anning; Fan, Jiwen; Fridlind, Ann M.; Ghan, Steven; Harrington, Jerry; Hoose, Corinna; Korolev, Alexei;

In Vivo Differentiation of Complementary Contrast Media at Dual-Energy CT

PubMed Central

Mongan, John; Rathnayake, Samira; Fu, Yanjun; Wang, Runtang; Jones, Ella F.; Gao, Dong-Wei

2012-01-01

Purpose: To evaluate the feasibility of using a commercially available clinical dual-energy computed tomographic (CT) scanner to differentiate the in vivo enhancement due to two simultaneously administered contrast media with complementary x-ray attenuation ratios. Materials and Methods: Approval from the institutional animal care and use committee was obtained, and National Institutes of Health guidelines for the care and use of laboratory animals were observed. Dual-energy CT was performed in a set of iodine and tungsten solution phantoms and in a rabbit in which iodinated intravenous and bismuth subsalicylate oral contrast media were administered. In addition, a second rabbit was studied after intravenous administration of iodinated and tungsten cluster contrast media. Images were processed to produce virtual monochromatic images that simulated the appearance of conventional single-energy scans, as well as material decomposition images that separate the attenuation due to each contrast medium. Results: Clear separation of each of the contrast media pairs was seen in the phantom and in both in vivo animal models. Separation of bowel lumen from vascular contrast medium allowed visualization of bowel wall enhancement that was obscured by intraluminal bowel contrast medium on conventional CT scans. Separation of two vascular contrast media in different vascular phases enabled acquisition of a perfectly coregistered CT angiogram and venous phase–enhanced CT scan simultaneously in a single examination. Conclusion: Commercially available clinical dual-energy CT scanners can help differentiate the enhancement of selected pairs of complementary contrast media in vivo. © RSNA, 2012 PMID:22778447

Large field-of-view tiled grating structures for X-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Schröter, Tobias J.; Koch, Frieder J.; Meyer, Pascal; Kunka, Danays; Meiser, Jan; Willer, Konstantin; Gromann, Lukas; Marco, Fabio D.; Herzen, Julia; Noel, Peter; Yaroshenko, Andre; Hofmann, Andreas; Pfeiffer, Franz; Mohr, Jürgen

2017-01-01

X-ray grating-based interferometry promises unique new diagnostic possibilities in medical imaging and materials analysis. To transfer this method from scientific laboratories or small-animal applications to clinical radiography applications, compact setups with a large field of view (FoV) are required. Currently the FoV is limited by the grating area, which is restricted due to the complex manufacturing process. One possibility to increase the FoV is tiling individual grating tiles to create one large area grating mounted on a carrier substrate. We investigate theoretically the accuracy needed for a tiling process in all degrees of freedom by applying a simulation approach. We show how the resulting precision requirements can be met using a custom-built frame for exact positioning. Precise alignment is achieved by comparing the fringe patterns of two neighboring grating tiles in a grating interferometer. With this method, the FoV can be extended to practically any desired length in one dimension. First results of a phase-contrast scanning setup with a full FoV of 384 mm × 24 mm show the suitability of this method.

Lifshitz phase: the microscopic structure of aqueous and ethanol mixtures of 1,n-diols.

PubMed

Požar, Martina; Perera, Aurélien

2017-06-14

We study binary mixtures of ethylene glycol and 1,3-propandiol with water or ethanol using computer simulations. Despite strong hydrogen bonding tendencies between all these molecules, we find that these mixtures are surprisingly homogeneous, in contrast to the strong micro-heterogeneity found in aqueous ethanol mixtures. The aqueous diol mixtures are found to be close to ideal mixtures, with near-ideal Kirkwood-Buff integrals. Ethanol-diol mixtures show weak non-ideality. The origin of this unexpected randomness is due to the fact that the two hydrogen bonding hydroxyl groups of the 1,n-diol are bound by the neutral alkyl bond, which prevents the micro-segregation of the different types of hydroxyl groups. These findings suggest that random disorder can arise in the presence of strong interactions - in contrast to the usual picture of random disorder due to weak interactions between the components. They point to the important role of molecular topology in tuning concentration fluctuations in complex liquids. We propose and justify herein the name of Lifshitz phases to designate such types of disordered systems.

Understanding the Impacts of Soil, Climate, and Farming Practices on Soil Organic Carbon Sequestration: A Simulation Study in Australia.

PubMed

Godde, Cécile M; Thorburn, Peter J; Biggs, Jody S; Meier, Elizabeth A

2016-01-01

Carbon sequestration in agricultural soils has the capacity to mitigate greenhouse gas emissions, as well as to improve soil biological, physical, and chemical properties. The review of literature pertaining to soil organic carbon (SOC) dynamics within Australian grain farming systems does not enable us to conclude on the best farming practices to increase or maintain SOC for a specific combination of soil and climate. This study aimed to further explore the complex interactions of soil, climate, and farming practices on SOC. We undertook a modeling study with the Agricultural Production Systems sIMulator modeling framework, by combining contrasting Australian soils, climates, and farming practices (crop rotations, and management within rotations, such as fertilization, tillage, and residue management) in a factorial design. This design resulted in the transposition of contrasting soils and climates in our simulations, giving soil-climate combinations that do not occur in the study area to help provide insights into the importance of the climate constraints on SOC. We statistically analyzed the model's outputs to determinate the relative contributions of soil parameters, climate, and farming practices on SOC. The initial SOC content had the largest impact on the value of SOC, followed by the climate and the fertilization practices. These factors explained 66, 18, and 15% of SOC variations, respectively, after 80 years of constant farming practices in the simulation. Tillage and stubble management had the lowest impacts on SOC. This study highlighted the possible negative impact on SOC of a chickpea phase in a wheat-chickpea rotation and the potential positive impact of a cover crop in a sub-tropical climate (QLD, Australia) on SOC. It also showed the complexities in managing to achieve increased SOC, while simultaneously aiming to minimize nitrous oxide (N2O) emissions and nitrate leaching in farming systems. The transposition of contrasting soils and climates in our simulations revealed the importance of the climate constraints on SOC.

Understanding the Impacts of Soil, Climate, and Farming Practices on Soil Organic Carbon Sequestration: A Simulation Study in Australia

PubMed Central

Godde, Cécile M.; Thorburn, Peter J.; Biggs, Jody S.; Meier, Elizabeth A.

2016-01-01

Carbon sequestration in agricultural soils has the capacity to mitigate greenhouse gas emissions, as well as to improve soil biological, physical, and chemical properties. The review of literature pertaining to soil organic carbon (SOC) dynamics within Australian grain farming systems does not enable us to conclude on the best farming practices to increase or maintain SOC for a specific combination of soil and climate. This study aimed to further explore the complex interactions of soil, climate, and farming practices on SOC. We undertook a modeling study with the Agricultural Production Systems sIMulator modeling framework, by combining contrasting Australian soils, climates, and farming practices (crop rotations, and management within rotations, such as fertilization, tillage, and residue management) in a factorial design. This design resulted in the transposition of contrasting soils and climates in our simulations, giving soil–climate combinations that do not occur in the study area to help provide insights into the importance of the climate constraints on SOC. We statistically analyzed the model’s outputs to determinate the relative contributions of soil parameters, climate, and farming practices on SOC. The initial SOC content had the largest impact on the value of SOC, followed by the climate and the fertilization practices. These factors explained 66, 18, and 15% of SOC variations, respectively, after 80 years of constant farming practices in the simulation. Tillage and stubble management had the lowest impacts on SOC. This study highlighted the possible negative impact on SOC of a chickpea phase in a wheat–chickpea rotation and the potential positive impact of a cover crop in a sub-tropical climate (QLD, Australia) on SOC. It also showed the complexities in managing to achieve increased SOC, while simultaneously aiming to minimize nitrous oxide (N2O) emissions and nitrate leaching in farming systems. The transposition of contrasting soils and climates in our simulations revealed the importance of the climate constraints on SOC. PMID:27242862

Effect of DM Actuator Errors on the WFIRST/AFTA Coronagraph Contrast Performance

NASA Technical Reports Server (NTRS)

Sidick, Erkin; Shi, Fang

2015-01-01

The WFIRST/AFTA 2.4 m space telescope currently under study includes a stellar coronagraph for the imaging and the spectral characterization of extrasolar planets. The coronagraph employs two sequential deformable mirrors (DMs) to compensate for phase and amplitude errors in creating dark holes. DMs are critical elements in high contrast coronagraphs, requiring precision and stability measured in picometers to enable detection of Earth-like exoplanets. Working with a low-order wavefront-sensor the DM that is conjugate to a pupil can also be used to correct low-order wavefront drift during a scientific observation. However, not all actuators in a DM have the same gain. When using such a DM in low-order wavefront sensing and control subsystem, the actuator gain errors introduce high-spatial frequency errors to the DM surface and thus worsen the contrast performance of the coronagraph. We have investigated the effects of actuator gain errors and the actuator command digitization errors on the contrast performance of the coronagraph through modeling and simulations, and will present our results in this paper.

X-ray phase-contrast imaging of the breast—advances towards clinical implementation

PubMed Central

Herzen, J; Willner, M; Grandl, S; Scherer, K; Bamberg, F; Reiser, M F; Pfeiffer, F; Hellerhoff, K

2014-01-01

Breast cancer constitutes about one-quarter of all cancers and is the leading cause of cancer death in women. To reduce breast cancer mortality, mammographic screening programmes have been implemented in many Western countries. However, these programmes remain controversial because of the associated radiation exposure and the need for improvement in terms of diagnostic accuracy. Phase-contrast imaging is a new X-ray-based technology that has been shown to provide enhanced soft-tissue contrast and improved visualization of cancerous structures. Furthermore, there is some indication that these improvements of image quality can be maintained at reduced radiation doses. Thus, X-ray phase-contrast mammography may significantly contribute to advancements in early breast cancer diagnosis. Feasibility studies of X-ray phase-contrast breast CT have provided images that allow resolution of the fine structure of tissue that can otherwise only be obtained by histology. This implies that X-ray phase-contrast imaging may also lead to the development of entirely new (micro-) radiological applications. This review provides a brief overview of the physical characteristics of this new technology and describes recent developments towards clinical implementation of X-ray phase-contrast imaging of the breast. PMID:24452106

High Resolution X-ray Phase Contrast Imaging with Acoustic Tissue-Selective Contrast Enhancement

DTIC Science & Technology

2008-06-01

Imaging with Acoustic Tissue-Selective Contrast Enhancement PRINCIPAL INVESTIGATOR: Gerald J. Diebold, Ph.D. CONTRACTING... Contrast Imaging with Acoustic Tissue-Selective Contrast Enhancement 5b. GRANT NUMBER W81XWH-04-1-0481 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...additional phase contrast features are visible at the interfaces of soft tissues as slight contrast enhancements . The image sequence in Fig. 2 shows an image

Multiphase-field model of small strain elasto-plasticity according to the mechanical jump conditions

NASA Astrophysics Data System (ADS)

Herrmann, Christoph; Schoof, Ephraim; Schneider, Daniel; Schwab, Felix; Reiter, Andreas; Selzer, Michael; Nestler, Britta

2018-04-01

We introduce a small strain elasto-plastic multiphase-field model according to the mechanical jump conditions. A rate-independent J_2 -plasticity model with linear isotropic hardening and without kinematic hardening is applied exemplary. Generally, any physically nonlinear mechanical model is compatible with the subsequently presented procedure. In contrast to models with interpolated material parameters, the proposed model is able to apply different nonlinear mechanical constitutive equations for each phase separately. The Hadamard compatibility condition and the static force balance are employed as homogenization approaches to calculate the phase-inherent stresses and strains. Several verification cases are discussed. The applicability of the proposed model is demonstrated by simulations of the martensitic transformation and quantitative parameters.

Circadian waveform bifurcation, but not phase-shifting, leaves cued fear memory intact.

PubMed

Harrison, E M; Carmack, S A; Block, C L; Sun, J; Anagnostaras, S G; Gorman, M R

2017-02-01

In mammals, memory acquisition and retrieval can be affected by time of day, as well as by manipulations of the light/dark cycle. Under bifurcation, a manipulation of circadian waveform, two subjective days and nights are experimentally induced in rodents. We examined the effect of bifurcation on Pavlovian fear conditioning, a prominent model of learning and memory. Here we demonstrate that bifurcation of the circadian waveform produces a small deficit in acquisition, but not on retrieval of fear memory. In contrast, repeated phase-shifting in a simulated jet-lag protocol impairs retrieval of memory for cued fear. The results have implications for those attempting to adjust to shift-work or other challenging schedules. Copyright © 2016 Elsevier Inc. All rights reserved.

Variability of 4D flow parameters when subjected to changes in MRI acquisition parameters using a realistic thoracic aortic phantom.

PubMed

Montalba, Cristian; Urbina, Jesus; Sotelo, Julio; Andia, Marcelo E; Tejos, Cristian; Irarrazaval, Pablo; Hurtado, Daniel E; Valverde, Israel; Uribe, Sergio

2018-04-01

To assess the variability of peak flow, mean velocity, stroke volume, and wall shear stress measurements derived from 3D cine phase contrast (4D flow) sequences under different conditions of spatial and temporal resolutions. We performed controlled experiments using a thoracic aortic phantom. The phantom was connected to a pulsatile flow pump, which simulated nine physiological conditions. For each condition, 4D flow data were acquired with different spatial and temporal resolutions. The 2D cine phase contrast and 4D flow data with the highest available spatio-temporal resolution were considered as a reference for comparison purposes. When comparing 4D flow acquisitions (spatial and temporal resolution of 2.0 × 2.0 × 2.0 mm 3 and 40 ms, respectively) with 2D phase-contrast flow acquisitions, the underestimation of peak flow, mean velocity, and stroke volume were 10.5, 10 and 5%, respectively. However, the calculated wall shear stress showed an underestimation larger than 70% for the former acquisition, with respect to 4D flow, with spatial and temporal resolution of 1.0 × 1.0 × 1.0 mm 3 and 20 ms, respectively. Peak flow, mean velocity, and stroke volume from 4D flow data are more sensitive to changes of temporal than spatial resolution, as opposed to wall shear stress, which is more sensitive to changes in spatial resolution. Magn Reson Med 79:1882-1892, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Propagation-based x-ray phase contrast imaging using an iterative phase diversity technique

NASA Astrophysics Data System (ADS)

Carroll, Aidan J.; van Riessen, Grant A.; Balaur, Eugeniu; Dolbnya, Igor P.; Tran, Giang N.; Peele, Andrew G.

2018-03-01

Through the use of a phase diversity technique, we demonstrate a near-field in-line x-ray phase contrast algorithm that provides improved object reconstruction when compared to our previous iterative methods for a homogeneous sample. Like our previous methods, the new technique uses the sample refractive index distribution during the reconstruction process. The technique complements existing monochromatic and polychromatic methods and is useful in situations where experimental phase contrast data is affected by noise.

Hydraulic fracturing fluid migration in the subsurface: A review and expanded modeling results

NASA Astrophysics Data System (ADS)

Birdsell, Daniel T.; Rajaram, Harihar; Dempsey, David; Viswanathan, Hari S.

2015-09-01

Understanding the transport of hydraulic fracturing (HF) fluid that is injected into the deep subsurface for shale gas extraction is important to ensure that shallow drinking water aquifers are not contaminated. Topographically driven flow, overpressured shale reservoirs, permeable pathways such as faults or leaky wellbores, the increased formation pressure due to HF fluid injection, and the density contrast of the HF fluid to the surrounding brine can encourage upward HF fluid migration. In contrast, the very low shale permeability and capillary imbibition of water into partially saturated shale may sequester much of the HF fluid, and well production will remove HF fluid from the subsurface. We review the literature on important aspects of HF fluid migration. Single-phase flow and transport simulations are performed to quantify how much HF fluid is removed via the wellbore with flowback and produced water, how much reaches overlying aquifers, and how much is permanently sequestered by capillary imbibition, which is treated as a sink term based on a semianalytical, one-dimensional solution for two-phase flow. These simulations include all of the important aspects of HF fluid migration identified in the literature review and are performed in five stages to faithfully represent the typical operation of a hydraulically fractured well. No fracturing fluid reaches the aquifer without a permeable pathway. In the presence of a permeable pathway, 10 times more fracturing fluid reaches the aquifer if well production and capillary imbibition are not included in the model.

Chiral extrapolations of the ρ ( 770 ) meson in N f = 2 + 1 lattice QCD simulations

DOE PAGES

Hu, B.; Molina, R.; Döring, M.; ...

2017-08-24

Recentmore » $$N_f=2+1$$ lattice data for meson-meson scattering in $p$-wave and isospin $I=1$ are analyzed using a unitarized model inspired by Chiral Perturbation Theory in the inverse-amplitude formulation for two and three flavors. We perform chiral extrapolations that postdict phase shifts extracted from experiment quite well. Additionally, the low-energy constants are compared to the ones from a recent analysis of $$N_f=2$$ lattice QCD simulations to check for the consistency of the hadronic model used here. Some inconsistencies are detected in the fits to $$N_f=2+1$$ data, in contrast to the previous analysis of $$N_f=2$$ data.« less

PHYSICAL EFFECTS OCCURRING DURING GENERATION AND AMPLIFICATION OF LASER RADIATION: Reversal of the contrast of optical radiation in round-trip amplifiers with a phase conjugation mirror

NASA Astrophysics Data System (ADS)

Afanas'ev, Anatolii A.; Samson, B. A.

1989-02-01

A description is given of a method for inversion of the contrast of optical radiation in a round-trip amplifier with a phase conjugation mirror and a phase nonreciprocal element. The system can be used to achieve high powers of contrast-reversed radiation because of compensation of phase distortions introduced by amplification.

High-throughput, high-resolution X-ray phase contrast tomographic microscopy for visualisation of soft tissue

NASA Astrophysics Data System (ADS)

McDonald, S. A.; Marone, F.; Hintermüller, C.; Bensadoun, J.-C.; Aebischer, P.; Stampanoni, M.

2009-09-01

The use of conventional absorption based X-ray microtomography can become limited for samples showing only very weak absorption contrast. However, a wide range of samples studied in biology and materials science can produce significant phase shifts of the X-ray beam, and thus the use of the phase signal can provide substantially increased contrast and therefore new and otherwise inaccessible information. The application of two approaches for high-throughput, high-resolution X-ray phase contrast tomography, both available on the TOMCAT beamline of the SLS, is illustrated. Differential Phase Contrast (DPC) imaging uses a grating interferometer and a phase-stepping technique. It has been integrated into the beamline environment on TOMCAT in terms of the fast acquisition and reconstruction of data and the availability to scan samples within an aqueous environment. The second phase contrast approach is a modified transfer of intensity approach that can yield the 3D distribution of the phase (refractive index) of a weakly absorbing object from a single tomographic dataset. These methods are being used for the evaluation of cell integrity in 3D, with the specific aim of following and analyzing progressive cell degeneration to increase knowledge of the mechanistic events of neurodegenerative disorders such as Parkinson's disease.

Motionless phase stepping in X-ray phase contrast imaging with a compact source

PubMed Central

Miao, Houxun; Chen, Lei; Bennett, Eric E.; Adamo, Nick M.; Gomella, Andrew A.; DeLuca, Alexa M.; Patel, Ajay; Morgan, Nicole Y.; Wen, Han

2013-01-01

X-ray phase contrast imaging offers a way to visualize the internal structures of an object without the need to deposit significant radiation, and thereby alleviate the main concern in X-ray diagnostic imaging procedures today. Grating-based differential phase contrast imaging techniques are compatible with compact X-ray sources, which is a key requirement for the majority of clinical X-ray modalities. However, these methods are substantially limited by the need for mechanical phase stepping. We describe an electromagnetic phase-stepping method that eliminates mechanical motion, thus removing the constraints in speed, accuracy, and flexibility. The method is broadly applicable to both projection and tomography imaging modes. The transition from mechanical to electromagnetic scanning should greatly facilitate the translation of X-ray phase contrast techniques into mainstream applications. PMID:24218599

X-ray phase-contrast imaging: the quantum perspective

NASA Astrophysics Data System (ADS)

Slowik, J. M.; Santra, R.

2013-08-01

Time-resolved phase-contrast imaging using ultrafast x-ray sources is an emerging method to investigate ultrafast dynamical processes in matter. Schemes to generate attosecond x-ray pulses have been proposed, bringing electronic timescales into reach and emphasizing the demand for a quantum description. In this paper, we present a method to describe propagation-based x-ray phase-contrast imaging in nonrelativistic quantum electrodynamics. We explain why the standard scattering treatment via Fermi’s golden rule cannot be applied. Instead, the quantum electrodynamical treatment of phase-contrast imaging must be based on a different approach. It turns out that it is essential to select a suitable observable. Here, we choose the quantum-mechanical Poynting operator. We determine the expectation value of our observable and demonstrate that the leading order term describes phase-contrast imaging. It recovers the classical expression of phase-contrast imaging. Thus, it makes the instantaneous electron density of non-stationary electronic states accessible to time-resolved imaging. Interestingly, inelastic (Compton) scattering does automatically not contribute in leading order, explaining the success of the semiclassical description.

Phase segregation in multiphase turbulent channel flow

NASA Astrophysics Data System (ADS)

Bianco, Federico; Soldati, Alfredo

2014-11-01

The phase segregation of a rapidly quenched mixture (namely spinodal decomposition) is numerically investigated. A phase field approach is considered. Direct numerical simulation of the coupled Navier-Stokes and Cahn-Hilliard equations is performed with spectral accuracy and focus has been put on domain growth scaling laws, in a wide range of regimes. The numerical method has been first validated against well known results of literature, then spinodal decomposition in a turbulent bounded flow (channel flow) has been considered. As for homogeneous isotropic case, turbulent fluctuations suppress the segregation process when surface tension at the interfaces is relatively low (namely low Weber number regimes). For these regimes, segregated domains size reaches a statistically steady state due to mixing and break-up phenomena. In contrast with homogenous and isotropic turbulence, the presence of mean shear, leads to a typical domain size that show a wall-distance dependence. Finally, preliminary results on the effects to the drag forces at the wall, due to phase segregation, have been discussed. Regione FVG, program PAR-FSC.

Transport Properties of the Nuclear Pasta Phase with Quantum Molecular Dynamics

NASA Astrophysics Data System (ADS)

Nandi, Rana; Schramm, Stefan

2018-01-01

We study the transport properties of nuclear pasta for a wide range of density, temperature, and proton fractions, relevant for different astrophysical scenarios adopting a quantum molecular dynamics model. In particular, we estimate the values of shear viscosity as well as electrical and thermal conductivities by calculating the static structure factor S(q) using simulation data. In the density and temperature range where the pasta phase appears, the static structure factor shows irregular behavior. The presence of a slab phase greatly enhances the peak in S(q). However, the effect of irregularities in S(q) on the transport coefficients is not very dramatic. The values of all three transport coefficients are found to have the same orders of magnitude as found in theoretical calculations for the inner crust matter of neutron stars without the pasta phase; therefore, the values are in contrast to earlier speculations that a pasta layer might be highly resistive, both thermally and electrically.

Thermo-structural analysis and electrical conductivity behavior of epoxy/metals composites

NASA Astrophysics Data System (ADS)

Boumedienne, N.; Faska, Y.; Maaroufi, A.; Pinto, G.; Vicente, L.; Benavente, R.

2017-05-01

This paper reports on the elaboration and characterization of epoxy resin filled with metallic particles powder (aluminum, tin and zinc) composites. The scanning electron microscopy (SEM) pictures, density measurements and x-ray diffraction analysis (DRX) showed a homogeneous phase of obtained composites. The differential scanning calorimetry revealed a good adherence at matrix-filler interfaces, confirming the SEM observations. The measured glass transition temperatures depend on composites fillers' nature. Afterwards, the electrical conductivity of composites versus their fillers' contents has been investigated. The obtained results depict a nonlinear behavior, indicating an insulator to conductor phase transition at a conduction threshold; with high contrast of ten decades. Hence, the elaborated materials give a possibility to obtain dielectric or electrically conducting phases, which can to be interesting in the choice of desired applications. Finally, the obtained results have been successfully simulated on the basis of different percolation models approach combined with structural characterization inferences.

Analysis of image formation in optical coherence elastography using a multiphysics approach

PubMed Central

Chin, Lixin; Curatolo, Andrea; Kennedy, Brendan F.; Doyle, Barry J.; Munro, Peter R. T.; McLaughlin, Robert A.; Sampson, David D.

2014-01-01

Image formation in optical coherence elastography (OCE) results from a combination of two processes: the mechanical deformation imparted to the sample and the detection of the resulting displacement using optical coherence tomography (OCT). We present a multiphysics model of these processes, validated by simulating strain elastograms acquired using phase-sensitive compression OCE, and demonstrating close correspondence with experimental results. Using the model, we present evidence that the approximation commonly used to infer sample displacement in phase-sensitive OCE is invalidated for smaller deformations than has been previously considered, significantly affecting the measurement precision, as quantified by the displacement sensitivity and the elastogram signal-to-noise ratio. We show how the precision of OCE is affected not only by OCT shot-noise, as is usually considered, but additionally by phase decorrelation due to the sample deformation. This multiphysics model provides a general framework that could be used to compare and contrast different OCE techniques. PMID:25401007

Grating-Based Phase-Contrast Imaging of Tumor Angiogenesis in Lung Metastases

PubMed Central

Li, Xiangting; Wang, Yujie; Ding, Bei; Shi, Chen; Liu, Huanhuan; Tang, Rongbiao; Sun, Jianqi; Yan, Fuhua; Zhang, Huan

2015-01-01

Purpose To assess the feasibility of the grating-based phase-contrast imaging (GPI) technique for studying tumor angiogenesis in nude BALB/c mice, without contrast agents. Methods We established lung metastatic models of human gastric cancer by injecting the moderately differentiated SGC-7901 gastric cancer cell line into the tail vein of nude mice. Samples were embedded in a 10% formalin suspension and dried before imaging. Grating-based X-ray phase-contrast images were obtained at the BL13W beamline of the Shanghai Synchrotron Radiation Facility (SSRF) and compared with histological sections. Results Without contrast agents, grating-based X-ray phase-contrast imaging still differentiated angiogenesis within metastatic tumors with high spatial resolution. Vessels, down to tens of microns, showed gray values that were distinctive from those of the surrounding tumors, which made them easily identifiable. The vessels depicted in the imaging study were similar to those identified on histopathology, both in size and shape. Conclusions Our preliminary study demonstrates that grating-based X-ray phase-contrast imaging has the potential to depict angiogenesis in lung metastases. PMID:25811626

Crystal structure, equation of state, and elasticity of phase H (MgSiO4H2) at Earth's lower mantle pressures.

PubMed

Tsuchiya, Jun; Mookherjee, Mainak

2015-10-23

Dense hydrous magnesium silicate (DHMS) phases play a crucial role in transporting water in to the Earth's interior. A newly discovered DHMS, phase H (MgSiO4H2), is stable at Earth's lower mantle, i.e., at pressures greater than 30 GPa. Here we report the crystal structure and elasticity of phase H and its evolution upon compression. Using first principles simulations, we have explored the relative energetics of the candidate crystal structures with ordered and disordered configurations of magnesium and silicon atoms in the octahedral sites. At conditions relevant to Earth's lower mantle, it is likely that phase H is able to incorporate a significant amount of aluminum, which may enhance the thermodynamic stability of phase H. The sound wave velocities of phase H are ~2-4% smaller than those of isostructural δ-AlOOH. The shear wave impedance contrast due to the transformation of phase D to a mixture of phase H and stishovite at pressures relevant to the upper part of the lower mantle could partly explain the geophysical observations. The calculated elastic wave velocities and anisotropies indicate that phase H can be a source of significant seismic anisotropy in the lower mantle.

Glancing angle Talbot-Lau grating interferometers for phase contrast imaging at high x-ray energy

NASA Astrophysics Data System (ADS)

Stutman, D.; Finkenthal, M.

2012-08-01

A Talbot-Lau interferometer is demonstrated using micro-periodic gratings inclined at a glancing angle along the light propagation direction. Due to the increase in the effective thickness of the absorption gratings, the device enables differential phase contrast imaging at high x-ray energy, with improved fringe visibility (contrast). For instance, at 28° glancing angle, we obtain up to ˜35% overall interferometer contrast with a spectrum having ˜43 keV mean energy, suitable for medical applications. In addition, glancing angle interferometers could provide high contrast at energies above 100 keV, enabling industrial and security applications of phase contrast imaging.

Equilibrium-phase MR angiography: Comparison of unspecific extracellular and protein-binding gadolinium-based contrast media with respect to image quality.

PubMed

Erb-Eigner, Katharina; Taupitz, Matthias; Asbach, Patrick

2016-01-01

The purpose of this study was to compare contrast and image quality of whole-body equilibrium-phase high-spatial-resolution MR angiography using a non-protein-binding unspecific extracellular gadolinium-based contrast medium with that of two contrast media with different protein-binding properties. 45 patients were examined using either 15 mL of gadobutrol (non-protein-binding, n = 15), 32 mL of gadobenate dimeglumine (weakly protein binding, n = 15) or 11 mL gadofosveset trisodium (protein binding, n = 15) followed by equilibrium-phase high-spatial-resolution MR-angiography of four consecutive anatomic regions. The time elapsed between the contrast injection and the beginning of the equilibrium-phase image acquisition in the respective region was measured and was up to 21 min. Signal intensity was measured in two vessels per region and in muscle tissue. Relative contrast (RC) values were calculated. Vessel contrast, artifacts and image quality were rated by two radiologists in consensus on a five-point scale. Compared with gadobutrol, gadofosveset trisodium revealed significantly higher RC values only when acquired later than 15 min after bolus injection. Otherwise, no significant differences between the three contrast media were found regarding vascular contrast and image quality. Equilibrium-phase high-spatial-resolution MR-angiography using a weakly protein-binding or even non-protein-binding contrast medium is equivalent to using a stronger protein-binding contrast medium when image acquisition is within the first 15 min after contrast injection, and allows depiction of the vasculature with high contrast and image quality. The protein-binding contrast medium was superior for imaging only later than 15 min after contrast medium injection. Copyright © 2015 John Wiley & Sons, Ltd.

Quantitative phase-contrast digital holographic microscopy for cell dynamic evaluation

NASA Astrophysics Data System (ADS)

Yu, Lingfeng; Mohanty, Samarendra; Berns, Michael W.; Chen, Zhongping

2009-02-01

The laser microbeam uses lasers to alter and/or to ablate intracellular organelles and cellular and tissue samples, and, today, has become an important tool for cell biologists to study the molecular mechanism of complex biological systems by removing individual cells or sub-cellular organelles. However, absolute quantitation of the localized alteration/damage to transparent phase objects, such as the cell membrane or chromosomes, was not possible using conventional phase-contrast or differential interference contrast microscopy. We report the development of phase-contrast digital holographic microscopy for quantitative evaluation of cell dynamic changes in real time during laser microsurgery. Quantitative phase images are recorded during the process of laser microsurgery and thus, the dynamic change in phase can be continuously evaluated. Out-of-focus organelles are re-focused by numerical reconstruction algorithms.

Edge turbulence and divertor heat flux width simulations of Alcator C-Mod discharges using an electromagnetic two-fluid model

NASA Astrophysics Data System (ADS)

Chen, B.; Xu, X. Q.; Xia, T. Y.; Porkolab, M.; Edlund, E.; LaBombard, B.; Terry, J.; Hughes, J. W.; Mao, S. F.; Ye, M. Y.; Wan, Y. X.

2017-11-01

The BOUT++ code has been exploited in order to improve the understanding of the role of turbulent modes in controlling edge transport and resulting scaling of the scrape-off layer (SOL) heat flux width. For the C-Mod enhanced D_α (EDA) H-mode discharges, BOUT++ six-field two-fluid nonlinear simulations show a reasonable agreement of upstream turbulence and divertor target heat flux behavior: (a) the simulated quasi-coherent modes show consistent characteristics of the frequency versus poloidal wave number spectra of the electromagnetic fluctuations when compared with experimental measurements: frequencies are around 60-120 kHz (experiment: about 70-110 kHz), k_θ are around 2.0 cm-1 which is similar to the phase contrast imaging data; (b) linear spectrum analysis is consistent with the nonlinear phase relationship calculation which indicates the dominance of resistive-ballooning modes and drift-Alfven wave instabilities; (c) the SOL heat flux width λq versus current I p scaling is reproduced by turbulent transport: the simulations yield similar λq to experimental measurements within a factor of 2. However the magnitudes of divertor heat fluxes can be varied, depending on the physics models, sources and sinks, sheath boundary conditions, or flux limiting coefficient; (d) Simple estimate by the ‘2-point model’ for λq is consistent with simulation. Moreover, blobby turbulent spreading is confirmed for these relatively high B p shots.

Phase-contrast Hounsfield units of fixated and non-fixated soft-tissue samples

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

Willner, Marian; Fior, Gabriel; Marschner, Mathias

X-ray phase-contrast imaging is a novel technology that achieves high soft-tissue contrast. Although its clinical impact is still under investigation, the technique may potentially improve clinical diagnostics. In conventional attenuation-based X-ray computed tomography, radiological diagnostics are quantified by Hounsfield units. Corresponding Hounsfield units for phase-contrast imaging have been recently introduced, enabling a setup-independent comparison and standardized interpretation of imaging results. Thus far, the experimental values of few tissue types have been reported; these values have been determined from fixated tissue samples. This study presents phase-contrast Hounsfield units for various types of non-fixated human soft tissues. A large variety of tissuemore » specimens ranging from adipose, muscle and connective tissues to liver, kidney and pancreas tissues were imaged by a grating interferometer with a rotating-anode X-ray tube and a photon-counting detector. In addition, we investigated the effects of formalin fixation on the quantitative phase-contrast imaging results.« less

Phase-Contrast Hounsfield Units of Fixated and Non-Fixated Soft-Tissue Samples

PubMed Central

Willner, Marian; Fior, Gabriel; Marschner, Mathias; Birnbacher, Lorenz; Schock, Jonathan; Braun, Christian; Fingerle, Alexander A.; Noël, Peter B.; Rummeny, Ernst J.; Pfeiffer, Franz; Herzen, Julia

2015-01-01

X-ray phase-contrast imaging is a novel technology that achieves high soft-tissue contrast. Although its clinical impact is still under investigation, the technique may potentially improve clinical diagnostics. In conventional attenuation-based X-ray computed tomography, radiological diagnostics are quantified by Hounsfield units. Corresponding Hounsfield units for phase-contrast imaging have been recently introduced, enabling a setup-independent comparison and standardized interpretation of imaging results. Thus far, the experimental values of few tissue types have been reported; these values have been determined from fixated tissue samples. This study presents phase-contrast Hounsfield units for various types of non-fixated human soft tissues. A large variety of tissue specimens ranging from adipose, muscle and connective tissues to liver, kidney and pancreas tissues were imaged by a grating interferometer with a rotating-anode X-ray tube and a photon-counting detector. Furthermore, we investigated the effects of formalin fixation on the quantitative phase-contrast imaging results. PMID:26322638

Phase-contrast Hounsfield units of fixated and non-fixated soft-tissue samples

DOE PAGES

Willner, Marian; Fior, Gabriel; Marschner, Mathias; ...

2015-08-31

X-ray phase-contrast imaging is a novel technology that achieves high soft-tissue contrast. Although its clinical impact is still under investigation, the technique may potentially improve clinical diagnostics. In conventional attenuation-based X-ray computed tomography, radiological diagnostics are quantified by Hounsfield units. Corresponding Hounsfield units for phase-contrast imaging have been recently introduced, enabling a setup-independent comparison and standardized interpretation of imaging results. Thus far, the experimental values of few tissue types have been reported; these values have been determined from fixated tissue samples. This study presents phase-contrast Hounsfield units for various types of non-fixated human soft tissues. A large variety of tissuemore » specimens ranging from adipose, muscle and connective tissues to liver, kidney and pancreas tissues were imaged by a grating interferometer with a rotating-anode X-ray tube and a photon-counting detector. In addition, we investigated the effects of formalin fixation on the quantitative phase-contrast imaging results.« less

In-line phase shift tomosynthesis

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

Hammonds, Jeffrey C.; Price, Ronald R.; Pickens, David R.

2013-08-15

Purpose: The purpose of this work is to (1) demonstrate laboratory measurements of phase shift images derived from in-line phase-contrast radiographs using the attenuation-partition based algorithm (APBA) of Yan et al.[Opt. Express 18(15), 16074–16089 (2010)], (2) verify that the APBA reconstructed images obey the linearity principle, and (3) reconstruct tomosynthesis phase shift images from a collection of angularly sampled planar phase shift images.Methods: An unmodified, commercially available cabinet x-ray system (Faxitron LX-60) was used in this experiment. This system contains a tungsten anode x-ray tube with a nominal focal spot size of 10 μm. The digital detector uses CsI/CMOS withmore » a pixel size of 50 × 50 μm. The phantoms used consisted of one acrylic plate, two polystyrene plates, and a habanero pepper. Tomosynthesis images were reconstructed from 51 images acquired over a ±25° arc. All phase shift images were reconstructed using the APBA.Results: Image contrast derived from the planar phase shift image of an acrylic plate of uniform thickness exceeded the contrast of the traditional attenuation image by an approximate factor of two. Comparison of the planar phase shift images from a single, uniform thickness polystyrene plate with two polystyrene plates demonstrated an approximate linearity of the estimated phase shift with plate thickness (−1600 rad vs −2970 rad). Tomographic phase shift images of the habanero pepper exhibited acceptable spatial resolution and contrast comparable to the corresponding attenuation image.Conclusions: This work demonstrated the feasibility of laboratory-based phase shift tomosynthesis and suggests that phase shift imaging could potentially provide a new imaging biomarker. Further investigation will be needed to determine if phase shift contrast will be able to provide new tissue contrast information or improved clinical performance.« less

Microfluidic droplet-based liquid-liquid extraction.

PubMed

Mary, Pascaline; Studer, Vincent; Tabeling, Patrick

2008-04-15

We study microfluidic systems in which mass exchanges take place between moving water droplets, formed on-chip, and an external phase (octanol). Here, no chemical reaction takes place, and the mass exchanges are driven by a contrast in chemical potential between the dispersed and continuous phases. We analyze the case where the microfluidic droplets, occupying the entire width of the channel, extract a solute-fluorescein-from the external phase (extraction) and the opposite case, where droplets reject a solute-rhodamine-into the external phase (purification). Four flow configurations are investigated, based on straight or zigzag microchannels. Additionally to the experimental work, we performed two-dimensional numerical simulations. In the experiments, we analyze the influence of different parameters on the process (channel dimensions, fluid viscosities, flow rates, drop size, droplet spacing, ...). Several regimes are singled out. In agreement with the mass transfer theory of Young et al. (Young, W.; Pumir, A.; Pomeau, Y. Phys. Fluids A 1989, 1, 462), we find that, after a short transient, the amount of matter transferred across the droplet interface grows as the square root of time and the time it takes for the transfer process to be completed decreases as Pe-2/3, where Pe is the Peclet number based on droplet velocity and radius. The numerical simulation is found in excellent consistency with the experiment. In practice, the transfer time ranges between a fraction and a few seconds, which is much faster than conventional systems.

Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy.

PubMed

Vöhringer-Martinez, E; Link, O; Lugovoy, E; Siefermann, K R; Wiederschein, F; Grubmüller, H; Abel, B

2014-09-28

Supercritical water and methanol have recently drawn much attention in the field of green chemistry. It is crucial to an understanding of supercritical solvents to know their dynamics and to what extent hydrogen (H) bonds persist in these fluids. Here, we show that with femtosecond infrared (IR) laser pulses water and methanol can be heated to temperatures near and above their critical temperature Tc and their molecular dynamics can be studied via ultrafast photoelectron spectroscopy at liquid jet interfaces with high harmonics radiation. As opposed to previous studies, the main focus here is the comparison between the hydrogen bonded systems of methanol and water and their interpretation by theory. Superheated water initially forms a dense hot phase with spectral features resembling those of monomers in gas phase water. On longer timescales, this phase was found to build hot aggregates, whose size increases as a function of time. In contrast, methanol heated to temperatures near Tc initially forms a broad distribution of aggregate sizes and some gas. These experimental features are also found and analyzed in extended molecular dynamics simulations. Additionally, the simulations enabled us to relate the origin of the different behavior of these two hydrogen-bonded liquids to the nature of the intermolecular potentials. The combined experimental and theoretical approach delivers new insights into both superheated phases and may contribute to understand their different chemical reactivities.

Transformation of binaural response properties in the ascending auditory pathway: influence of time-varying interaural phase disparity.

PubMed

Spitzer, M W; Semple, M N

1998-12-01

Transformation of binaural response properties in the ascending auditory pathway: influence of time-varying interaural phase disparity. J. Neurophysiol. 80: 3062-3076, 1998. Previous studies demonstrated that tuning of inferior colliculus (IC) neurons to interaural phase disparity (IPD) is often profoundly influenced by temporal variation of IPD, which simulates the binaural cue produced by a moving sound source. To determine whether sensitivity to simulated motion arises in IC or at an earlier stage of binaural processing we compared responses in IC with those of two major IPD-sensitive neuronal classes in the superior olivary complex (SOC), neurons whose discharges were phase locked (PL) to tonal stimuli and those that were nonphase locked (NPL). Time-varying IPD stimuli consisted of binaural beats, generated by presenting tones of slightly different frequencies to the two ears, and interaural phase modulation (IPM), generated by presenting a pure tone to one ear and a phase modulated tone to the other. IC neurons and NPL-SOC neurons were more sharply tuned to time-varying than to static IPD, whereas PL-SOC neurons were essentially uninfluenced by the mode of stimulus presentation. Preferred IPD was generally similar in responses to static and time-varying IPD for all unit populations. A few IC neurons were highly influenced by the direction and rate of simulated motion, but the major effect for most IC neurons and all SOC neurons was a linear shift of preferred IPD at high rates-attributable to response latency. Most IC and NPL-SOC neurons were strongly influenced by IPM stimuli simulating motion through restricted ranges of azimuth; simulated motion through partially overlapping azimuthal ranges elicited discharge profiles that were highly discontiguous, indicating that the response associated with a particular IPD is dependent on preceding portions of the stimulus. In contrast, PL-SOC responses tracked instantaneous IPD throughout the trajectory of simulated motion, resulting in highly contiguous discharge profiles for overlapping stimuli. This finding indicates that responses of PL-SOC units to time-varying IPD reflect only instantaneous IPD with no additional influence of dynamic stimulus attributes. Thus the neuronal representation of auditory spatial information undergoes a major transformation as interaural delay is initially processed in the SOC and subsequently reprocessed in IC. The finding that motion sensitivity in IC emerges from motion-insensitive input suggests that information about change of position is crucial to spatial processing at higher levels of the auditory system.

Multi-wavelength speckle reduction for laser pico-projectors using diffractive optics

NASA Astrophysics Data System (ADS)

Thomas, Weston H.

Personal electronic devices, such as cell phones and tablets, continue to decrease in size while the number of features and add-ons keep increasing. One particular feature of great interest is an integrated projector system. Laser pico-projectors have been considered, but the technology has not been developed enough to warrant integration. With new advancements in diode technology and MEMS devices, laser-based projection is currently being advanced for pico-projectors. A primary problem encountered when using a pico-projector is coherent interference known as speckle. Laser speckle can lead to eye irritation and headaches after prolonged viewing. Diffractive optical elements known as diffusers have been examined as a means to lower speckle contrast. Diffusers are often rotated to achieve temporal averaging of the spatial phase pattern provided by diffuser surface. While diffusers are unable to completely eliminate speckle, they can be utilized to decrease the resultant contrast to provide a more visually acceptable image. This dissertation measures the reduction in speckle contrast achievable through the use of diffractive diffusers. A theoretical Fourier optics model is used to provide the diffuser's stationary and in-motion performance in terms of the resultant contrast level. Contrast measurements of two diffractive diffusers are calculated theoretically and compared with experimental results. In addition, a novel binary diffuser design based on Hadamard matrices will be presented. Using two static in-line Hadamard diffusers eliminates the need for rotation or vibration of the diffuser for temporal averaging. Two Hadamard diffusers were fabricated and contrast values were subsequently measured, showing good agreement with theory and simulated values. Monochromatic speckle contrast values of 0.40 were achieved using the Hadamard diffusers. Finally, color laser projection devices require the use of red, green, and blue laser sources; therefore, using a monochromatic diffractive diffuser may not optimal for color speckle contrast reduction. A simulation of the Hadamard diffusers is conducted to determine the optimum spacing between the two diffusers for polychromatic speckle reduction. Experimental measured results are presented using the optimal spacing of Hadamard diffusers for RGB color speckle reduction, showing 60% reduction in contrast.

Kernel-Phase Interferometry for Super-Resolution Detection of Faint Companions

NASA Astrophysics Data System (ADS)

Factor, Samuel M.; Kraus, Adam L.

2017-06-01

Direct detection of close in companions (exoplanets or binary systems) is notoriously difficult. While coronagraphs and point spread function (PSF) subtraction can be used to reduce contrast and dig out signals of companions under the PSF, there are still significant limitations in separation and contrast near λ/D. Non-redundant aperture masking (NRM) interferometry can be used to detect companions well inside the PSF of a diffraction limited image, though the mask discards ˜ 95% of the light gathered by the telescope and thus the technique is severely flux limited. Kernel-phase analysis applies interferometric techniques similar to NRM to a diffraction limited image utilizing the full aperture. Instead of non-redundant closure-phases, kernel-phases are constructed from a grid of points on the full aperture, simulating a redundant interferometer. I have developed a new, easy to use, faint companion detection pipeline which analyzes kernel-phases utilizing Bayesian model comparison. I demonstrate this pipeline on archival images from HST/NICMOS, searching for new companions in order to constrain binary formation models at separations inaccessible to previous techniques. Using this method, it is possible to detect a companion well within the classical λ/D Rayleigh diffraction limit using a fraction of the telescope time as NRM. Since the James Webb Space Telescope (JWST) will be able to perform NRM observations, further development and characterization of kernel-phase analysis will allow efficient use of highly competitive JWST telescope time. As no mask is needed, this technique can easily be applied to archival data and even target acquisition images (e.g. from JWST), making the detection of close in companions cheap and simple as no additional observations are needed.

X-Ray Phase Imaging for Breast Cancer Detection

DTIC Science & Technology

2011-09-01

the inline phase contrast imaging has good potential of greatly enhanc - ing the detection sensitivity and reducing radiation doses involved in the...the edge- enhancement generated by phase- contrast is generally useful for imaging the wrap, however, such edge- enhancements may lead interpretation...Kotre and I. P. Birch, “Phase contrast enhancement of x-ray mam- mography: A design study,” Phys. Med. Biol. 44, 2853–2866 (1999). 6F. Arfelli et al

Contrast and autoshaping in multiple schedules varying reinforcer rate and duration.

PubMed

Hamilton, B E; Silberberg, A

1978-07-01

Thirteen master pigeons were exposed to multiple schedules in which reinforcement frequency (Experiment I) or duration (Experiment II) was varied. In Phases 1 and 3 of Experiment I, the values of the first and second components' random-interval schedules were 33 and 99 seconds, respectively. In Phase 2, these values were 99 seconds for both components. In Experiment II, a random-interval 33-second schedule was associated with each component. During Phases 1 and 3, the first and second components had hopper durations of 7.5 and 2.5 seconds respectively. During Phase 2, both components' hopper durations were 2.5 seconds. In each experiment, positive contrast obtained for about half the master subjects. The rest showed a rate increase in both components (positive induction). Each master subject's key colors and reinforcers were synchronously presented on a response-independent basis to a yoked control. Richer component key-pecking occurred during each experiment's Phases 1 and 3 among half these subjects. However, none responded during the contrast condition (unchanged component of each experiment's Phase 2). From this it is inferred that autoshaping did not contribute to the contrast and induction findings among master birds. Little evidence of local contrast (highest rate at beginning of richer component) was found in any subject. These data show that (a) contrast can occur independently from autoshaping, (b) contrast assays during equal-valued components may produce induction, (c) local contrast in multiple schedules often does not occur, and (d) differential hopper durations can produce autoshaping and contrast.

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

Müller, Mark, E-mail: mark-mueller@ph.tum.de; Yaroshenko, Andre; Velroyen, Astrid

In the field of biomedical X-ray imaging, novel techniques, such as phase-contrast and dark-field imaging, have the potential to enhance the contrast and provide complementary structural information about a specimen. In this paper, a first prototype of a preclinical X-ray phase-contrast CT scanner based on a Talbot-Lau interferometer is characterized. We present a study of the contrast-to-noise ratios for attenuation and phase-contrast images acquired with the prototype scanner. The shown results are based on a series of projection images and tomographic data sets of a plastic phantom in phase and attenuation-contrast recorded with varying acquisition settings. Subsequently, the signal andmore » noise distribution of different regions in the phantom were determined. We present a novel method for estimation of contrast-to-noise ratios for projection images based on the cylindrical geometry of the phantom. Analytical functions, representing the expected signal in phase and attenuation-contrast for a circular object, are fitted to individual line profiles of the projection data. The free parameter of the fit function is used to estimate the contrast and the goodness of the fit is determined to assess the noise in the respective signal. The results depict the dependence of the contrast-to-noise ratios on the applied source voltages, the number of steps of the phase stepping routine, and the exposure times for an individual step. Moreover, the influence of the number of projection angles on the image quality of CT slices is investigated. Finally, the implications for future imaging purposes with the scanner are discussed.« less

Characterization of a high-energy in-line phase contrast tomosynthesis prototype.

PubMed

Wu, Di; Yan, Aimin; Li, Yuhua; Wong, Molly D; Zheng, Bin; Wu, Xizeng; Liu, Hong

2015-05-01

In this research, a high-energy in-line phase contrast tomosynthesis prototype was developed and characterized through quantitative investigations and phantom studies. The prototype system consists of an x-ray source, a motorized rotation stage, and a CMOS detector with a pixel pitch of 0.05 mm. The x-ray source was operated at 120 kVp for this study, and the objects were mounted on the rotation stage 76.2 cm (R1) from the source and 114.3 cm (R2) from the detector. The large air gap between the object and detector guarantees sufficient phase-shift effects. The quantitative evaluation of this prototype included modulation transfer function and noise power spectrum measurements conducted under both projection mode and tomosynthesis mode. Phantom studies were performed including three custom designed phantoms with complex structures: a five-layer bubble wrap phantom, a fishbone phantom, and a chicken breast phantom with embedded fibrils and mass structures extracted from an ACR phantom. In-plane images of the phantoms were acquired to investigate their image qualities through observation, intensity profile plots, edge enhancement evaluations, and/or contrast-to-noise ratio calculations. In addition, the robust phase-attenuation duality (PAD)-based phase retrieval method was applied to tomosynthesis for the first time in this research. It was utilized as a preprocessing method to fully exhibit phase contrast on the angular projection before reconstruction. The resolution and noise characteristics of this high-energy in-line phase contrast tomosynthesis prototype were successfully investigated and demonstrated. The phantom studies demonstrated that this imaging prototype can successfully remove the structure overlapping in phantom projections, obtain delineate interfaces, and achieve better contrast-to-noise ratio after applying phase retrieval to the angular projections. This research successfully demonstrated a high-energy in-line phase contrast tomosynthesis prototype. In addition, the PAD-based method of phase retrieval was combined with tomosynthesis imaging for the first time, which demonstrated its capability in significantly improving the contrast-to-noise ratios in the images.

Contrast features of breast cancer in frequency-domain laser scanning mammography

NASA Astrophysics Data System (ADS)

Moesta, K. Thomas; Fantini, Sergio; Jess, Helge; Totkas, Susan; Franceschini, Maria-Angela; Kaschke, Michael; Schlag, Peter M.

1998-04-01

Frequency-domain optical mammography has been advocated to improve contrast and thus cancer detectability in breast transillumination. To the best of our knowledge, this report provides the first systematic clinical results of a frequency-domain laser scanning mammograph (FLM). The instrument provides monochromatic light at 690 and 810 nm, whose intensity is modulated at 110.0008 MHz, respectively. The breast is scanned by stepwise positioning of source and detector, and amplitude and phase for both wavelengths are measured by a photomultiplier tube using heterodyne detection. Images are formed representing amplitude or phase data on linear gray scales. Furthermore, various algorithms carrying on more than one signal were essayed. Twenty visible cancers out of 25 cancers in the first 59 investigations were analyzed for their quantitative contrast with respect to the whole breast or to defined reference areas. Contrast definitions refer to the signal itself, to the signal noise, or were based on nonparametric comparison. The amplitude signal provides better contrast than the phase signal. Ratio images between red and IR amplitudes gave variable results; in some cases the tumor contrast was canceled. The algorithms to determine (mu) a and (mu) sPRM from amplitude and phase data did not significantly improve upon objective contrast. The N algorithm, using the phase signal to flatten the amplitude signal did significantly improve upon contrast according to contrast definitions 1 and 2, however, did not improve upon nonparametric contrast. Thus, with the current instrumentation, the phase signal is helpful to correct for the complex and variable geometry of the breast. However, an independent informational content for tumor differentiation could not be determined. The flat field algorithm did greatly enhance optical contrast in comparison with amplitude or amplitude ratio images. Further evaluation of FLM will have to be based on the N-algorithm images.

Effects of Uncertainties in Electric Field Boundary Conditions for Ring Current Simulations

NASA Astrophysics Data System (ADS)

Chen, Margaret W.; O'Brien, T. Paul; Lemon, Colby L.; Guild, Timothy B.

2018-01-01

Physics-based simulation results can vary widely depending on the applied boundary conditions. As a first step toward assessing the effect of boundary conditions on ring current simulations, we analyze the uncertainty of cross-polar cap potentials (CPCP) on electric field boundary conditions applied to the Rice Convection Model-Equilibrium (RCM-E). The empirical Weimer model of CPCP is chosen as the reference model and Defense Meteorological Satellite Program CPCP measurements as the reference data. Using temporal correlations from a statistical analysis of the "errors" between the reference model and data, we construct a Monte Carlo CPCP discrete time series model that can be generalized to other model boundary conditions. RCM-E simulations using electric field boundary conditions from the reference model and from 20 randomly generated Monte Carlo discrete time series of CPCP are performed for two large storms. During the 10 August 2000 storm main phase, the proton density at 10 RE at midnight was observed to be low (< 1.4 cm-3) and the observed disturbance Dst index is bounded by the simulated Dst values. In contrast, the simulated Dst values during the recovery phases of the 10 August 2000 and 31 August 2005 storms tend to underestimate systematically the observed late Dst recovery. This suggests a need to improve the accuracy of particle loss calculations in the RCM-E model. Application of this technique can aid modelers to make efficient choices on either investing more effort on improving specification of boundary conditions or on improving descriptions of physical processes.

Phase-field model of insulator-to-metal transition in VO2 under an electric field

NASA Astrophysics Data System (ADS)

Shi, Yin; Chen, Long-Qing

2018-05-01

The roles of an electric field and electronic doping in insulator-to-metal transitions are still not well understood. Here we formulated a phase-field model of insulator-to-metal transitions by taking into account both structural and electronic instabilities as well as free electrons and holes in VO2, a strongly correlated transition-metal oxide. Our phase-field simulations demonstrate that in a VO2 slab under a uniform electric field, an abrupt universal resistive transition occurs inside the supercooling region, in sharp contrast to the conventional Landau-Zener smooth electric breakdown. We also show that hole doping may decouple the structural and electronic phase transitions in VO2, leading to a metastable metallic monoclinic phase which could be stabilized through a geometrical confinement and the size effect. This work provides a general mesoscale thermodynamic framework for understanding the influences of electric field, electronic doping, and stress and strain on insulator-to-metal transitions and the corresponding mesoscale domain structure evolution in VO2 and related strongly correlated systems.

Anisotropy of Earth's D'' layer and stacking faults in the MgSiO3 post-perovskite phase.

PubMed

Oganov, Artem R; Martonák, Roman; Laio, Alessandro; Raiteri, Paolo; Parrinello, Michele

2005-12-22

The post-perovskite phase of (Mg,Fe)SiO3 is believed to be the main mineral phase of the Earth's lowermost mantle (the D'' layer). Its properties explain numerous geophysical observations associated with this layer-for example, the D'' discontinuity, its topography and seismic anisotropy within the layer. Here we use a novel simulation technique, first-principles metadynamics, to identify a family of low-energy polytypic stacking-fault structures intermediate between the perovskite and post-perovskite phases. Metadynamics trajectories identify plane sliding involving the formation of stacking faults as the most favourable pathway for the phase transition, and as a likely mechanism for plastic deformation of perovskite and post-perovskite. In particular, the predicted slip planes are {010} for perovskite (consistent with experiment) and {110} for post-perovskite (in contrast to the previously expected {010} slip planes). Dominant slip planes define the lattice preferred orientation and elastic anisotropy of the texture. The {110} slip planes in post-perovskite require a much smaller degree of lattice preferred orientation to explain geophysical observations of shear-wave anisotropy in the D'' layer.

Improved Homogeneity of the Transmit Field by Simultaneous Transmission with Phased Array and Volume Coil

PubMed Central

Avdievich, Nikolai I.; Oh, Suk-Hoon; Hetherington, Hoby P.; Collins, Christopher M.

2010-01-01

Purpose To improve the homogeneity of transmit volume coils at high magnetic fields (≥ 4 T). Due to RF field/ tissue interactions at high fields, 4–8 T, the transmit profile from head-sized volume coils shows a distinctive pattern with relatively strong RF magnetic field B1 in the center of the brain. Materials and Methods In contrast to conventional volume coils at high field strengths, surface coil phased arrays can provide increased RF field strength peripherally. In theory, simultaneous transmission from these two devices could produce a more homogeneous transmission field. To minimize interactions between the phased array and the volume coil, counter rotating current (CRC) surface coils consisting of two parallel rings carrying opposite currents were used for the phased array. Results Numerical simulations and experimental data demonstrate that substantial improvements in transmit field homogeneity can be obtained. Conclusion We have demonstrated the feasibility of using simultaneous transmission with human head-sized volume coils and CRC phased arrays to improve homogeneity of the transmit RF B1 field for high-field MRI systems. PMID:20677280

Characteristics and issues of an EUVL mask applying phase-shifting thinner absorber for device fabrication

NASA Astrophysics Data System (ADS)

Seo, Hwan-Seok; Lee, Dong-Gun; Ahn, Byung-Sup; Han, Hakseung; Huh, Sungmin; Kang, In-Yong; Kim, Hoon; Kim, Dongwan; Kim, Seong-Sue; Cho, Han-Ku

2009-03-01

Phase-shifting EUVL masks applying thinner absorber are investigated to design optimum mask structure with less shadowing problems. Simulations using S-Litho show that H-V bias in Si capping structure is higher than that of Ru capping since the high n (= 0.999) of Si increases sensible absorber height. Phase differences obtained from the patterned masks using the EUV CSM are well-matched with the calculated values using the practical refractive index of absorber materials. Although the mask with 62.4-nm-thick absorber, among the in-house masks, shows the closest phase ΔΦ(= 176°) to the out-of-phase condition, higher NILS and contrast as well as lower H-V bias are obtained with 52.4-nm-thick absorber (ΔΦ = 151°) which has higher R/R0 ratio. MET results also show that lithography performances including MEEF, PW, and resist threshold (dose), are improved with thinner absorber structure. However, low OD in EUVL mask, especially in thinner absorber structure, results in light leakage from the neighboring exposure shots, and thus an appropriate light-shielding layer should be introduced.

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

Effect of a relative phase of waves constituting the initial perturbation and the wave interference on the dynamics of strong-shock-driven Richtmyer-Meshkov flows

NASA Astrophysics Data System (ADS)

Pandian, Arun; Stellingwerf, Robert F.; Abarzhi, Snezhana I.

2017-07-01

While it is a common wisdom that initial conditions influence the evolution of the Richtmyer-Meshkov instability (RMI), the research in this area is focused primarily on the effects of the wavelength and amplitude of the interface perturbation. The information has hitherto largely ignored the influences on RMI dynamics of the relative phase of waves constituting a multiwave initial perturbation and the interference of the perturbation waves. In this work we systematically study the influence of the relative phase and the interference of waves constituting a multiwave initial perturbation on a strong-shock-driven Richtmyer-Meshkov unstable interface separating ideal fluids with contrast densities. We apply group theory analysis and smoothed particle hydrodynamics numerical simulations. For verification and validation of the simulations, qualitative and quantitative comparisons are performed with rigorous zeroth-order, linear, and nonlinear theories as well as with gas dynamics experiments achieving good agreement. For a sample case of a two-wave (two-mode) initial perturbation we select the first-wave amplitude enabling the maximum initial growth rate of the RMI and we vary the second-wave amplitude from 1% to 100% of the first-wave amplitude. We also vary the relative phase of the first and second waves and consider the in-phase, the antiphase and the random-phase cases. We find that the relative phase and the interference of waves are important factors of RMI dynamics influencing qualitatively and quantitatively the symmetry, morphology, and growth rate of the Richtmyer-Meshkov unstable interface, as well as the order and disorder in strong-shock-driven RMI.

Mesh-based phase contrast Fourier transform imaging

NASA Astrophysics Data System (ADS)

Tahir, Sajjad; Bashir, Sajid; MacDonald, C. A.; Petruccelli, Jonathan C.

2017-04-01

Traditional x-ray radiography is limited by low attenuation contrast in materials of low electron density. Phase contrast imaging offers the potential to improve the contrast between such materials, but due to the requirements on the spatial coherence of the x-ray beam, practical implementation of such systems with tabletop (i.e. non-synchrotron) sources has been limited. One phase imaging technique employs multiple fine-pitched gratings. However, the strict manufacturing tolerances and precise alignment requirements have limited the widespread adoption of grating-based techniques. In this work, we have investigated a recently developed technique that utilizes a single grid of much coarser pitch. Our system consisted of a low power 100 μm spot Mo source, a CCD with 22 μm pixel pitch, and either a focused mammography linear grid or a stainless steel woven mesh. Phase is extracted from a single image by windowing and comparing data localized about harmonics of the mesh in the Fourier domain. The effects on the diffraction phase contrast and scattering amplitude images of varying grid types and periods, and of varying the width of the window function used to separate the harmonics were investigated. Using the wire mesh, derivatives of the phase along two orthogonal directions were obtained and combined to form improved phase contrast images.

Flat (0 0 1) surfaces of II-VI semiconductors: a lattice gas model

NASA Astrophysics Data System (ADS)

Ahr, Martin; Biehl, Michael

2002-05-01

We present a two-dimensional lattice gas with anisotropic interactions which model the known properties of the surface reconstructions of CdTe and ZnSe. In contrast to an earlier publication [M. Biehl, M. Ahr, W. Kinzel, M. Sokolowski, T. Volkmann, Europhys. Lett. 53 (2001) 169] the formation of anion dimers is considered. This alters the behaviour of the model considerably. We determine the phase diagram of this model by means of transfer matrix calculations and Monte Carlo simulations. We find qualitative agreement with the results of various experimental investigations.

Near-Field Imaging of Free Carriers in ZnO Nanowires with a Scanning Probe Tip Made of Heavily Doped Germanium

NASA Astrophysics Data System (ADS)

Sakat, Emilie; Giliberti, Valeria; Bollani, Monica; Notargiacomo, Andrea; Pea, Marialilia; Finazzi, Marco; Pellegrini, Giovanni; Hugonin, Jean-Paul; Weber-Bargioni, Alexander; Melli, Mauro; Sassolini, Simone; Cabrini, Stefano; Biagioni, Paolo; Ortolani, Michele; Baldassarre, Leonetta

2017-11-01

A novel scanning probe tip made of heavily doped semiconductor is fabricated and used instead of standard gold-coated tips in infrared scattering-type near-field microscopy. Midinfrared near-field microscopy experiments are conducted on ZnO nanowires with a lateral resolution better than 100 nm, using tips made of heavily electron-doped germanium with a plasma frequency in the midinfrared (plasma wavelength of 9.5 μ m ). Nanowires embedded in a dielectric matrix are imaged at two wavelengths, 11.3 and 8.0 μ m , above and below the plasma wavelength of the tips. An opposite sign of the imaging contrasts between the nanowire and the dielectric matrix is observed at the two infrared wavelengths, indicating a clear role of the free-electron plasma in the heavily doped germanium tip in building the imaging contrast. Electromagnetic simulations with a multispherical dipole model accounting for the finite size of the tip are well consistent with the experiments. By comparison of the simulated and measured imaging contrasts, an estimate for the local free-carrier density in the investigated ZnO nanowires in the low 1019 cm-3 range is retrieved. The results are benchmarked against the scattering intensity and phase maps obtained on the same sample with a gold-coated probe tip in pseudoheterodyne detection mode.

Poster — Thur Eve — 16: 4DCT simulation with synchronized contrast injection of liver SBRT patients

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

Karotki, A.; Korol, R.; Milot, L.

2014-08-15

Stereotactic body radiation therapy (SBRT) has recently emerged as a valid option for treating liver metastases. SBRT delivers highly conformai dose over a small number of fractions. As such it is particularly sensitive to the accuracy of target volume delineation by the radiation oncologist. However, contouring liver metastases remains challenging for the following reasons. First, the liver usually undergoes significant motion due to respiration. Second, liver metastases are often nearly indistinguishable from the surrounding tissue when using computed tomography (CT) for imaging making it difficult to identify and delineate them. Both problems can be overcome by using four dimensional CTmore » (4DCT) synchronized with intravenous contrast injection. We describe a novel CT simulation process which involves two 4DCT scans. The first scan captures the tumor and immediately surrounding tissue which in turn reduces the 4DCT scan time so that it can be optimally timed with intravenous contrast injection. The second 4DCT scan covers a larger volume and is used as the primary CT dataset for dose calculation, as well as patient setup verification on the treatment unit. The combination of two 4DCT scans, short and long, allows visualization of the liver metastases over all phases of breathing cycle while simultaneously acquiring long enough 4DCT dataset suitable for planning and patient setup verification.« less

3D visualization of subcellular structures of Schizosaccharomyces pombe by hard X-ray tomography.

PubMed

Yang, Y; Li, W; Liu, G; Zhang, X; Chen, J; Wu, W; Guan, Y; Xiong, Y; Tian, Y; Wu, Z

2010-10-01

Cellular structures of the fission yeast, Schizosaccharomyces pombe, were examined by using hard X-ray tomography. Since cells are nearly transparent to hard X-rays, Zernike phase contrast and heavy metal staining were introduced to improve image contrast. Through using such methods, images taken at 8 keV displayed sufficient contrast for observing cellular structures. The cell wall, the intracellular organelles and the entire structural organization of the whole cells were visualized in three-dimensional at a resolution better than 100 nm. Comparison between phase contrast and absorption contrast was also made, indicating the obvious advantage of phase contrast for cellular imaging at this energy. Our results demonstrate that hard X-ray tomography with Zernike phase contrast is suitable for cellular imaging. Its unique abilities make it have potential to become a useful tool for revealing structural information from cells, especially thick eukaryotic cells. © 2010 The Authors Journal compilation © 2010 The Royal Microscopical Society.

Contrast of Backscattered Electron SEM Images of Nanoparticles on Substrates with Complex Structure

PubMed Central

Müller, Erich; Fritsch-Decker, Susanne; Hettler, Simon; Störmer, Heike; Weiss, Carsten; Gerthsen, Dagmar

2017-01-01

This study is concerned with backscattered electron scanning electron microscopy (BSE SEM) contrast of complex nanoscaled samples which consist of SiO2 nanoparticles (NPs) deposited on indium-tin-oxide covered bulk SiO2 and glassy carbon substrates. BSE SEM contrast of NPs is studied as function of the primary electron energy and working distance. Contrast inversions are observed which prevent intuitive interpretation of NP contrast in terms of material contrast. Experimental data is quantitatively compared with Monte-Carlo- (MC-) simulations. Quantitative agreement between experimental data and MC-simulations is obtained if the transmission characteristics of the annular semiconductor detector are taken into account. MC-simulations facilitate the understanding of NP contrast inversions and are helpful to derive conditions for optimum material and topography contrast. PMID:29109816

Contrast of Backscattered Electron SEM Images of Nanoparticles on Substrates with Complex Structure.

PubMed

Kowoll, Thomas; Müller, Erich; Fritsch-Decker, Susanne; Hettler, Simon; Störmer, Heike; Weiss, Carsten; Gerthsen, Dagmar

2017-01-01

This study is concerned with backscattered electron scanning electron microscopy (BSE SEM) contrast of complex nanoscaled samples which consist of SiO 2 nanoparticles (NPs) deposited on indium-tin-oxide covered bulk SiO 2 and glassy carbon substrates. BSE SEM contrast of NPs is studied as function of the primary electron energy and working distance. Contrast inversions are observed which prevent intuitive interpretation of NP contrast in terms of material contrast. Experimental data is quantitatively compared with Monte-Carlo- (MC-) simulations. Quantitative agreement between experimental data and MC-simulations is obtained if the transmission characteristics of the annular semiconductor detector are taken into account. MC-simulations facilitate the understanding of NP contrast inversions and are helpful to derive conditions for optimum material and topography contrast.

Accelerated radial Fourier-velocity encoding using compressed sensing.

PubMed

Hilbert, Fabian; Wech, Tobias; Hahn, Dietbert; Köstler, Herbert

2014-09-01

Phase Contrast Magnetic Resonance Imaging (MRI) is a tool for non-invasive determination of flow velocities inside blood vessels. Because Phase Contrast MRI only measures a single mean velocity per voxel, it is only applicable to vessels significantly larger than the voxel size. In contrast, Fourier Velocity Encoding measures the entire velocity distribution inside a voxel, but requires a much longer acquisition time. For accurate diagnosis of stenosis in vessels on the scale of spatial resolution, it is important to know the velocity distribution of a voxel. Our aim was to determine velocity distributions with accelerated Fourier Velocity Encoding in an acquisition time required for a conventional Phase Contrast image. We imaged the femoral artery of healthy volunteers with ECG-triggered, radial CINE acquisition. Data acquisition was accelerated by undersampling, while missing data were reconstructed by Compressed Sensing. Velocity spectra of the vessel were evaluated by high resolution Phase Contrast images and compared to spectra from fully sampled and undersampled Fourier Velocity Encoding. By means of undersampling, it was possible to reduce the scan time for Fourier Velocity Encoding to the duration required for a conventional Phase Contrast image. Acquisition time for a fully sampled data set with 12 different Velocity Encodings was 40 min. By applying a 12.6-fold retrospective undersampling, a data set was generated equal to 3:10 min acquisition time, which is similar to a conventional Phase Contrast measurement. Velocity spectra from fully sampled and undersampled Fourier Velocity Encoded images are in good agreement and show the same maximum velocities as compared to velocity maps from Phase Contrast measurements. Compressed Sensing proved to reliably reconstruct Fourier Velocity Encoded data. Our results indicate that Fourier Velocity Encoding allows an accurate determination of the velocity distribution in vessels in the order of the voxel size. Thus, compared to normal Phase Contrast measurements delivering only mean velocities, no additional scan time is necessary to retrieve meaningful velocity spectra in small vessels. Copyright © 2013. Published by Elsevier GmbH.

Feedback first: the surprisingly weak effects of magnetic fields, viscosity, conduction and metal diffusion on sub-L* galaxy formation

NASA Astrophysics Data System (ADS)

Su, Kung-Yi; Hopkins, Philip F.; Hayward, Christopher C.; Faucher-Giguère, Claude-André; Kereš, Dušan; Ma, Xiangcheng; Robles, Victor H.

2017-10-01

Using high-resolution simulations with explicit treatment of stellar feedback physics based on the FIRE (Feedback In Realistic Environments) project, we study how galaxy formation and the interstellar medium (ISM) are affected by magnetic fields, anisotropic Spitzer-Braginskii conduction and viscosity, and sub-grid metal diffusion from unresolved turbulence. We consider controlled simulations of isolated (non-cosmological) galaxies but also a limited set of cosmological 'zoom-in' simulations. Although simulations have shown significant effects from these physics with weak or absent stellar feedback, the effects are much weaker than those of stellar feedback when the latter is modelled explicitly. The additional physics have no systematic effect on galactic star formation rates (SFRs). In contrast, removing stellar feedback leads to SFRs being overpredicted by factors of ˜10-100. Without feedback, neither galactic winds nor volume-filling hot-phase gas exist, and discs tend to runaway collapse to ultra-thin scaleheights with unphysically dense clumps congregating at the galactic centre. With stellar feedback, a multi-phase, turbulent medium with galactic fountains and winds is established. At currently achievable resolutions and for the investigated halo mass range 1010-1013 M⊙, the additional physics investigated here (magnetohydrodynamic, conduction, viscosity, metal diffusion) have only weak (˜10 per cent-level) effects on regulating SFR and altering the balance of phases, outflows or the energy in ISM turbulence, consistent with simple equipartition arguments. We conclude that galactic star formation and the ISM are primarily governed by a combination of turbulence, gravitational instabilities and feedback. We add the caveat that active galactic nucleus feedback is not included in the present work.

SU-E-J-226: Propagation of Pancreas Target Contours On Respiratory Correlated CT Images Using Deformable Image Registration

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

Liu, F; Yorke, E; Mageras, G

2014-06-01

Purpose: Respiratory Correlated CT (RCCT) scans to assess intra-fraction motion among pancreatic cancer patients undergoing radiotherapy allow for dose sparing of normal tissues, in particular for the duodenum. Contour propagation of the gross tumor volume (GTV) from one reference respiratory phase to 9 other phases is time consuming. Deformable image registration (DIR) has been successfully used for high contrast disease sites but lower contrast for pancreatic tumors may compromise accuracy. This study evaluates the accuracy of Fast Free Form (FFF) registration-based contour propagation of the GTV on RCCT scans of pancreas cancer patients. Methods: Twenty-four pancreatic cancer patients were retrospectivelymore » studied; 20 had tumors in the pancreatic head/neck, 4 in the body/tail. Patients were simulated with RCCT and images were sorted into 10 respiratory phases. A radiation oncologist manually delineated the GTV for 5 phases (0%, 30%, 50%, 70% and 90%). The FFF algorithm was used to map deformations between the EE (50%) phase and each of the other 4 phases. The resultant deformation fields served to propagate GTV contours from EE to the other phases. The Dice Similarity Coefficient (DSC), which measures agreement between the DIR-propagated and manually-delineated GTVs, was used to quantitatively examine DIR accuracy. Results: Average DSC over all scans and patients is 0.82 and standard deviation is 0.09 (DSC range 0.97–0.57). For GTV volumes above and below the median volume of 20.2 cc, a Wilcoxon rank-sum test shows significantly different DSC (p=0.0000002). For the GTVs above the median volume, average +/− SD is 0.85 +/− 0.07; and for the GTVs below, the average +/− SD is 0.75 +/−0.08. Conclusion: For pancreatic tumors, the FFF DIR algorithm accurately propagated the GTV between the images in different phases of RCCT, with improved performance for larger tumors.« less

Contrast and autoshaping in multiple schedules varying reinforcer rate and duration

PubMed Central

Hamilton, Bruce E.; Silberberg, Alan

1978-01-01

Thirteen master pigeons were exposed to multiple schedules in which reinforcement frequency (Experiment I) or duration (Experiment II) was varied. In Phases 1 and 3 of Experiment I, the values of the first and second components' random-interval schedules were 33 and 99 seconds, respectively. In Phase 2, these values were 99 seconds for both components. In Experiment II, a random-interval 33-second schedule was associated with each component. During Phases 1 and 3, the first and second components had hopper durations of 7.5 and 2.5 seconds respectively. During Phase 2, both components' hopper durations were 2.5 seconds. In each experiment, positive contrast obtained for about half the master subjects. The rest showed a rate increase in both components (positive induction). Each master subject's key colors and reinforcers were synchronously presented on a response-independent basis to a yoked control. Richer component key-pecking occurred during each experiment's Phases 1 and 3 among half these subjects. However, none responded during the contrast condition (unchanged component of each experiment's Phase 2). From this it is inferred that autoshaping did not contribute to the contrast and induction findings among master birds. Little evidence of local contrast (highest rate at beginning of richer component) was found in any subject. These data show that (a) contrast can occur independently from autoshaping, (b) contrast assays during equal-valued components may produce induction, (c) local contrast in multiple schedules often does not occur, and (d) differential hopper durations can produce autoshaping and contrast. PMID:16812081

A parametric study of the dynamic failure of energetic composites

NASA Astrophysics Data System (ADS)

Tanasoiu, Bogdan; Koslowski, Marisol

2017-09-01

Heating by frictional sliding of cracks is often considered to be one of the most important causes of localized melting and ignition in solid explosives. Furthermore, recent high speed X-ray phase contrast experiments on energetic composites under dynamic compression [Parab et al., Appl. Phys. Lett. 109(13) (2016)] show that most fracture events appear inside the particles. Initial cracks develop in regions where particles are close, and widespread fragmentation is observed in the interior of the particles as the stress waves propagate through the sample. However, most simulations have focused on interface debonding of energetic composites and, in general, do not include fracture of the particles explicitly. A phase field damage approach is used to model the dynamic response of a system of cyclotetramethylene-tetranitramine particles embedded in a Sylgard matrix. The simulations show several damage mechanisms observed in the experiments. The effects of the energy release rate and the initial crack distribution on the energy dissipation due to fracture are studied. The numerical results confirm that initial cracks play an important role in the evolution of damage, energy dissipation and consequently, the formation of hot-spots.

Selection for production-related traits in Pelargonium zonale: improved design and analysis make all the difference

PubMed Central

Molenaar, Heike; Glawe, Martin; Boehm, Robert; Piepho, Hans-Peter

2017-01-01

Ornamental plant variety improvement is limited by current phenotyping approaches and neglected use of experimental designs. The present study was conducted to show the benefits of using an experimental design and corresponding analysis in ornamental breeding regarding simulated response to selection in Pelargonium zonale for production-related traits. This required establishment of phenotyping protocols for root formation and stem cutting counts, with which 974 genotypes were assessed in a two-phase experimental design. The present paper evaluates this protocol. The possibility of varietal improvement through indirect selection on secondary traits such as branch count and flower count was assessed by genetic correlations. Simulated response to selection varied greatly, depending on the genotypic variances of the breeding population and traits. A varietal improvement of over 20% is possible for stem cutting count, root formation, branch count and flower count. In contrast, indirect selection of stem cutting count by branch count or flower count was found to be ineffective. The established phenotypic protocols and two-phase experimental designs are valuable tools for breeding of P. zonale. PMID:28243453

Selection for production-related traits in Pelargonium zonale: improved design and analysis make all the difference.

PubMed

Molenaar, Heike; Glawe, Martin; Boehm, Robert; Piepho, Hans-Peter

2017-01-01

Ornamental plant variety improvement is limited by current phenotyping approaches and neglected use of experimental designs. The present study was conducted to show the benefits of using an experimental design and corresponding analysis in ornamental breeding regarding simulated response to selection in Pelargonium zonale for production-related traits. This required establishment of phenotyping protocols for root formation and stem cutting counts, with which 974 genotypes were assessed in a two-phase experimental design. The present paper evaluates this protocol. The possibility of varietal improvement through indirect selection on secondary traits such as branch count and flower count was assessed by genetic correlations. Simulated response to selection varied greatly, depending on the genotypic variances of the breeding population and traits. A varietal improvement of over 20% is possible for stem cutting count, root formation, branch count and flower count. In contrast, indirect selection of stem cutting count by branch count or flower count was found to be ineffective. The established phenotypic protocols and two-phase experimental designs are valuable tools for breeding of P. zonale .

Project ARGO: Gas phase formation in simulated microgravity

NASA Technical Reports Server (NTRS)

Powell, Michael R.; Waligora, James M.; Norfleet, William T.; Kumar, K. Vasantha

1993-01-01

The ARGO study investigated the reduced incidence of joint pain decompression sickness (DCS) encountered in microgravity as compared with an expected incidence of joint pain DCS experienced by test subjects in Earth-based laboratories (unit gravity) with similar protocols. Individuals who are decompressed from saturated conditions usually acquire joint pain DCS in the lower extremities. Our hypothesis is that the incidence of joint pain DCS can be limited by a significant reduction in the tissue gas micronuclei formed by stress-assisted nucleation. Reductions in dynamic and kinetic stresses in vivo are linked to hypokinetic and adynamic conditions of individuals in zero g. We employed the Doppler ultrasound bubble detection technique in simulated microgravity studies to determine quantitatively the degree of gas phase formation in the upper and lower extremities of test subjects during decompression. We found no evidence of right-to-left shunting through pulmonary vasculature. The volume of gas bubble following decompression was examined and compared with the number following saline contrast injection. From this, we predict a reduced incidence of DCS on orbit, although the incidence of predicted mild DCS still remains larger than that encountered on orbit.

Numerical Simulation of Transient Liquid Phase Bonding under Temperature Gradient

NASA Astrophysics Data System (ADS)

Ghobadi Bigvand, Arian

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

Studying methane migration mechanisms at Walker Ridge, Gulf of Mexico, via 3D methane hydrate reservoir modeling

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

Nole, Michael; Daigle, Hugh; Mohanty, Kishore

We have developed a 3D methane hydrate reservoir simulator to model marine methane hydrate systems. Our simulator couples highly nonlinear heat and mass transport equations and includes heterogeneous sedimentation, in-situ microbial methanogenesis, the influence of pore size contrast on solubility gradients, and the impact of salt exclusion from the hydrate phase on dissolved methane equilibrium in pore water. Using environmental parameters from Walker Ridge in the Gulf of Mexico, we first simulate hydrate formation in and around a thin, dipping, planar sand stratum surrounded by clay lithology as it is buried to 295mbsf. We find that with sufficient methane beingmore » supplied by organic methanogenesis in the clays, a 200x pore size contrast between clays and sands allows for a strong enough concentration gradient to significantly drop the concentration of methane hydrate in clays immediately surrounding a thin sand layer, a phenomenon that is observed in well log data. Building upon previous work, our simulations account for the increase in sand-clay solubility contrast with depth from about 1.6% near the top of the sediment column to 8.6% at depth, which leads to a progressive strengthening of the diffusive flux of methane with time. By including an exponentially decaying organic methanogenesis input to the clay lithology with depth, we see a decrease in the aqueous methane supplied to the clays surrounding the sand layer with time, which works to further enhance the contrast in hydrate saturation between the sand and surrounding clays. Significant diffusive methane transport is observed in a clay interval of about 11m above the sand layer and about 4m below it, which matches well log observations. The clay-sand pore size contrast alone is not enough to completely eliminate hydrate (as observed in logs), because the diffusive flux of aqueous methane due to a contrast in pore size occurs slower than the rate at which methane is supplied via organic methanogenesis. Therefore, it is likely that additional mechanisms are at play, notably bound water activity reduction in clays. Three-dimensionality allows for inclusion of lithologic heterogeneities, which focus fluid flow and subsequently allow for heterogeneity in the methane migration mechanisms that dominate in marine sediments at a local scale. Incorporating recently acquired 3D seismic data from Walker Ridge to inform the lithologic structure of our modeled reservoir, we show that even with deep adjective sourcing of methane along highly permeable pathways, local hydrate accumulations can be sourced either by diffusive or advective methane flux; advectively-sourced hydrates accumulate evenly in highly permeable strata, while diffusively-sourced hydrates are characterized by thin strata-bound intervals with high clay-sand pore size contrasts.« less

Diffuse-interface approach to rotating Hele-Shaw flows.

PubMed

Chen, Ching-Yao; Huang, Yu-Sheng; Miranda, José A

2011-10-01

When two fluids of different densities move in a rotating Hele-Shaw cell, the interface between them becomes centrifugally unstable and deforms. Depending on the viscosity contrast of the system, distinct types of complex patterns arise at the fluid-fluid boundary. Deformations can also induce the emergence of interfacial singularities and topological changes such as droplet pinch-off and self-intersection. We present numerical simulations based on a diffuse-interface model for this particular two-phase displacement that capture a variety of pattern-forming behaviors. This is implemented by employing a Boussinesq Hele-Shaw-Cahn-Hilliard approach, considering the whole range of possible values for the viscosity contrast, and by including inertial effects due to the Coriolis force. The role played by these two physical contributions on the development of interface singularities is illustrated and discussed.

Glycerol extracting dealcoholization for the biodiesel separation process.

PubMed

Ye, Jianchu; Sha, Yong; Zhang, Yun; Yuan, Yunlong; Wu, Housheng

2011-04-01

By means of utilizing sunflower oil and Jatropha oil as raw oil respectively, the biodiesel transesterification production and the multi-stage extracting separation were carried out experimentally. Results indicate that dealcoholized crude glycerol can be utilized as the extracting agent to achieve effective separation of methanol from the methyl ester phase, and the glycerol content in the dealcoholized methyl esters is as low as 0.02 wt.%. For the biodiesel separation process utilizing glycerol extracting dealcoholization, its technical and equipment information were acquired through the rigorous process simulation in contrast to the traditional biodiesel distillation separation process, and results show that its energy consumption decrease about 35% in contrast to that of the distillation separation process. The glycerol extracting dealcoholization has sufficient feasibility and superiority for the biodiesel separation process. Copyright © 2011 Elsevier Ltd. All rights reserved.

Leveraging Gibbs Ensemble Molecular Dynamics and Hybrid Monte Carlo/Molecular Dynamics for Efficient Study of Phase Equilibria.

PubMed

Gartner, Thomas E; Epps, Thomas H; Jayaraman, Arthi

2016-11-08

We describe an extension of the Gibbs ensemble molecular dynamics (GEMD) method for studying phase equilibria. Our modifications to GEMD allow for direct control over particle transfer between phases and improve the method's numerical stability. Additionally, we found that the modified GEMD approach had advantages in computational efficiency in comparison to a hybrid Monte Carlo (MC)/MD Gibbs ensemble scheme in the context of the single component Lennard-Jones fluid. We note that this increase in computational efficiency does not compromise the close agreement of phase equilibrium results between the two methods. However, numerical instabilities in the GEMD scheme hamper GEMD's use near the critical point. We propose that the computationally efficient GEMD simulations can be used to map out the majority of the phase window, with hybrid MC/MD used as a follow up for conditions under which GEMD may be unstable (e.g., near-critical behavior). In this manner, we can capitalize on the contrasting strengths of these two methods to enable the efficient study of phase equilibria for systems that present challenges for a purely stochastic GEMC method, such as dense or low temperature systems, and/or those with complex molecular topologies.

Effect of Charge Patterning on the Phase Behavior of Polymer Coacervates for Charge Driven Self Assembly

NASA Astrophysics Data System (ADS)

Radhakrishna, Mithun; Sing, Charles E.

Oppositely charged polymers can undergo associative liquid-liquid phase separation when mixed under suitable conditions of ionic strength, temperature and pH to form what are known as `polymeric complex coacervates'. Polymer coacervates find use in diverse array of applications like microencapsulation, drug delivery, membrane filtration and underwater adhesives. The similarity between complex coacervate environments and those in biological systems has also found relevance in areas of bio-mimicry. Our previous works have demonstrated how local charge correlations and molecular connectivity can drastically affect the phase behavior of coacervates. The precise location of charges along the chain therefore dramatically influences the local charge correlations, which consequently influences the phase behavior of coacervates. We investigate the effect of charge patterning along the polymer chain on the phase behavior of coacervates in the framework of the Restricted Primitive Model using Gibbs Ensemble Monte Carlo simulations. Our results show that charge patterning dramatically changes the phase behavior of polymer coacervates, which contrasts with the predictions of the classical Voorn-Overbeek theory. This provides the basis for designing new materials through charge driven self assembly by controlling the positioning of the charged monomers along the chain.

Enhancing Tabletop X-Ray Phase Contrast Imaging with Nano-Fabrication

PubMed Central

Miao, Houxun; Gomella, Andrew A.; Harmon, Katherine J.; Bennett, Eric E.; Chedid, Nicholas; Znati, Sami; Panna, Alireza; Foster, Barbara A.; Bhandarkar, Priya; Wen, Han

2015-01-01

X-ray phase-contrast imaging is a promising approach for improving soft-tissue contrast and lowering radiation dose in biomedical applications. While current tabletop imaging systems adapt to common x-ray tubes and large-area detectors by employing absorptive elements such as absorption gratings or monolithic crystals to filter the beam, we developed nanometric phase gratings which enable tabletop x-ray far-field interferometry with only phase-shifting elements, leading to a substantial enhancement in the performance of phase contrast imaging. In a general sense the method transfers the demands on the spatial coherence of the x-ray source and the detector resolution to the feature size of x-ray phase masks. We demonstrate its capabilities in hard x-ray imaging experiments at a fraction of clinical dose levels and present comparisons with the existing Talbot-Lau interferometer and with conventional digital radiography. PMID:26315891

Theory and preliminary experimental verification of quantitative edge illumination x-ray phase contrast tomography.

PubMed

Hagen, C K; Diemoz, P C; Endrizzi, M; Rigon, L; Dreossi, D; Arfelli, F; Lopez, F C M; Longo, R; Olivo, A

2014-04-07

X-ray phase contrast imaging (XPCi) methods are sensitive to phase in addition to attenuation effects and, therefore, can achieve improved image contrast for weakly attenuating materials, such as often encountered in biomedical applications. Several XPCi methods exist, most of which have already been implemented in computed tomographic (CT) modality, thus allowing volumetric imaging. The Edge Illumination (EI) XPCi method had, until now, not been implemented as a CT modality. This article provides indications that quantitative 3D maps of an object's phase and attenuation can be reconstructed from EI XPCi measurements. Moreover, a theory for the reconstruction of combined phase and attenuation maps is presented. Both reconstruction strategies find applications in tissue characterisation and the identification of faint, weakly attenuating details. Experimental results for wires of known materials and for a biological object validate the theory and confirm the superiority of the phase over conventional, attenuation-based image contrast.

Towards a standardized method to assess straylight in earth observing optical instruments

NASA Astrophysics Data System (ADS)

Caron, J.; Taccola, M.; Bézy, J.-L.

2017-09-01

Straylight is a spurious effect that can seriously degrade the radiometric accuracy achieved by Earth observing optical instruments, as a result of the high contrast in the observed Earth radiance scenes and spectra. It is considered critical for several ESA missions such as Sentinel-5, FLEX and potential successors to CarbonSat. Although it is traditionally evaluated by Monte-Carlo simulations performed with commercial softwares (e.g. ASAP, Zemax, LightTools), semi-analytical approximate methods [1,2] have drawn some interest in recent years due to their faster computing time and the greater insight they provide in straylight mechanisms. They cannot replace numerical simulations, but may be more advantageous in contexts where many iterations are needed, for instance during the early phases of an instrument design.

A tone-aided dual vestigial sideband system for digital communications on fading channels

NASA Technical Reports Server (NTRS)

Hladik, Stephen M.; Saulnier, Gary J.; Rafferty, William

1989-01-01

A spectrally efficient tone-aided dual vestigial sideband (TA/DVSB) system for digital data communications on fading channels is presented and described analytically. This PSK (phase-shift-keying) system incorporates a feed-forward, tone-aided demodulation technique to compensate for Doppler frequency shift and channel- induced, multipath fading. In contrast to other tone-in-band-type systems, receiver synchronization is derived from the complete data VSBs. Simulation results for the Rician fading channel are presented. These results demonstrate the receiver's ability to mitigate performance degradation due to fading and to obtain proper data carrier synchronization, suggesting that the proposed TA/DVSB system has promise for this application. Simulated BER (bit-error rate) data indicate that the TA/DVSB system effectively alleviates the channel distortions of the land mobile satellite application.

Intact Imaging of Human Heart Structure Using X-ray Phase-Contrast Tomography.

PubMed

Kaneko, Yukihiro; Shinohara, Gen; Hoshino, Masato; Morishita, Hiroyuki; Morita, Kiyozo; Oshima, Yoshihiro; Takahashi, Masashi; Yagi, Naoto; Okita, Yutaka; Tsukube, Takuro

2017-02-01

Structural examination of human heart specimens at the microscopic level is a prerequisite for understanding congenital heart diseases. It is desirable not to destroy or alter the properties of such specimens because of their scarcity. However, many of the currently available imaging techniques either destroy the specimen through sectioning or alter the chemical and mechanical properties of the specimen through staining and contrast agent injection. As a result, subsequent studies may not be possible. X-ray phase-contrast tomography is an imaging modality for biological soft tissues that does not destroy or alter the properties of the specimen. The feasibility of X-ray phase-contrast tomography for the structural examination of heart specimens was tested using infantile and fetal heart specimens without congenital diseases. X-ray phase-contrast tomography was carried out at the SPring-8 synchrotron radiation facility using the Talbot grating interferometer at the bending magnet beamline BL20B2 to visualize the structure of five non-pretreated whole heart specimens obtained by autopsy. High-resolution, three-dimensional images were obtained for all specimens. The images clearly showed the myocardial structure, coronary vessels, and conduction bundle. X-ray phase-contrast tomography allows high-resolution, three-dimensional imaging of human heart specimens. Intact imaging using X-ray phase-contrast tomography can contribute to further structural investigation of heart specimens with congenital heart diseases.

Phase contrast imaging with coherent high energy X-rays

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

Snigireva, I.

X-ray imaging concern high energy domain (>6 keV) like a contact radiography, projection microscopy and tomography is used for many years to discern the features of the internal structure non destructively in material science, medicine and biology. In so doing the main contrast formation is absorption that makes some limitations for imaging of the light density materials and what is more the resolution of these techniques is not better than 10-100 {mu}m. It was turned out that there is now way in which to overcome 1{mu}m or even sub-{mu}m resolution limit except phase contrast imaging. It is well known inmore » optics that the phase contrast is realised when interference between reference wave front and transmitted through the sample take place. Examples of this imaging are: phase contrast microscopy suggested by Zernike and Gabor (in-line) holography. Both of this techniques: phase contrast x-ray microscopy and holography are successfully progressing now in soft x-ray region. For imaging in the hard X-rays to enhance the contrast and to be able to resolve phase variations across the beam the high degree of the time and more importantly spatial coherence is needed. Because of this it was reasonable that the perfect crystal optics was involved like Bonse-Hart interferometry, double-crystal and even triple-crystal set-up using Laue and Bragg geometry with asymmetrically cut crystals.« less

Amide-induced phase separation of hexafluoroisopropanol-water mixtures depending on the hydrophobicity of amides.

PubMed

Takamuku, Toshiyuki; Wada, Hiroshi; Kawatoko, Chiemi; Shimomura, Takuya; Kanzaki, Ryo; Takeuchi, Munetaka

2012-06-21

Amide-induced phase separation of hexafluoro-2-propanol (HFIP)-water mixtures has been investigated to elucidate solvation properties of the mixtures by means of small-angle neutron scattering (SANS), (1)H and (13)C NMR, and molecular dynamics (MD) simulation. The amides included N-methylformamide (NMF), N-methylacetamide (NMA), and N-methylpropionamide (NMP). The phase diagrams of amide-HFIP-water ternary systems at 298 K showed that phase separation occurs in a closed-loop area of compositions as well as an N,N-dimethylformamide (DMF) system previously reported. The phase separation area becomes wider as the hydrophobicity of amides increases in the order of NMF < NMA < DMF < NMP. Thus, the evolution of HFIP clusters around amides due to the hydrophobic interaction gives rise to phase separation of the mixtures. In contrast, the disruption of HFIP clusters causes the recovery of the homogeneity of the ternary systems. The present results showed that HFIP clusters are evolved with increasing amide content to the lower phase separation concentration in the same mechanism among the four amide systems. However, the disruption of HFIP clusters in the NMP and DMF systems with further increasing amide content to the upper phase separation concentration occurs in a different way from those in the NMF and NMA systems.

Binocular combination in abnormal binocular vision

PubMed Central

Ding, Jian; Klein, Stanley A.; Levi, Dennis M.

2013-01-01

We investigated suprathreshold binocular combination in humans with abnormal binocular visual experience early in life. In the first experiment we presented the two eyes with equal but opposite phase shifted sine waves and measured the perceived phase of the cyclopean sine wave. Normal observers have balanced vision between the two eyes when the two eyes' images have equal contrast (i.e., both eyes contribute equally to the perceived image and perceived phase = 0°). However, in observers with strabismus and/or amblyopia, balanced vision requires a higher contrast image in the nondominant eye (NDE) than the dominant eye (DE). This asymmetry between the two eyes is larger than predicted from the contrast sensitivities or monocular perceived contrast of the two eyes and is dependent on contrast and spatial frequency: more asymmetric with higher contrast and/or spatial frequency. Our results also revealed a surprising NDE-to-DE enhancement in some of our abnormal observers. This enhancement is not evident in normal vision because it is normally masked by interocular suppression. However, in these abnormal observers the NDE-to-DE suppression was weak or absent. In the second experiment, we used the identical stimuli to measure the perceived contrast of a cyclopean grating by matching the binocular combined contrast to a standard contrast presented to the DE. These measures provide strong constraints for model fitting. We found asymmetric interocular interactions in binocular contrast perception, which was dependent on both contrast and spatial frequency in the same way as in phase perception. By introducing asymmetric parameters to the modified Ding-Sperling model including interocular contrast gain enhancement, we succeeded in accounting for both binocular combined phase and contrast simultaneously. Adding binocular contrast gain control to the modified Ding-Sperling model enabled us to predict the results of dichoptic and binocular contrast discrimination experiments and provides new insights into the mechanisms of abnormal binocular vision. PMID:23397039

Binocular combination in abnormal binocular vision.

PubMed

Ding, Jian; Klein, Stanley A; Levi, Dennis M

2013-02-08

We investigated suprathreshold binocular combination in humans with abnormal binocular visual experience early in life. In the first experiment we presented the two eyes with equal but opposite phase shifted sine waves and measured the perceived phase of the cyclopean sine wave. Normal observers have balanced vision between the two eyes when the two eyes' images have equal contrast (i.e., both eyes contribute equally to the perceived image and perceived phase = 0°). However, in observers with strabismus and/or amblyopia, balanced vision requires a higher contrast image in the nondominant eye (NDE) than the dominant eye (DE). This asymmetry between the two eyes is larger than predicted from the contrast sensitivities or monocular perceived contrast of the two eyes and is dependent on contrast and spatial frequency: more asymmetric with higher contrast and/or spatial frequency. Our results also revealed a surprising NDE-to-DE enhancement in some of our abnormal observers. This enhancement is not evident in normal vision because it is normally masked by interocular suppression. However, in these abnormal observers the NDE-to-DE suppression was weak or absent. In the second experiment, we used the identical stimuli to measure the perceived contrast of a cyclopean grating by matching the binocular combined contrast to a standard contrast presented to the DE. These measures provide strong constraints for model fitting. We found asymmetric interocular interactions in binocular contrast perception, which was dependent on both contrast and spatial frequency in the same way as in phase perception. By introducing asymmetric parameters to the modified Ding-Sperling model including interocular contrast gain enhancement, we succeeded in accounting for both binocular combined phase and contrast simultaneously. Adding binocular contrast gain control to the modified Ding-Sperling model enabled us to predict the results of dichoptic and binocular contrast discrimination experiments and provides new insights into the mechanisms of abnormal binocular vision.

Development of a preoperative simulation technique for carotid endarterectomy in patients with contrast contraindications.

PubMed

Nomura, Shunsuke; Hayashi, Motohiro; Ishikawa, Tatsuya; Yamaguchi, Koji; Kawamata, Takakazu

2018-05-19

Vascular and osteological parameters, such as the heights of the carotid bifurcation and distal end of the plaque, are important preoperative considerations for patients undergoing carotid stenosis procedures such as carotid endarterectomy. However, for patients with contrast contraindications such as allergies or nephropathies, three-dimensional computed tomography angiography (3D-CTA) is unavailable, and preoperative evaluation remains challenging. In the present study, we aimed to develop a preoperative simulation for use in patients with contrast-contraindicated carotid stenosis. Images from non-contrast neck CT and magnetic resonance imaging obtained without the Leksell stereotactic frame were uploaded to GammaPlan. Following delineation of various structures, we performed preoperative simulations to determine the relationships between vascular and osteological structures. We applied this technique in 10 patients with carotid stenosis to verify the accuracy of the simulation. In all patients, the GammaPlan simulation successfully visualized the heights of the carotid bifurcation and distal end of the plaque without the use of contrast medium. Furthermore, information regarding the location of internal arterial structures, such as calcifications and unstable plaques, could be incorporated into GammaPlan images. Thereafter, we verified simulation accuracy by comparing the simulation results with 3D-CTA and operative findings. Simulations created using GammaPlan can be used to obtain accurate vascular and osteological information regarding the heights of the carotid bifurcation and distal end of the plaque, without the use of contrast medium. The reconstruction of delineated structures using this technique may be effective for preoperative evaluation in patients with contrast-contraindicated carotid stenosis. Copyright © 2018 Elsevier Inc. All rights reserved.

Modeling laser speckle imaging of perfusion in the skin (Conference Presentation)

NASA Astrophysics Data System (ADS)

Regan, Caitlin; Hayakawa, Carole K.; Choi, Bernard

2016-02-01

Laser speckle imaging (LSI) enables visualization of relative blood flow and perfusion in the skin. It is frequently applied to monitor treatment of vascular malformations such as port wine stain birthmarks, and measure changes in perfusion due to peripheral vascular disease. We developed a computational Monte Carlo simulation of laser speckle contrast imaging to quantify how tissue optical properties, blood vessel depths and speeds, and tissue perfusion affect speckle contrast values originating from coherent excitation. The simulated tissue geometry consisted of multiple layers to simulate the skin, or incorporated an inclusion such as a vessel or tumor at different depths. Our simulation used a 30x30mm uniform flat light source to optically excite the region of interest in our sample to better mimic wide-field imaging. We used our model to simulate how dynamically scattered photons from a buried blood vessel affect speckle contrast at different lateral distances (0-1mm) away from the vessel, and how these speckle contrast changes vary with depth (0-1mm) and flow speed (0-10mm/s). We applied the model to simulate perfusion in the skin, and observed how different optical properties, such as epidermal melanin concentration (1%-50%) affected speckle contrast. We simulated perfusion during a systolic forearm occlusion and found that contrast decreased by 35% (exposure time = 10ms). Monte Carlo simulations of laser speckle contrast give us a tool to quantify what regions of the skin are probed with laser speckle imaging, and measure how the tissue optical properties and blood flow affect the resulting images.

Large-field high-contrast hard x-ray Zernike phase-contrast nano-imaging beamline at Pohang Light Source.

PubMed

Lim, Jun; Park, So Yeong; Huang, Jung Yun; Han, Sung Mi; Kim, Hong-Tae

2013-01-01

We developed an off-axis-illuminated zone-plate-based hard x-ray Zernike phase-contrast microscope beamline at Pohang Light Source. Owing to condenser optics-free and off-axis illumination, a large field of view was achieved. The pinhole-type Zernike phase plate affords high-contrast images of a cell with minimal artifacts such as the shade-off and halo effects. The setup, including the optics and the alignment, is simple and easy, and allows faster and easier imaging of large bio-samples.

Tomographic image reconstruction using x-ray phase information

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji; Hirano, Keiichi

1996-04-01

We have been developing phase-contrast x-ray computed tomography (CT) to make possible the observation of biological soft tissues without contrast enhancement. Phase-contrast x-ray CT requires for its input data the x-ray phase-shift distributions or phase-mapping images caused by an object. These were measured with newly developed fringe-scanning x-ray interferometry. Phase-mapping images at different projection directions were obtained by rotating the object in an x-ray interferometer, and were processed with a standard CT algorithm. A phase-contrast x-ray CT image of a nonstained cancerous tissue was obtained using 17.7 keV synchrotron x rays with 12 micrometer voxel size, although the size of the observation area was at most 5 mm. The cancerous lesions were readily distinguishable from normal tissues. Moreover, fine structures corresponding to cancerous degeneration and fibrous tissues were clearly depicted. It is estimated that the present system is sensitive down to a density deviation of 4 mg/cm3.

Multiphase contrast medium injection for optimization of computed tomographic coronary angiography.

PubMed

Budoff, Matthew Jay; Shinbane, Jerold S; Child, Janis; Carson, Sivi; Chau, Alex; Liu, Stephen H; Mao, SongShou

2006-02-01

Electron beam angiography is a minimally invasive imaging technique. Adequate vascular opacification throughout the study remains a critical issue for image quality. We hypothesized that vascular image opacification and uniformity of vascular enhancement between slices can be improved using multiphase contrast medium injection protocols. We enrolled 244 consecutive patients who were randomized to three different injection protocols: single-phase contrast medium injection (Group 1), dual-phase contrast medium injection with each phase at a different injection rate (Group 2), and a three-phase injection with two phases of contrast medium injection followed by a saline injection phase (Group 3). Parameters measured were aortic opacification based on Hounsfield units and uniformity of aortic enhancement at predetermined slices (locations from top [level 1] to base [level 60]). In Group 1, contrast opacification differed across seven predetermined locations (scan levels: 1st versus 60th, P < .05), demonstrating significant nonuniformity. In Group 2, there was more uniform vascular enhancement, with no significant differences between the first 50 slices (P > .05). In Group 3, there was greater uniformity of vascular enhancement and higher mean Hounsfield units value across all 60 images, from the aortic root to the base of the heart (P < .05). The three-phase injection protocol improved vascular opacification at the base of the heart, as well as uniformity of arterial enhancement throughout the study.

Adaptive windowing in contrast-enhanced intravascular ultrasound imaging

PubMed Central

Lindsey, Brooks D.; Martin, K. Heath; Jiang, Xiaoning; Dayton, Paul A.

2016-01-01

Intravascular ultrasound (IVUS) is one of the most commonly-used interventional imaging techniques and has seen recent innovations which attempt to characterize the risk posed by atherosclerotic plaques. One such development is the use of microbubble contrast agents to image vasa vasorum, fine vessels which supply oxygen and nutrients to the walls of coronary arteries and typically have diameters less than 200 µm. The degree of vasa vasorum neovascularization within plaques is positively correlated with plaque vulnerability. Having recently presented a prototype dual-frequency transducer for contrast agent-specific intravascular imaging, here we describe signal processing approaches based on minimum variance (MV) beamforming and the phase coherence factor (PCF) for improving the spatial resolution and contrast-to-tissue ratio (CTR) in IVUS imaging. These approaches are examined through simulations, phantom studies, ex vivo studies in porcine arteries, and in vivo studies in chicken embryos. In phantom studies, PCF processing improved CTR by a mean of 4.2 dB, while combined MV and PCF processing improved spatial resolution by 41.7%. Improvements of 2.2 dB in CTR and 37.2% in resolution were observed in vivo. Applying these processing strategies can enhance image quality in conventional B-mode IVUS or in contrast-enhanced IVUS, where signal-to-noise ratio is relatively low and resolution is at a premium. PMID:27161022

Characterization of a high-energy in-line phase contrast tomosynthesis prototype

PubMed Central

Wu, Di; Yan, Aimin; Li, Yuhua; Wong, Molly D.; Zheng, Bin; Wu, Xizeng; Liu, Hong

2015-01-01

Purpose: In this research, a high-energy in-line phase contrast tomosynthesis prototype was developed and characterized through quantitative investigations and phantom studies. Methods: The prototype system consists of an x-ray source, a motorized rotation stage, and a CMOS detector with a pixel pitch of 0.05 mm. The x-ray source was operated at 120 kVp for this study, and the objects were mounted on the rotation stage 76.2 cm (R1) from the source and 114.3 cm (R2) from the detector. The large air gap between the object and detector guarantees sufficient phase-shift effects. The quantitative evaluation of this prototype included modulation transfer function and noise power spectrum measurements conducted under both projection mode and tomosynthesis mode. Phantom studies were performed including three custom designed phantoms with complex structures: a five-layer bubble wrap phantom, a fishbone phantom, and a chicken breast phantom with embedded fibrils and mass structures extracted from an ACR phantom. In-plane images of the phantoms were acquired to investigate their image qualities through observation, intensity profile plots, edge enhancement evaluations, and/or contrast-to-noise ratio calculations. In addition, the robust phase-attenuation duality (PAD)-based phase retrieval method was applied to tomosynthesis for the first time in this research. It was utilized as a preprocessing method to fully exhibit phase contrast on the angular projection before reconstruction. Results: The resolution and noise characteristics of this high-energy in-line phase contrast tomosynthesis prototype were successfully investigated and demonstrated. The phantom studies demonstrated that this imaging prototype can successfully remove the structure overlapping in phantom projections, obtain delineate interfaces, and achieve better contrast-to-noise ratio after applying phase retrieval to the angular projections. Conclusions: This research successfully demonstrated a high-energy in-line phase contrast tomosynthesis prototype. In addition, the PAD-based method of phase retrieval was combined with tomosynthesis imaging for the first time, which demonstrated its capability in significantly improving the contrast-to-noise ratios in the images. PMID:25979035

A user-friendly LabVIEW software platform for grating based X-ray phase-contrast imaging.

PubMed

Wang, Shenghao; Han, Huajie; Gao, Kun; Wang, Zhili; Zhang, Can; Yang, Meng; Wu, Zhao; Wu, Ziyu

2015-01-01

X-ray phase-contrast imaging can provide greatly improved contrast over conventional absorption-based imaging for weakly absorbing samples, such as biological soft tissues and fibre composites. In this study, we introduced an easy and fast way to develop a user-friendly software platform dedicated to the new grating-based X-ray phase-contrast imaging setup at the National Synchrotron Radiation Laboratory of the University of Science and Technology of China. The control of 21 motorized stages, of a piezoelectric stage and of an X-ray tube are achieved with this software, it also covers image acquisition with a flat panel detector for automatic phase stepping scan. Moreover, a data post-processing module for signals retrieval and other custom features are in principle available. With a seamless integration of all the necessary functions in one software package, this platform greatly facilitate users' activities during experimental runs with this grating based X-ray phase contrast imaging setup.

Table-top phase-contrast imaging employing photon-counting detectors towards mammographic applications

NASA Astrophysics Data System (ADS)

Palma, K. D.; Pichotka, M.; Hasn, S.; Granja, C.

2017-02-01

In mammography the difficult task to detect microcalcifications (≈ 100 μm) and low contrast structures in the breast has been a topic of interest from its beginnings. The possibility to improve the image quality requires the effort to employ novel X-ray imaging techniques, such as phase-contrast, and high resolution detectors. Phase-contrast techniques are promising tools for medical diagnosis because they provide additional and complementary information to traditional absorption-based X-ray imaging methods. In this work a Hamamatsu microfocus X-ray source with tungsten anode and a photon counting detector (Timepix operated in Medipix mode) was used. A significant improvement in the detection of phase-effects using Medipix detector was observed in comparison to an standard flat-panel detector. An optimization of geometrical parameters reveals the dependency on the X-ray propagation path and the small angle deviation. The quantification of these effects was achieved taking into account the image noise, contrast, spatial resolution of the phase-enhancement, absorbed dose, and energy dependence.

Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods.

PubMed

Wan, Xiaohua; Katchalski, Tsvi; Churas, Christopher; Ghosh, Sreya; Phan, Sebastien; Lawrence, Albert; Hao, Yu; Zhou, Ziying; Chen, Ruijuan; Chen, Yu; Zhang, Fa; Ellisman, Mark H

2017-05-01

Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography. Copyright © 2017 Elsevier Inc. All rights reserved.

Simulated space weathering of Fe- and Mg-rich aqueously altered minerals using pulsed laser irradiation

NASA Astrophysics Data System (ADS)

Kaluna, H. M.; Ishii, H. A.; Bradley, J. P.; Gillis-Davis, J. J.; Lucey, P. G.

2017-08-01

Simulated space weathering experiments on volatile-rich carbonaceous chondrites (CCs) have resulted in contrasting spectral behaviors (e.g. reddening vs bluing). The aim of this work is to investigate the origin of these contrasting trends by simulating space weathering on a subset of minerals found in these meteorites. We use pulsed laser irradiation to simulate micrometeorite impacts on aqueously altered minerals and observe their spectral and physical evolution as a function of irradiation time. Irradiation of the mineral lizardite, a Mg-phyllosilicate, produces a small degree of reddening and darkening, but a pronounced reduction in band depths with increasing irradiation. In comparison, irradiation of an Fe-rich aqueously altered mineral assemblage composed of cronstedtite, pyrite and siderite, produces significant darkening and band depth suppression. The spectral slopes of the Fe-rich assemblage initially redden then become bluer with increasing irradiation time. Post-irradiation analyses of the Fe-rich assemblage using scanning and transmission electron microscopy reveal the presence of micron sized carbon-rich particles that contain notable fractions of nitrogen and oxygen. Radiative transfer modeling of the Fe-rich assemblage suggests that nanometer sized metallic iron (npFe0) particles result in the initial spectral reddening of the samples, but the increasing production of micron sized carbon particles (μpC) results in the subsequent spectral bluing. The presence of npFe0 and the possible catalytic nature of cronstedtite, an Fe-rich phyllosilicate, likely promotes the synthesis of these carbon-rich, organic-like compounds. These experiments indicate that space weathering processes may enable organic synthesis reactions on the surfaces of volatile-rich asteroids. Furthermore, Mg-rich and Fe-rich aqueously altered minerals are dominant at different phases of the aqueous alteration process. Thus, the contrasting spectral slope evolution between the Fe- and Mg-rich samples in these experiments may indicate that space weathering trends of volatile-rich asteroids have a compositional dependency that could be used to determine the aqueous histories of asteroid parent bodies.

Grating-based x-ray differential phase contrast imaging with twin peaks in phase-stepping curves—phase retrieval and dewrapping

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

Yang, Yi; Xie, Huiqiao; Tang, Xiangyang, E-mail: xiangyang.tang@emory.edu

Purpose: X-ray differential phase contrast CT implemented with Talbot interferometry employs phase-stepping to extract information of x-ray attenuation, phase shift, and small-angle scattering. Since inaccuracy may exist in the absorption grating G{sub 2} due to an imperfect fabrication, the effective period of G{sub 2} can be as large as twice the nominal period, leading to a phenomenon of twin peaks that differ remarkably in their heights. In this work, the authors investigate how to retrieve and dewrap the phase signal from the phase-stepping curve (PSC) with the feature of twin peaks for x-ray phase contrast imaging. Methods: Based on themore » paraxial Fresnel–Kirchhoff theory, the analytical formulae to characterize the phenomenon of twin peaks in the PSC are derived. Then an approach to dewrap the retrieved phase signal by jointly using the phases of the first- and second-order Fourier components is proposed. Through an experimental investigation using a prototype x-ray phase contrast imaging system implemented with Talbot interferometry, the authors evaluate and verify the derived analytic formulae and the proposed approach for phase retrieval and dewrapping. Results: According to theoretical analysis, the twin-peak phenomenon in PSC is a consequence of combined effects, including the inaccuracy in absorption grating G{sub 2}, mismatch between phase grating and x-ray source spectrum, and finite size of x-ray tube’s focal spot. The proposed approach is experimentally evaluated by scanning a phantom consisting of organic materials and a lab mouse. The preliminary data show that compared to scanning G{sub 2} over only one single nominal period and correcting the measured phase signal with an intuitive phase dewrapping method that is being used in the field, stepping G{sub 2} over twice its nominal period and dewrapping the measured phase signal with the proposed approach can significantly improve the quality of x-ray differential phase contrast imaging in both radiograph and CT. Conclusions: Using the phase retrieval and dewrapping methods proposed to deal with the phenomenon of twin peaks in PSCs and phase wrapping, the performance of grating-based x-ray differential phase contrast radiography and CT can be significantly improved.« less

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

NASA Astrophysics Data System (ADS)

Kou, Jisheng; Sun, Shuyu

2016-08-01

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

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

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

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

2016-08-01

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

Breast tumor segmentation in high resolution x-ray phase contrast analyzer based computed tomography.

PubMed

Brun, E; Grandl, S; Sztrókay-Gaul, A; Barbone, G; Mittone, A; Gasilov, S; Bravin, A; Coan, P

2014-11-01

Phase contrast computed tomography has emerged as an imaging method, which is able to outperform present day clinical mammography in breast tumor visualization while maintaining an equivalent average dose. To this day, no segmentation technique takes into account the specificity of the phase contrast signal. In this study, the authors propose a new mathematical framework for human-guided breast tumor segmentation. This method has been applied to high-resolution images of excised human organs, each of several gigabytes. The authors present a segmentation procedure based on the viscous watershed transform and demonstrate the efficacy of this method on analyzer based phase contrast images. The segmentation of tumors inside two full human breasts is then shown as an example of this procedure's possible applications. A correct and precise identification of the tumor boundaries was obtained and confirmed by manual contouring performed independently by four experienced radiologists. The authors demonstrate that applying the watershed viscous transform allows them to perform the segmentation of tumors in high-resolution x-ray analyzer based phase contrast breast computed tomography images. Combining the additional information provided by the segmentation procedure with the already high definition of morphological details and tissue boundaries offered by phase contrast imaging techniques, will represent a valuable multistep procedure to be used in future medical diagnostic applications.

Reactive Burn Model Calibration for PETN Using Ultra-High-Speed Phase Contrast Imaging

NASA Astrophysics Data System (ADS)

Johnson, Carl; Ramos, Kyle; Bolme, Cindy; Sanchez, Nathaniel; Barber, John; Montgomery, David

2017-06-01

A 1D reactive burn model (RBM) calibration for a plastic bonded high explosive (HE) requires run-to-detonation data. In PETN (pentaerythritol tetranitrate, 1.65 g/cc) the shock to detonation transition (SDT) is on the order of a few millimeters. This rapid SDT imposes experimental length scales that preclude application of traditional calibration methods such as embedded electromagnetic gauge methods (EEGM) which are very effective when used to study 10 - 20 mm thick HE specimens. In recent work at Argonne National Laboratory's Advanced Photon Source we have obtained run-to-detonation data in PETN using ultra-high-speed dynamic phase contrast imaging (PCI). A reactive burn model calibration valid for 1D shock waves is obtained using density profiles spanning the transition to detonation as opposed to particle velocity profiles from EEGM. Particle swarm optimization (PSO) methods were used to operate the LANL hydrocode FLAG iteratively to refine SURF RBM parameters until a suitable parameter set attained. These methods will be presented along with model validation simulations. The novel method described is generally applicable to `sensitive' energetic materials particularly those with areal densities amenable to radiography.

X-ray fast tomography and its applications in dynamical phenomena studies in geosciences at Advanced Photon Source

NASA Astrophysics Data System (ADS)

Xiao, Xianghui; Fusseis, Florian; De Carlo, Francesco

2012-10-01

State-of-art synchrotron radiation based micro-computed tomography provides high spatial and temporal resolution. This matches the needs of many research problems in geosciences. In this letter we report the current capabilities in microtomography at sector 2BM at the Advanced Photon Source (APS) of Argonne National Laboratory. The beamline is well suited to routinely acquire three-dimensional data of excellent quality with sub-micron resolution. Fast cameras in combination with a polychromatic beam allow time-lapse experiments with temporal resolutions of down to 200 ms. Data processing utilizes quantitative phase retrieval to optimize contrast in phase contrast tomographic data. The combination of these capabilities with purpose-designed experimental cells allows for a wide range of dynamic studies on geoscientific topics, two of which are summarized here. In the near future, new experimental cells capable of simulating conditions in most geological reservoirs will be available for general use. Ultimately, these advances will be matched by a new wide-field imaging beam line, which will be constructed as part of the APS upgrade. It is expected that even faster tomography with larger field of view can be conducted at this beam line, creating new opportunities for geoscientific studies.

TRIS buffer in simulated body fluid distorts the assessment of glass-ceramic scaffold bioactivity.

PubMed

Rohanová, Dana; Boccaccini, Aldo Roberto; Yunos, Darmawati Mohamad; Horkavcová, Diana; Březovská, Iva; Helebrant, Aleš

2011-06-01

The paper deals with the characterisation of the bioactive phenomena of glass-ceramic scaffold derived from Bioglass® (containing 77 wt.% of crystalline phases Na(2)O·2CaO·3SiO(2) and CaO·SiO(2) and 23 wt.% of residual glass phase) using simulated body fluid (SBF) buffered with tris-(hydroxymethyl) aminomethane (TRIS). A significant effect of the TRIS buffer on glass-ceramic scaffold dissolution in SBF was detected. To better understand the influence of the buffer, the glass-ceramic scaffold was exposed to a series of in vitro tests using different media as follows: (i) a fresh liquid flow of SBF containing tris (hydroxymethyl) aminomethane; (ii) SBF solution without TRIS buffer; (iii) TRIS buffer alone; and (iv) demineralised water. The in vitro tests were provided under static and dynamic arrangements. SBF buffered with TRIS dissolved both the crystalline and residual glass phases of the scaffold and a crystalline form of hydroxyapatite (HAp) developed on the scaffold surface. In contrast, when TRIS buffer was not present in the solutions only the residual glassy phase dissolved and an amorphous calcium phosphate (Ca-P) phase formed on the scaffold surface. It was confirmed that the TRIS buffer primarily dissolved the crystalline phase of the glass-ceramic, doubled the dissolving rate of the scaffold and moreover supported the formation of crystalline HAp. This significant effect of the buffer TRIS on bioactive glass-ceramic scaffold degradation in SBF has not been demonstrated previously and should be considered when analysing the results of SBF immersion bioactivity tests of such systems. Copyright © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Anomalous finite-size effect due to quasidegenerate phases in triangular antiferromagnets with long-range interactions and mapping to the generalized six-state clock model

NASA Astrophysics Data System (ADS)

Nishino, Masamichi; Miyashita, Seiji

2016-11-01

The effect of long-range (LR) interactions on frustrated-spin models is an interesting problem, which provides rich ordering processes. We study the effect of LR interactions on triangular Ising antiferromagnets with the next-nearest-neighbor ferromagnetic interaction (TIAFF). In the thermodynamic limit, the LRTIAFF model should reproduce the corresponding mean-field results, in which successive phase transitions occur among various phases, i.e., the disordered paramagnetic phase, so-called partially disordered phase, three-sublattice ferrimagnetic phase, and two-sublattice ferrimagnetic phase. In the present paper we focus on the magnetic susceptibility at the transition point between the two-sublattice ferrimagnetic and the disordered paramagnetic phases at relatively large ferromagnetic interactions. In the mean-field analysis, the magnetic susceptibility shows no divergence at the transition point. In contrast, a divergencelike enhancement of the susceptibility is observed in Monte Carlo simulations in finite-size systems. We investigate the origin of this difference and find that it is attributed to a virtual degeneracy of the free energies of the partially disordered and 2-FR phases. We also exploit a generalized six-state clock model with an LR interaction, which is a more general system with Z6 symmetry. We discuss the phase diagram of this model and find that it exhibits richer transition patterns and contains the physics of the LRTIAFF model.

Observation of human tissue with phase-contrast x-ray computed tomography

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji; Tu, Jinhong; Hirano, Keiichi

1999-05-01

Human tissues obtained from cancerous kidneys fixed in formalin were observed with phase-contrast X-ray computed tomography (CT) using 17.7-keV synchrotron X-rays. By measuring the distributions of the X-ray phase shift caused by samples using an X-ray interferometer, sectional images that map the distribution of the refractive index were reconstructed. Because of the high sensitivity of phase- contrast X-ray CT, a cancerous lesion was differentiated from normal tissue and a variety of other structures were revealed without the need for staining.

Analysis of speckle patterns in phase-contrast images of lung tissue

NASA Astrophysics Data System (ADS)

Kitchen, M. J.; Paganin, D.; Lewis, R. A.; Yagi, N.; Uesugi, K.

2005-08-01

Propagation-based phase-contrast images of mice lungs have been obtained at the SPring-8 synchrotron research facility. Such images exhibit a speckled intensity pattern that bears a superficial resemblance to alveolar structures. This speckle results from focussing effects as projected air-filled alveoli form aberrated compound refractive lenses. An appropriate phase-retrieval algorithm has been utilized to reconstruct the approximate projected lung tissue thickness from single-phase-contrast mice chest radiographs. The results show projected density variations across the lung, highlighting regions of low density corresponding to air-filled regions. Potentially, this offers a better method than conventional radiography for detecting lung diseases such as fibrosis, emphysema and cancer, though this has yet to be demonstrated. As such, the approach can assist in continuing studies of lung function utilizing propagation-based phase-contrast imaging.

The effective χ parameter in polarizable polymeric systems: One-loop perturbation theory and field-theoretic simulations.

PubMed

Grzetic, Douglas J; Delaney, Kris T; Fredrickson, Glenn H

2018-05-28

We derive the effective Flory-Huggins parameter in polarizable polymeric systems, within a recently introduced polarizable field theory framework. The incorporation of bead polarizabilities in the model self-consistently embeds dielectric response, as well as van der Waals interactions. The latter generate a χ parameter (denoted χ̃) between any two species with polarizability contrast. Using one-loop perturbation theory, we compute corrections to the structure factor Sk and the dielectric function ϵ^(k) for a polarizable binary homopolymer blend in the one-phase region of the phase diagram. The electrostatic corrections to S(k) can be entirely accounted for by a renormalization of the excluded volume parameter B into three van der Waals-corrected parameters B AA , B AB , and B BB , which then determine χ̃. The one-loop theory not only enables the quantitative prediction of χ̃ but also provides useful insight into the dependence of χ̃ on the electrostatic environment (for example, its sensitivity to electrostatic screening). The unapproximated polarizable field theory is amenable to direct simulation via complex Langevin sampling, which we employ here to test the validity of the one-loop results. From simulations of S(k) and ϵ^(k) for a system of polarizable homopolymers, we find that the one-loop theory is best suited to high concentrations, where it performs very well. Finally, we measure χ̃N in simulations of a polarizable diblock copolymer melt and obtain excellent agreement with the one-loop theory. These constitute the first fully fluctuating simulations conducted within the polarizable field theory framework.

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.

PubMed

Horn, Hans W; Swope, William C; Pitera, Jed W

2005-11-15

The liquid-vapor-phase equilibrium properties of the previously developed TIP4P-Ew water model have been studied using thermodynamic integration free-energy simulation techniques in the temperature range of 274-400 K. We stress that free-energy results from simulations need to be corrected in order to be compared to the experiment. This is due to the fact that the thermodynamic end states accessible through simulations correspond to fictitious substances (classical rigid liquids and classical rigid ideal gases) while experiments operate on real substances (liquids and real gases, with quantum effects). After applying analytical corrections the vapor pressure curve obtained from simulated free-energy changes is in excellent agreement with the experimental vapor pressure curve. The boiling point of TIP4P-Ew water under ambient pressure is found to be at 370.3+/-1.9 K, about 7 K higher than the boiling point of TIP4P water (363.7+/-5.1 K; from simulations that employ finite range treatment of electrostatic and Lennard-Jones interactions). This is in contrast to the approximately +15 K by which the temperature of the density maximum and the melting temperature of TIP4P-Ew are shifted relative to TIP4P, indicating that the temperature range over which the liquid phase of TIP4P-Ew is stable is narrower than that of TIP4P and resembles more that of real water. The quality of the vapor pressure results highlights the success of TIP4P-Ew in describing the energetic and entropic aspects of intermolecular interactions in liquid water.

The effective χ parameter in polarizable polymeric systems: One-loop perturbation theory and field-theoretic simulations

NASA Astrophysics Data System (ADS)

Grzetic, Douglas J.; Delaney, Kris T.; Fredrickson, Glenn H.

2018-05-01

We derive the effective Flory-Huggins parameter in polarizable polymeric systems, within a recently introduced polarizable field theory framework. The incorporation of bead polarizabilities in the model self-consistently embeds dielectric response, as well as van der Waals interactions. The latter generate a χ parameter (denoted χ ˜ ) between any two species with polarizability contrast. Using one-loop perturbation theory, we compute corrections to the structure factor S (k ) and the dielectric function ɛ ^ (k ) for a polarizable binary homopolymer blend in the one-phase region of the phase diagram. The electrostatic corrections to S(k) can be entirely accounted for by a renormalization of the excluded volume parameter B into three van der Waals-corrected parameters BAA, BAB, and BBB, which then determine χ ˜ . The one-loop theory not only enables the quantitative prediction of χ ˜ but also provides useful insight into the dependence of χ ˜ on the electrostatic environment (for example, its sensitivity to electrostatic screening). The unapproximated polarizable field theory is amenable to direct simulation via complex Langevin sampling, which we employ here to test the validity of the one-loop results. From simulations of S(k) and ɛ ^ (k ) for a system of polarizable homopolymers, we find that the one-loop theory is best suited to high concentrations, where it performs very well. Finally, we measure χ ˜ N in simulations of a polarizable diblock copolymer melt and obtain excellent agreement with the one-loop theory. These constitute the first fully fluctuating simulations conducted within the polarizable field theory framework.

Preliminary studies of enhanced contrast radiography in anatomy and embryology of insects with Elettra synchrotron light

NASA Astrophysics Data System (ADS)

Hönnicke, M. G.; Foerster, L. A.; Navarro-Silva, M. A.; Menk, R.-H.; Rigon, L.; Cusatis, C.

2005-08-01

Enhanced contrast X-ray imaging is achieved by exploiting the real part of the refraction index, which is responsible for the phase shifts, in addition to the imaginary part, which is responsible for the absorption. Such techniques are called X-ray phase contrast imaging. An analyzer-based X-ray phase contrast imaging set-up with Diffraction Enhanced Imaging processing (DEI) were used for preliminary studies in anatomy and embryology of insects. Parasitized stinkbug and moth eggs used as control agents of pests in vegetables and adult stinkbugs and mosquitoes ( Aedes aegypti) were used as samples. The experimental setup was mounted in the SYRMEP beamline at ELETTRA. Images were obtained using a high spatial resolution CCD detector (pixel size 14×14 μm 2) coupled with magnifying optics. Analyzer-based X-ray phase contrast images (PCI) and edge detection images show contrast and details not observed with conventional synchrotron radiography and open the possibility for future study in the embryonic development of insects.

Differential phase contrast with a segmented detector in a scanning X-ray microprobe

PubMed Central

Hornberger, B.; de Jonge, M. D.; Feser, M.; Holl, P.; Holzner, C.; Jacobsen, C.; Legnini, D.; Paterson, D.; Rehak, P.; Strüder, L.; Vogt, S.

2008-01-01

Scanning X-ray microprobes are unique tools for the nanoscale investigation of specimens from the life, environmental, materials and other fields of sciences. Typically they utilize absorption and fluorescence as contrast mechanisms. Phase contrast is a complementary technique that can provide strong contrast with reduced radiation dose for weakly absorbing structures in the multi-keV range. In this paper the development of a segmented charge-integrating silicon detector which provides simultaneous absorption and differential phase contrast is reported. The detector can be used together with a fluorescence detector for the simultaneous acquisition of transmission and fluorescence data. It can be used over a wide range of photon energies, photon rates and exposure times at third-generation synchrotron radiation sources, and is currently operating at two beamlines at the Advanced Photon Source. Images obtained at around 2 keV and 10 keV demonstrate the superiority of phase contrast over absorption for specimens composed of light elements. PMID:18552427

In Vitro Validation of an Artefact Suppression Algorithm in X-Ray Phase-Contrast Computed Tomography.

PubMed

Sunaguchi, Naoki; Yuasa, Tetsuya; Hirano, Shin-Ichi; Gupta, Rajiv; Ando, Masami

2015-01-01

X-ray phase-contrast tomography can significantly increase the contrast-resolution of conventional attenuation-contrast imaging, especially for soft-tissue structures that have very similar attenuation. Just as in attenuation-based tomography, phase contrast tomography requires a linear dependence of aggregate beam direction on the incremental direction alteration caused by individual voxels along the path of the X-ray beam. Dense objects such as calcifications in biological specimens violate this condition. There are extensive beam deflection artefacts in the vicinity of such structures because they result in large distortion of wave front due to the large difference of refractive index; for such large changes in beam direction, the transmittance of the silicon analyzer crystal saturates and is no longer linearly dependent on the angle of refraction. This paper describes a method by which these effects can be overcome and excellent soft-tissue contrast of phase tomography can be preserved in the vicinity of such artefact-producing structures.

Compositional and strain analysis of In(Ga)N/GaN short period superlattices

NASA Astrophysics Data System (ADS)

Dimitrakopulos, G. P.; Vasileiadis, I. G.; Bazioti, C.; Smalc-Koziorowska, J.; Kret, S.; Dimakis, E.; Florini, N.; Kehagias, Th.; Suski, T.; Karakostas, Th.; Moustakas, T. D.; Komninou, Ph.

2018-01-01

Extensive high resolution transmission and scanning transmission electron microscopy observations were performed in In(Ga)N/GaN multi-quantum well short period superlattices comprising two-dimensional quantum wells (QWs) of nominal thicknesses 1, 2, and 4 monolayers (MLs) in order to obtain a correlation between their average composition, geometry, and strain. The high angle annular dark field Z-contrast observations were quantified for such layers, regarding the indium content of the QWs, and were correlated to their strain state using peak finding and geometrical phase analysis. Image simulations taking into thorough account the experimental imaging conditions were employed in order to associate the observed Z-contrast to the indium content. Energetically relaxed supercells calculated with a Tersoff empirical interatomic potential were used as the input for such simulations. We found a deviation from the tetragonal distortion prescribed by continuum elasticity for thin films, i.e., the strain in the relaxed cells was lower than expected for the case of 1 ML QWs. In all samples, the QW thickness and strain were confined in up to 2 ML with possible indium enrichment of the immediately abutting MLs. The average composition of the QWs was quantified in the form of alloy content.

Relating Standardized Visual Perception Measures to Simulator Visual System Performance

NASA Technical Reports Server (NTRS)

Kaiser, Mary K.; Sweet, Barbara T.

2013-01-01

Human vision is quantified through the use of standardized clinical vision measurements. These measurements typically include visual acuity (near and far), contrast sensitivity, color vision, stereopsis (a.k.a. stereo acuity), and visual field periphery. Simulator visual system performance is specified in terms such as brightness, contrast, color depth, color gamut, gamma, resolution, and field-of-view. How do these simulator performance characteristics relate to the perceptual experience of the pilot in the simulator? In this paper, visual acuity and contrast sensitivity will be related to simulator visual system resolution, contrast, and dynamic range; similarly, color vision will be related to color depth/color gamut. Finally, we will consider how some characteristics of human vision not typically included in current clinical assessments could be used to better inform simulator requirements (e.g., relating dynamic characteristics of human vision to update rate and other temporal display characteristics).

Contrast enhanced liver MRI in patients with primary sclerosing cholangitis: inverse appearance of focal confluent fibrosis on delayed phase MR images with hepatocyte specific versus extracellular gadolinium based contrast agents.

PubMed

Husarik, Daniela B; Gupta, Rajan T; Ringe, Kristina I; Boll, Daniel T; Merkle, Elmar M

2011-12-01

To assess the enhancement pattern of focal confluent fibrosis (FCF) on contrast-enhanced hepatic magnetic resonance imaging (MRI) using hepatocyte-specific (Gd-EOB-DTPA) and extracellular (ECA) gadolinium-based contrast agents in patients with primary sclerosing cholangitis (PSC). After institutional review board approval, 10 patients with PSC (6 male, 4 female; 33-61 years) with 13 FCF were included in this retrospective study. All patients had a Gd-EOB-DTPA-enhanced liver MRI exam, and a comparison ECA-enhanced MRI. On each T1-weighted dynamic dataset, the signal intensity (SI) of FCF and the surrounding liver as well as the paraspinal muscle (M) were measured. In the Gd-EOB-DTPA group, hepatocyte phase images were also included. SI FCF/SI M, SI liver/SI M, and [(SI liver - SI FCF)/SI liver] were compared between the different contrast agents for each dynamic phase using the paired Student's t-test. There was no significant difference in SI FCF/SI M in all imaging phases. SI liver/SI M was significantly higher for the Gd-EOB-DTPA group in the delayed phase (P < .001), whereas there was no significant difference in all other imaging phases. In the Gd-EOB-DTPA group, mean [(SI liver - SI FCF)/SI liver] were as follows (values for ECA group in parentheses): unenhanced phase: 0.26 (0.26); arterial phase: 0.01 (-0.31); portal venous phase (PVP): -0.05 (-0.26); delayed phase (DP): 0.14 (-0.54); and hepatocyte phase: 0.26. Differences were significant for the DP (P < .001). On delayed phase MR images the FCF-to-liver contrast is reversed with the lesions appearing hyperintense on ECA enhanced images and hypointense on Gd-EOB-DTPA-enhanced images. Copyright © 2011 AUR. Published by Elsevier Inc. All rights reserved.

The Impact of Galactic Winds on the Angular Momentum of Disk Galaxies in the Illustris Simulation

NASA Astrophysics Data System (ADS)

DeFelippis, Daniel; Genel, Shy; Bryan, Greg L.; Fall, S. Michael

2017-05-01

Observed galactic disks have specific angular momenta similar to expectations for typical dark matter halos in ΛCDM. Cosmological hydrodynamical simulations have recently reproduced this similarity in large galaxy samples by including strong galactic winds, but the exact mechanism that achieves this is not yet clear. Here we present an analysis of key aspects contributing to this relation: angular momentum selection and evolution of Lagrangian mass elements as they accrete onto dark matter halos, condense into Milky-Way-scale galaxies, and join the z = 0 stellar phase. We contrast this evolution in the Illustris simulation with that in a simulation without galactic winds, where the z = 0 angular momentum is ≈ 0.6 {dex} lower. We find that winds induce differences between these simulations in several ways: increasing angular momentum, preventing angular momentum loss, and causing z = 0 stars to sample the accretion-time angular momentum distribution of baryons in a biased way. In both simulations, gas loses on average ≈ 0.4 {dex} between accreting onto halos and first accreting onto central galaxies. In Illustris, this is followed by ≈ 0.2 {dex} gains in the “galactic wind fountain” and no further net evolution past the final accretion onto the galaxy. Without feedback, further losses of ≈ 0.2 {dex} occur in the gas phase inside the galaxies. An additional ≈ 0.15 {dex} difference arises from feedback preferentially selecting higher angular momentum gas at accretion by expelling gas that is poorly aligned. These and additional effects of similar magnitude are discussed, suggesting a complex origin of the similarity between the specific angular momenta of galactic disks and typical halos.

Kinetic theory-based numerical modeling and analysis of bi-disperse segregated mixture fluidized bed

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

Konan, N. A.; Huckaby, E. D.

We discuss a series of continuum Euler-Euler simulations of an initially mixed bi-disperse fluidized bed which segregates under certain operating conditions. The simulations use the multi-phase kinetic theory-based description of the momentum and energy exchanges between the phases by Simonin’s Group [see e.g. Gourdel, Simonin and Brunier (1999). Proceedings of 6th International Conference on Circulating Fluidized Beds, Germany, pp. 205-210]. The discussion and analysis of the results focus on the fluid-particle momentum exchange (i.e. drag). Simulations using mono- and poly-disperse fluid-particle drag correlations are analyzed for the Geldart D-type size bi-disperse gas-solid experiments performed by Goldschmidt et al. [Powder Tech.,more » pp. 135-159 (2003)]. The poly-disperse gas-particle drag correlations account for the local particle size distribution by using an effective mixture diameter when calculating the Reynolds number and then correcting the resulting force coefficient. Simulation results show very good predictions of the segregation index for bidisperse beds with the mono-disperse drag correlations contrary to the poly-disperse drag correlations for which the segregation rate is systematically under-predicted. The statistical analysis of the results shows a clear separation in the distribution of the gas-particle mean relaxation times of the small and large particles with simulations using the mono-disperse drag. In contrast, the poly-disperse drag simulations have a significant overlap and also a smaller difference in the mean particle relaxation times. This results in the small and large particles in the bed to respond to the gas similarly without enough relative time lag. The results suggest that the difference in the particle response time induce flow dynamics favorable to a force imbalance which results in the segregation.« less

Kinetic theory-based numerical modeling and analysis of bi-disperse segregated mixture fluidized bed

DOE PAGES

Konan, N. A.; Huckaby, E. D.

2017-06-21

We discuss a series of continuum Euler-Euler simulations of an initially mixed bi-disperse fluidized bed which segregates under certain operating conditions. The simulations use the multi-phase kinetic theory-based description of the momentum and energy exchanges between the phases by Simonin’s Group [see e.g. Gourdel, Simonin and Brunier (1999). Proceedings of 6th International Conference on Circulating Fluidized Beds, Germany, pp. 205-210]. The discussion and analysis of the results focus on the fluid-particle momentum exchange (i.e. drag). Simulations using mono- and poly-disperse fluid-particle drag correlations are analyzed for the Geldart D-type size bi-disperse gas-solid experiments performed by Goldschmidt et al. [Powder Tech.,more » pp. 135-159 (2003)]. The poly-disperse gas-particle drag correlations account for the local particle size distribution by using an effective mixture diameter when calculating the Reynolds number and then correcting the resulting force coefficient. Simulation results show very good predictions of the segregation index for bidisperse beds with the mono-disperse drag correlations contrary to the poly-disperse drag correlations for which the segregation rate is systematically under-predicted. The statistical analysis of the results shows a clear separation in the distribution of the gas-particle mean relaxation times of the small and large particles with simulations using the mono-disperse drag. In contrast, the poly-disperse drag simulations have a significant overlap and also a smaller difference in the mean particle relaxation times. This results in the small and large particles in the bed to respond to the gas similarly without enough relative time lag. The results suggest that the difference in the particle response time induce flow dynamics favorable to a force imbalance which results in the segregation.« less

High resolution laboratory grating-based x-ray phase-contrast CT

NASA Astrophysics Data System (ADS)

Viermetz, Manuel P.; Birnbacher, Lorenz J. B.; Fehringer, Andreas; Willner, Marian; Noel, Peter B.; Pfeiffer, Franz; Herzen, Julia

2017-03-01

Grating-based phase-contrast computed tomography (gbPC-CT) is a promising imaging method for imaging of soft tissue contrast without the need of any contrast agent. The focus of this study is the increase in spatial resolution without loss in sensitivity to allow visualization of pathologies comparable to the convincing results obtained at the synchrotron. To improve the effective pixel size a super-resolution reconstruction based on subpixel shifts involving a deconvolution of the image is applied on differential phase-contrast data. In our study we could achieve an effective pixel sizes of 28mm without any drawback in terms of sensitivity or the ability to measure quantitative data.

Enhanced renal image contrast by ethanol fixation in phase-contrast X-ray computed tomography.

PubMed

Shirai, Ryota; Kunii, Takuya; Yoneyama, Akio; Ooizumi, Takahito; Maruyama, Hiroko; Lwin, Thet Thet; Hyodo, Kazuyuki; Takeda, Tohoru

2014-07-01

Phase-contrast X-ray imaging using a crystal X-ray interferometer can depict the fine structures of biological objects without the use of a contrast agent. To obtain higher image contrast, fixation techniques have been examined with 100% ethanol and the commonly used 10% formalin, since ethanol causes increased density differences against background due to its physical properties and greater dehydration of soft tissue. Histological comparison was also performed. A phase-contrast X-ray system was used, fitted with a two-crystal X-ray interferometer at 35 keV X-ray energy. Fine structures, including cortex, tubules in the medulla, and the vessels of ethanol-fixed kidney could be visualized more clearly than that of formalin-fixed tissues. In the optical microscopic images, shrinkage of soft tissue and decreased luminal space were observed in ethanol-fixed kidney; and this change was significantly shown in the cortex and outer stripe of the outer medulla. The ethanol fixation technique enhances image contrast by approximately 2.7-3.2 times in the cortex and the outer stripe of the outer medulla; the effect of shrinkage and the physical effect of ethanol cause an increment of approximately 78% and 22%, respectively. Thus, the ethanol-fixation technique enables the image contrast to be enhanced in phase-contrast X-ray imaging.

A study on high NA and evanescent imaging with polarized illumination

NASA Astrophysics Data System (ADS)

Yang, Seung-Hune

Simulation techniques are developed for high NA polarized microscopy with Babinet's principle, partial coherence and vector diffraction for non-periodic geometries. A mathematical model for the Babinet approach is developed and interpreted. Simulation results of the Babinet's principle approach are compared with those of Rigorous Coupled Wave Theory (RCWT) for periodic structures to investigate the accuracy of this approach and its limitations. A microscope system using a special solid immersion lens (SIL) is introduced to image Blu-Ray (BD) optical disc samples without removing the protective cover layer. Aberration caused by the cover layer is minimized with a truncated SIL. Sub-surface imaging simulation is achieved by RCWT, partial coherence, vector diffraction and Babinet's Principle. Simulated results are compared with experimental images and atomic force microscopy (AFM) measurement. A technique for obtaining native and induced using a significant amount of evanescent energy is described for a solid immersion lens (SIL) microscope. Characteristics of native and induced polarization images for different object structures and materials are studied in detail. Experiments are conducted with a NA = 1.48 at lambda = 550nm microscope. Near-field images are simulated and analyzed with an RCWT approach. Contrast curve versus object spatial frequency calculations are compared with experimental measurements. Dependencies of contrast versus source polarization angles and air gap for native and induced polarization image profiles are evaluated. By using the relationship between induced polarization and topographical structure, an induced polarization image of an alternating phase shift mask (PSM) is converted into a topographical image, which shows very good agreement with AFM measurement. Images of other material structures include a dielectric grating, chrome-on-glass grating, silicon CPU structure, BD-R and BD-ROM.

Constraining ammonia dairy emissions during NASA DISCOVER-AQ California: surface and airborne observation comparisons with CMAQ simulations

NASA Astrophysics Data System (ADS)

Miller, D. J.; Liu, Z.; Sun, K.; Tao, L.; Nowak, J. B.; Bambha, R.; Michelsen, H. A.; Zondlo, M. A.

2014-12-01

Agricultural ammonia (NH3) emissions are highly uncertain in current bottom-up inventories. Ammonium nitrate is a dominant component of fine aerosols in agricultural regions such as the Central Valley of California, especially during winter. Recent high resolution regional modeling efforts in this region have found significant ammonium nitrate and gas-phase NH3 biases during summer. We compare spatially-resolved surface and boundary layer gas-phase NH3 observations during NASA DISCOVER-AQ California with Community Multi-Scale Air Quality (CMAQ) regional model simulations driven by the EPA NEI 2008 inventory to constrain wintertime NH3 model biases. We evaluate model performance with respect to aerosol partitioning, mixing and deposition to constrain contributions to modeled NH3 concentration biases in the Central Valley Tulare dairy region. Ammonia measurements performed with an open-path mobile platform on a vehicle are gridded to 4 km resolution hourly background concentrations. A peak detection algorithm is applied to remove local feedlot emission peaks. Aircraft NH3, NH4+ and NO3- observations are also compared with simulations extracted along the flight tracks. We find NH3 background concentrations in the dairy region are underestimated by three to five times during winter and NH3 simulations are moderately correlated with observations (r = 0.36). Although model simulations capture NH3 enhancements in the dairy region, these simulations are biased low by 30-60 ppbv NH3. Aerosol NH4+ and NO3- are also biased low in CMAQ by three and four times respectively. Unlike gas-phase NH3, CMAQ simulations do not capture typical NH4+ or NO3- enhancements observed in the dairy region. In contrast, boundary layer height simulations agree well with observations within 13%. We also address observational constraints on simulated NH3 deposition fluxes. These comparisons suggest that NEI 2008 wintertime dairy emissions are underestimated by a factor of three to five. We test sensitivity to emissions by increasing the NEI 2008 NH3 emissions uniformly across the dairy region and evaluate the impact on modeled concentrations. These results are applicable to improving predictions of ammoniated aerosol loading and highlight the value of mobile platform spatial NH3 measurements to constrain emission inventories.

Aerosol-cloud interactions in mixed-phase convective clouds - Part 1: Aerosol perturbations

NASA Astrophysics Data System (ADS)

Miltenberger, Annette K.; Field, Paul R.; Hill, Adrian A.; Rosenberg, Phil; Shipway, Ben J.; Wilkinson, Jonathan M.; Scovell, Robert; Blyth, Alan M.

2018-03-01

Changes induced by perturbed aerosol conditions in moderately deep mixed-phase convective clouds (cloud top height ˜ 5 km) developing along sea-breeze convergence lines are investigated with high-resolution numerical model simulations. The simulations utilise the newly developed Cloud-AeroSol Interacting Microphysics (CASIM) module for the Unified Model (UM), which allows for the representation of the two-way interaction between cloud and aerosol fields. Simulations are evaluated against observations collected during the COnvective Precipitation Experiment (COPE) field campaign over the southwestern peninsula of the UK in 2013. The simulations compare favourably with observed thermodynamic profiles, cloud base cloud droplet number concentrations (CDNC), cloud depth, and radar reflectivity statistics. Including the modification of aerosol fields by cloud microphysical processes improves the correspondence with observed CDNC values and spatial variability, but reduces the agreement with observations for average cloud size and cloud top height. Accumulated precipitation is suppressed for higher-aerosol conditions before clouds become organised along the sea-breeze convergence lines. Changes in precipitation are smaller in simulations with aerosol processing. The precipitation suppression is due to less efficient precipitation production by warm-phase microphysics, consistent with parcel model predictions. In contrast, after convective cells organise along the sea-breeze convergence zone, accumulated precipitation increases with aerosol concentrations. Condensate production increases with the aerosol concentrations due to higher vertical velocities in the convective cores and higher cloud top heights. However, for the highest-aerosol scenarios, no further increase in the condensate production occurs, as clouds grow into an upper-level stable layer. In these cases, the reduced precipitation efficiency (PE) dominates the precipitation response and no further precipitation enhancement occurs. Previous studies of deep convective clouds have related larger vertical velocities under high-aerosol conditions to enhanced latent heating from freezing. In the presented simulations changes in latent heating above the 0°C are negligible, but latent heating from condensation increases with aerosol concentrations. It is hypothesised that this increase is related to changes in the cloud field structure reducing the mixing of environmental air into the convective core. The precipitation response of the deeper mixed-phase clouds along well-established convergence lines can be the opposite of predictions from parcel models. This occurs when clouds interact with a pre-existing thermodynamic environment and cloud field structural changes occur that are not captured by simple parcel model approaches.

A New Concept of Coronagraph using Axicon Lenses

NASA Astrophysics Data System (ADS)

Choi, Jae Ho

2017-06-01

High-contrast direct imaging of faint objects nearby bright stellar is essential to investigate planetary systems. The goal of such effort is to find and characterize planets similar to Earth that is a challenging task due to it requires a high angular resolution and high dynamic range detections concurrently. A coronagraph that can be suppressed the bright stellar light or active galactic nuclei during the direct detection of astrophysical activities became one of the essential instruments to image exoplanets. In this presentation, a novel concept of a coronagraph using axicon-lenses is will be presented that is conjunction with a method of noninterferometric quantitative phase imaging for direct imaging of exoplanets. The essential scheme of the axicon-lenses coronagraph is the apodization carried out by excluding evaginated images of the planetary systems by a pair of axicon lens. The laboratory based coronagraph imaging is carried out with the axicon-lenses coronagraph setup which included the axicon lenses optics and phase contrast imaging unit. A simulated stellar and its companion are provided by illuminating light through small holes drilled on a thin metal plate. Those diffracted light at the edge of the holes bears a similarity to the light from the bright stellar. The images are evaginated about the optical axis by passing the first axicon lens. Then the evaginated beams of its external area have cut off by an iris which means the suppressed its central light of the bright stellar light preferentially. A symbolic calculation also is carried out to verify the scheme of the the axicon-lenses coronagraph using the symbolic computation program. The simulation results are shown that the the axicon-lenses coronagraph has feature of ability to achieve the IWA smaller than l/D. The laboratory based coronagraph imaging and simulation results support its potentials in direct imaging for finding exo-planet and various astrophysical activities.

Comparison of 4D Phase-Contrast MRI Flow Measurements to Computational Fluid Dynamics Simulations of Cerebrospinal Fluid Motion in the Cervical Spine

PubMed Central

Yiallourou, Theresia I.; Kröger, Jan Robert; Stergiopulos, Nikolaos; Maintz, David

2012-01-01

Cerebrospinal fluid (CSF) dynamics in the cervical spinal subarachnoid space (SSS) have been thought to be important to help diagnose and assess craniospinal disorders such as Chiari I malformation (CM). In this study we obtained time-resolved three directional velocity encoded phase-contrast MRI (4D PC MRI) in three healthy volunteers and four CM patients and compared the 4D PC MRI measurements to subject-specific 3D computational fluid dynamics (CFD) simulations. The CFD simulations considered the geometry to be rigid-walled and did not include small anatomical structures such as nerve roots, denticulate ligaments and arachnoid trabeculae. Results were compared at nine axial planes along the cervical SSS in terms of peak CSF velocities in both the cranial and caudal direction and visual interpretation of thru-plane velocity profiles. 4D PC MRI peak CSF velocities were consistently greater than the CFD peak velocities and these differences were more pronounced in CM patients than in healthy subjects. In the upper cervical SSS of CM patients the 4D PC MRI quantified stronger fluid jets than the CFD. Visual interpretation of the 4D PC MRI thru-plane velocity profiles showed greater pulsatile movement of CSF in the anterior SSS in comparison to the posterior and reduction in local CSF velocities near nerve roots. CFD velocity profiles were relatively uniform around the spinal cord for all subjects. This study represents the first comparison of 4D PC MRI measurements to CFD of CSF flow in the cervical SSS. The results highlight the utility of 4D PC MRI for evaluation of complex CSF dynamics and the need for improvement of CFD methodology. Future studies are needed to investigate whether integration of fine anatomical structures and gross motion of the brain and/or spinal cord into the computational model will lead to a better agreement between the two techniques. PMID:23284970

Constructing local integrals of motion in the many-body localized phase

NASA Astrophysics Data System (ADS)

Chandran, Anushya; Kim, Isaac H.; Vidal, Guifre; Abanin, Dmitry A.

2015-02-01

Many-body localization provides a generic mechanism of ergodicity breaking in quantum systems. In contrast to conventional ergodic systems, many-body-localized (MBL) systems are characterized by extensively many local integrals of motion (LIOM), which underlie the absence of transport and thermalization in these systems. Here we report a physically motivated construction of local integrals of motion in the MBL phase. We show that any local operator (e.g., a local particle number or a spin-flip operator), evolved with the system's Hamiltonian and averaged over time, becomes a LIOM in the MBL phase. Such operators have a clear physical meaning, describing the response of the MBL system to a local perturbation. In particular, when a local operator represents a density of some globally conserved quantity, the corresponding LIOM describes how this conserved quantity propagates through the MBL phase. Being uniquely defined and experimentally measurable, these LIOMs provide a natural tool for characterizing the properties of the MBL phase, in both experiments and numerical simulations. We demonstrate the latter by numerically constructing an extensive set of LIOMs in the MBL phase of a disordered spin-chain model. We show that the resulting LIOMs are quasilocal and use their decay to extract the localization length and establish the location of the transition between the MBL and ergodic phases.

Focal-plane electric field sensing with pupil-plane holograms

NASA Astrophysics Data System (ADS)

Por, Emiel H.; Keller, Christoph U.

2016-07-01

The direct detection and spectral characterization of exoplanets requires a coronagraph to suppress the diffracted star light. Amplitude and phase aberrations in the optical train fill the dark zone of the coronagraph with quasi-static speckles that limit the achievable contrast. Focal-plane electric field sensing, such as phase diversity introduced by a deformable mirror (DM), is a powerful tool to minimize this residual star light. The residual electric field can be estimated by sequentially applying phase probes on the DM to inject star light with a well-known amplitude and phase into the dark zone and analyzing the resulting intensity images. The DM can then be used to add light with the same amplitude but opposite phase to destructively interfere with this residual star light. Using a static phase-only pupil-plane element we create holographic copies of the point spread function (PSF), each superimposed with a certain pupil-plane phase probe. We therefore obtain all intensity images simultaneously while still retaining a central, unaltered science PSF. The electric field sensing method only makes use of the holographic copies, allowing for correction of the residual electric field while retaining the central PSF for uninterrupted science data collection. In this paper we demonstrate the feasibility of this method with numerical simulations.

Longitudinal design considerations to optimize power to detect variances and covariances among rates of change: Simulation results based on actual longitudinal studies

PubMed Central

Rast, Philippe; Hofer, Scott M.

2014-01-01

We investigated the power to detect variances and covariances in rates of change in the context of existing longitudinal studies using linear bivariate growth curve models. Power was estimated by means of Monte Carlo simulations. Our findings show that typical longitudinal study designs have substantial power to detect both variances and covariances among rates of change in a variety of cognitive, physical functioning, and mental health outcomes. We performed simulations to investigate the interplay among number and spacing of occasions, total duration of the study, effect size, and error variance on power and required sample size. The relation between growth rate reliability (GRR) and effect size to the sample size required to detect power ≥ .80 was non-linear, with rapidly decreasing sample sizes needed as GRR increases. The results presented here stand in contrast to previous simulation results and recommendations (Hertzog, Lindenberger, Ghisletta, & von Oertzen, 2006; Hertzog, von Oertzen, Ghisletta, & Lindenberger, 2008; von Oertzen, Ghisletta, & Lindenberger, 2010), which are limited due to confounds between study length and number of waves, error variance with GCR, and parameter values which are largely out of bounds of actual study values. Power to detect change is generally low in the early phases (i.e. first years) of longitudinal studies but can substantially increase if the design is optimized. We recommend additional assessments, including embedded intensive measurement designs, to improve power in the early phases of long-term longitudinal studies. PMID:24219544

X-ray phase contrast imaging of biological specimens with femtosecond pulses of betatron radiation from a compact laser plasma wakefield accelerator

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

Kneip, S.; Center for Ultrafast Optical Science, University of Michigan, Ann Arbor 48109; McGuffey, C.

2011-08-29

We show that x-rays from a recently demonstrated table top source of bright, ultrafast, coherent synchrotron radiation [Kneip et al., Nat. Phys. 6, 980 (2010)] can be applied to phase contrast imaging of biological specimens. Our scheme is based on focusing a high power short pulse laser in a tenuous gas jet, setting up a plasma wakefield accelerator that accelerates and wiggles electrons analogously to a conventional synchrotron, but on the centimeter rather than tens of meter scale. We use the scheme to record absorption and phase contrast images of a tetra fish, damselfly and yellow jacket, in particular highlightingmore » the contrast enhancement achievable with the simple propagation technique of phase contrast imaging. Coherence and ultrafast pulse duration will allow for the study of various aspects of biomechanics.« less

Flash Infrared Thermography Contrast Data Analysis Technique

NASA Technical Reports Server (NTRS)

Koshti, Ajay

2014-01-01

This paper provides information on an IR Contrast technique that involves extracting normalized contrast versus time evolutions from the flash thermography inspection infrared video data. The analysis calculates thermal measurement features from the contrast evolution. In addition, simulation of the contrast evolution is achieved through calibration on measured contrast evolutions from many flat-bottom holes in the subject material. The measurement features and the contrast simulation are used to evaluate flash thermography data in order to characterize delamination-like anomalies. The thermal measurement features relate to the anomaly characteristics. The contrast evolution simulation is matched to the measured contrast evolution over an anomaly to provide an assessment of the anomaly depth and width which correspond to the depth and diameter of the equivalent flat-bottom hole (EFBH) similar to that used as input to the simulation. A similar analysis, in terms of diameter and depth of an equivalent uniform gap (EUG) providing a best match with the measured contrast evolution, is also provided. An edge detection technique called the half-max is used to measure width and length of the anomaly. Results of the half-max width and the EFBH/EUG diameter are compared to evaluate the anomaly. The information provided here is geared towards explaining the IR Contrast technique. Results from a limited amount of validation data on reinforced carbon-carbon (RCC) hardware are included in this paper.

Invited Review Article: Methods for imaging weak-phase objects in electron microscopy

PubMed Central

Glaeser, Robert M.

2013-01-01

Contrast has traditionally been produced in electron-microscopy of weak phase objects by simply defocusing the objective lens. There now is renewed interest, however, in using devices that apply a uniform quarter-wave phase shift to the scattered electrons relative to the unscattered beam, or that generate in-focus image contrast in some other way. Renewed activity in making an electron-optical equivalent of the familiar “phase-contrast” light microscope is based in part on the improved possibilities that are now available for device microfabrication. There is also a better understanding that it is important to take full advantage of contrast that can be had at low spatial frequency when imaging large, macromolecular objects. In addition, a number of conceptually new phase-plate designs have been proposed, thus increasing the number of options that are available for development. The advantages, disadvantages, and current status of each of these options is now compared and contrasted. Experimental results that are, indeed, superior to what can be accomplished with defocus-based phase contrast have been obtained recently with two different designs of phase-contrast aperture. Nevertheless, extensive work also has shown that fabrication of such devices is inconsistent, and that their working lifetime is short. The main limitation, in fact, appears to be electrostatic charging of any device that is placed into the electron diffraction pattern. The challenge in fabricating phase plates that are practical to use for routine work in electron microscopy thus may be more in the area of materials science than in the area of electron optics. PMID:24289381

Chiral anomaly, Berry phase, and chiral kinetic theory from worldlines in quantum field theory

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

Mueller, Niklas; Venugopalan, Raju

Here, we outline a novel chiral kinetic theory framework for systematic computations of the Chiral Magnetic Effect (CME) in ultrarelativistic heavy-ion collisions. The real part of the fermion determinant in the QCD effective action is expressed as a supersymmetric world-line action of spinning, colored, Grassmanian point particles in background gauge fields, with equations of motion that are covariant generalizations of the Bargmann-Michel-Telegdi and Wong equations. Berry’s phase is obtained in a consistent non-relativistic adiabatic limit. The chiral anomaly, in contrast, arises from the phase of the fermion determinant; its topological properties are therefore distinct from those of the Berry phase.more » We show that the imaginary contribution to the fermion determinant too can be expressed as a point particle world-line path integral and derive the corresponding anomalous axial vector current. Our results can be used to derive a covariant relativistic chiral kinetic theory including the effects of topological fluctuations that has overlap with classical-statistical simulations of the CME at early times and anomalous hydrodynamics at late times.« less

Chiral anomaly, Berry phase, and chiral kinetic theory from worldlines in quantum field theory

DOE PAGES

Mueller, Niklas; Venugopalan, Raju

2018-03-21

Here, we outline a novel chiral kinetic theory framework for systematic computations of the Chiral Magnetic Effect (CME) in ultrarelativistic heavy-ion collisions. The real part of the fermion determinant in the QCD effective action is expressed as a supersymmetric world-line action of spinning, colored, Grassmanian point particles in background gauge fields, with equations of motion that are covariant generalizations of the Bargmann-Michel-Telegdi and Wong equations. Berry’s phase is obtained in a consistent non-relativistic adiabatic limit. The chiral anomaly, in contrast, arises from the phase of the fermion determinant; its topological properties are therefore distinct from those of the Berry phase.more » We show that the imaginary contribution to the fermion determinant too can be expressed as a point particle world-line path integral and derive the corresponding anomalous axial vector current. Our results can be used to derive a covariant relativistic chiral kinetic theory including the effects of topological fluctuations that has overlap with classical-statistical simulations of the CME at early times and anomalous hydrodynamics at late times.« less

Focusing light through scattering media by polarization modulation based generalized digital optical phase conjugation

NASA Astrophysics Data System (ADS)

Yang, Jiamiao; Shen, Yuecheng; Liu, Yan; Hemphill, Ashton S.; Wang, Lihong V.

2017-11-01

Optical scattering prevents light from being focused through thick biological tissue at depths greater than ˜1 mm. To break this optical diffusion limit, digital optical phase conjugation (DOPC) based wavefront shaping techniques are being actively developed. Previous DOPC systems employed spatial light modulators that modulated either the phase or the amplitude of the conjugate light field. Here, we achieve optical focusing through scattering media by using polarization modulation based generalized DOPC. First, we describe an algorithm to extract the polarization map from the measured scattered field. Then, we validate the algorithm through numerical simulations and find that the focusing contrast achieved by polarization modulation is similar to that achieved by phase modulation. Finally, we build a system using an inexpensive twisted nematic liquid crystal based spatial light modulator (SLM) and experimentally demonstrate light focusing through 3-mm thick chicken breast tissue. Since the polarization modulation based SLMs are widely used in displays and are having more and more pixel counts with the prevalence of 4 K displays, these SLMs are inexpensive and valuable devices for wavefront shaping.

X-ray phase contrast tomography by tracking near field speckle

PubMed Central

Wang, Hongchang; Berujon, Sebastien; Herzen, Julia; Atwood, Robert; Laundy, David; Hipp, Alexander; Sawhney, Kawal

2015-01-01

X-ray imaging techniques that capture variations in the x-ray phase can yield higher contrast images with lower x-ray dose than is possible with conventional absorption radiography. However, the extraction of phase information is often more difficult than the extraction of absorption information and requires a more sophisticated experimental arrangement. We here report a method for three-dimensional (3D) X-ray phase contrast computed tomography (CT) which gives quantitative volumetric information on the real part of the refractive index. The method is based on the recently developed X-ray speckle tracking technique in which the displacement of near field speckle is tracked using a digital image correlation algorithm. In addition to differential phase contrast projection images, the method allows the dark-field images to be simultaneously extracted. After reconstruction, compared to conventional absorption CT images, the 3D phase CT images show greatly enhanced contrast. This new imaging method has advantages compared to other X-ray imaging methods in simplicity of experimental arrangement, speed of measurement and relative insensitivity to beam movements. These features make the technique an attractive candidate for material imaging such as in-vivo imaging of biological systems containing soft tissue. PMID:25735237

Simple broadband implementation of a phase contrast wavefront sensor for adaptive optics

NASA Technical Reports Server (NTRS)

Bloemhof, E. E.; Wallace, J. K.

2004-01-01

The most critical element of an adaptive optics system is its wavefront sensor, which must measure the closed-loop difference between the corrected wavefront and an ideal template at high speed, in real time, over a dense sampling of the pupil. Most high-order systems have used Shack-Hartmann wavefront sensors, but a novel approach based on Zernike's phase contrast principle appears promising. In this paper we discuss a simple way to achromatize such a phase contrast wavefront sensor, using the pi/2 phase difference between reflected and transmitted rays in a thin, symmetric beam splitter. We further model the response at a range of wavelengths to show that the required transverse dimension of the focal-plane phase-shifting spot, nominally lambda/D, may not be very sensitive to wavelength, and so in practice additional optics to introduce wavelength-dependent transverse magnification achromatizing this spot diameter may not be required. A very simple broadband implementation of the phase contrast wavefront sensor results.

High-Fidelity Contrast Reaction Simulation Training: Performance Comparison of Faculty, Fellows, and Residents.

PubMed

Pfeifer, Kyle; Staib, Lawrence; Arango, Jennifer; Kirsch, John; Arici, Mel; Kappus, Liana; Pahade, Jay

2016-01-01

Reactions to contrast material are uncommon in diagnostic radiology, and vary in clinical presentation from urticaria to life-threatening anaphylaxis. Prior studies have demonstrated a high error rate in contrast reaction management, with smaller studies using simulation demonstrating variable data on effectiveness. We sought to assess the effectiveness of high-fidelity simulation in teaching contrast reaction management for residents, fellows, and attendings. A 20-question multiple-choice test assessing contrast reaction knowledge, with Likert-scale questions assessing subjective comfort levels of management of contrast reactions, was created. Three simulation scenarios that represented a moderate reaction, a severe reaction, and a contrast reaction mimic were completed in a one-hour period in a simulation laboratory. All participants completed a pretest and a posttest at one month. A six-month delayed posttest was given, but was optional for all participants. A total of 150 radiologists participated (residents = 52; fellows = 24; faculty = 74) in the pretest and posttest; and 105 participants completed the delayed posttest (residents = 31; fellows = 17; faculty = 57). A statistically significant increase was found in the one-month posttest (P < .00001) and the six-month posttest scores (P < .00001) and Likert scores (P < .001) assessing comfort level in managing all contrast reactions, compared with the pretest. Test scores and comfort level for moderate and severe reactions significantly decreased at six months, compared with the one-month posttest (P < .05). High-fidelity simulation is an effective learning tool, allowing practice of "high-acuity" situation management in a nonthreatening environment; the simulation training resulted in significant improvement in test scores, as well as an increase in subjective comfort in management of reactions, across all levels of training. A six-month refresher course is suggested, to maintain knowledge and comfort level in contrast reaction management. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Simulation, Design, and Test of Square, Apodized Photon Sieves for High Contrast, Exoplanet Imaging

DTIC Science & Technology

reason, square apodized photon sieves were simulated, designed, and tested for high-contrast performance and use in an exoplanet imaging telescope...for apodizing sieves, measuring PSFs, and characterizing high-contrast performance. Tests indicated that square apodized sieves could detect

Recent advances in synchrotron-based hard x-ray phase contrast imaging

NASA Astrophysics Data System (ADS)

Liu, Y.; Nelson, J.; Holzner, C.; Andrews, J. C.; Pianetta, P.

2013-12-01

Ever since the first demonstration of phase contrast imaging (PCI) in the 1930s by Frits Zernike, people have realized the significant advantage of phase contrast over conventional absorption-based imaging in terms of sensitivity to ‘transparent’ features within specimens. Thus, x-ray phase contrast imaging (XPCI) holds great potential in studies of soft biological tissues, typically containing low Z elements such as C, H, O and N. Particularly when synchrotron hard x-rays are employed, the favourable brightness, energy tunability, monochromatic characteristics and penetration depth have dramatically enhanced the quality and variety of XPCI methods, which permit detection of the phase shift associated with 3D geometry of relatively large samples in a non-destructive manner. In this paper, we review recent advances in several synchrotron-based hard x-ray XPCI methods. Challenges and key factors in methodological development are discussed, and biological and medical applications are presented.

Tribological Properties of AlCrCuFeNi2 High-Entropy Alloy in Different Conditions

NASA Astrophysics Data System (ADS)

Liu, Yong; Ma, Shengguo; Gao, Michael C.; Zhang, Chuan; Zhang, Teng; Yang, Huijun; Wang, Zhihua; Qiao, Junwei

2016-07-01

In order to understand the environmental effect on the mechanical behavior of high-entropy alloys, the tribological properties of AlCrCuFeNi2 are studied systematically in dry, simulated rainwater, and deionized water conditions against the Si3N4 ceramic ball at a series of different normal loads. The present study shows that both the friction and wear rate in simulated rainwater are the lowest. The simulated rainwater plays a significant role in the tribological behavior with the effect of forming passive film, lubricating, cooling, cleaning, and corrosion. The wear mechanism in simulated rainwater is mainly adhesive wear accompanied by abrasive wear as well as corrosive wear. In contrast, those in dry condition and deionized water are abrasive wear, adhesive wear, and surface plastic deformation. Oxidation contributes to the wear behavior in dry condition but is prevented in liquid condition. In addition, the phase diagram of Al x CrCuFeNi2 is predicted using CALPHAD modeling, which is in good agreement with the literature report and the present study.

Computational carbohydrate chemistry: what theoretical methods can tell us

PubMed Central

Woods, Robert J.

2014-01-01

Computational methods have had a long history of application to carbohydrate systems and their development in this regard is discussed. The conformational analysis of carbohydrates differs in several ways from that of other biomolecules. Many glycans appear to exhibit numerous conformations coexisting in solution at room temperature and a conformational analysis of a carbohydrate must address both spatial and temporal properties. When solution nuclear magnetic resonance data are used for comparison, the simulation must give rise to ensemble-averaged properties. In contrast, when comparing to experimental data obtained from crystal structures a simulation of a crystal lattice, rather than of an isolated molecule, is appropriate. Molecular dynamics simulations are well suited for such condensed phase modeling. Interactions between carbohydrates and other biological macromolecules are also amenable to computational approaches. Having obtained a three-dimensional structure of the receptor protein, it is possible to model with accuracy the conformation of the carbohydrate in the complex. An example of the application of free energy perturbation simulations to the prediction of carbohydrate-protein binding energies is presented. PMID:9579797

An Analytical-Numerical Model for Two-Phase Slug Flow through a Sudden Area Change in Microchannels

DOE PAGES

Momen, A. Mehdizadeh; Sherif, S. A.; Lear, W. E.

2016-01-01

In this article, two new analytical models have been developed to calculate two-phase slug flow pressure drop in microchannels through a sudden contraction. Even though many studies have been reported on two-phase flow in microchannels, considerable discrepancies still exist, mainly due to the difficulties in experimental setup and measurements. Numerical simulations were performed to support the new analytical models and to explore in more detail the physics of the flow in microchannels with a sudden contraction. Both analytical and numerical results were compared to the available experimental data and other empirical correlations. Results show that models, which were developed basedmore » on the slug and semi-slug assumptions, agree well with experiments in microchannels. Moreover, in contrast to the previous empirical correlations which were tuned for a specific geometry, the new analytical models are capable of taking geometrical parameters as well as flow conditions into account.« less

Third order harmonic imaging for biological tissues using three phase-coded pulses.

PubMed

Ma, Qingyu; Gong, Xiufen; Zhang, Dong

2006-12-22

Compared to the fundamental and the second harmonic imaging, the third harmonic imaging shows significant improvements in image quality due to the better resolution, but it is degraded by the lower sound pressure and signal-to-noise ratio (SNR). In this study, a phase-coded pulse technique is proposed to selectively enhance the sound pressure of the third harmonic by 9.5 dB whereas the fundamental and the second harmonic components are efficiently suppressed and SNR is also increased by 4.7 dB. Based on the solution of the KZK nonlinear equation, the axial and lateral beam profiles of harmonics radiated from a planar piston transducer were theoretically simulated and experimentally examined. Finally, the third harmonic images using this technique were performed for several biological tissues and compared with the images obtained by the fundamental and the second harmonic imaging. Results demonstrate that the phase-coded pulse technique yields a dramatically cleaner and sharper contrast image.

Threefold rotational symmetry in hexagonally shaped core-shell (In,Ga)As/GaAs nanowires revealed by coherent X-ray diffraction imaging.

PubMed

Davtyan, Arman; Krause, Thilo; Kriegner, Dominik; Al-Hassan, Ali; Bahrami, Danial; Mostafavi Kashani, Seyed Mohammad; Lewis, Ryan B; Küpers, Hanno; Tahraoui, Abbes; Geelhaar, Lutz; Hanke, Michael; Leake, Steven John; Loffeld, Otmar; Pietsch, Ullrich

2017-06-01

Coherent X-ray diffraction imaging at symmetric hhh Bragg reflections was used to resolve the structure of GaAs/In 0.15 Ga 0.85 As/GaAs core-shell-shell nanowires grown on a silicon (111) substrate. Diffraction amplitudes in the vicinity of GaAs 111 and GaAs 333 reflections were used to reconstruct the lost phase information. It is demonstrated that the structure of the core-shell-shell nanowire can be identified by means of phase contrast. Interestingly, it is found that both scattered intensity in the (111) plane and the reconstructed scattering phase show an additional threefold symmetry superimposed with the shape function of the investigated hexagonal nanowires. In order to find the origin of this threefold symmetry, elasticity calculations were performed using the finite element method and subsequent kinematic diffraction simulations. These suggest that a non-hexagonal (In,Ga)As shell covering the hexagonal GaAs core might be responsible for the observation.

The chimera state in colloidal phase oscillators with hydrodynamic interaction

NASA Astrophysics Data System (ADS)

Hamilton, Evelyn; Bruot, Nicolas; Cicuta, Pietro

2017-12-01

The chimera state is the incongruous situation where coherent and incoherent populations coexist in sets of identical oscillators. Using driven non-linear oscillators interacting purely through hydrodynamic forces at low Reynolds number, previously studied as a simple model of motile cilia supporting waves, we find concurrent incoherent and synchronised subsets in small arrays. The chimeras seen in simulation display a "breathing" aspect, reminiscent of uniformly interacting phase oscillators. In contrast to other systems where chimera has been observed, this system has a well-defined interaction metric, and we know that the emergent dynamics inherit the symmetry of the underlying Oseen tensor eigenmodes. The chimera state can thus be connected to a superposition of eigenstates, whilst considering the mean interaction strength within and across subsystems allows us to make a connection to more generic (and abstract) chimeras in populations of Kuramoto phase oscillators. From this work, we expect the chimera state to emerge in experimental observations of oscillators coupled through hydrodynamic forces.

Research on Robust Control Strategies for VSC-HVDC

NASA Astrophysics Data System (ADS)

Zhu, Kaicheng; Bao, Hai

2018-01-01

In the control system of VSC-HVDC, the phase locked loop provides phase signals to voltage vector control and trigger pulses to generate the required reference phase. The PLL is a typical second-order system. When the system is in unstable state, it will oscillate, make the trigger angle shift, produce harmonic, and make active power and reactive power coupled. Thus, considering the external disturbances introduced by the PLL in VSC-HVDC control system, the parameter perturbations of the controller and the model uncertainties, a H∞ robust controller of mixed sensitivity optimization problem is designed by using the Hinf function provided by the robust control toolbox. Then, compare it with the proportional integral controller through the MATLAB simulation experiment. By contrast, when the H∞ robust controller is added, active and reactive power of the converter station can track the change of reference values more accurately and quickly, and reduce overshoot. When the step change of active and reactive power occurs, mutual influence is reduced and better independent regulation is achieved.

Nonlinearity in the rotational dynamics of Haidinger's brushes

NASA Astrophysics Data System (ADS)

Rothmayer, Mark; Dultz, Wolfgang; Frins, Erna; Zhan, Qiwen; Tierney, Dennis; Schmitzer, Heidrun

2007-10-01

Haidinger's brushes are an entoptic effect of the human visual system that enables us to detect polarized light. However, individual perceptions of Haidinger's brushes can vary significantly. We find that the birefringence of the cornea influences the rotational motion and the contrast of Haidinger's brushes and may offer an explanation for individual differences. We have devised an experimental setup to simulate various phase shifts of the cornea and found a switching effect in the rotational dynamics of Haidinger's brushes. In addition, age related macular degeneration reduces the polarization effect of the macula and thus also leads to changes in the brush pattern.

How many photons are needed to reconstruct random objects in coherent X-ray diffractive imaging?

PubMed

Jahn, T; Wilke, R N; Chushkin, Y; Salditt, T

2017-01-01

This paper presents an investigation of the reconstructibility of coherent X-ray diffractive imaging diffraction patterns for a class of binary random `bitmap' objects. Combining analytical results and numerical simulations, the critical fluence per bitmap pixel is determined, for arbitrary contrast values (absorption level and phase shift), both for the optical near- and far-field. This work extends previous investigations based on information theory, enabling a comparison of the amount of information carried by single photons in different diffraction regimes. The experimental results show an order-of-magnitude agreement.

Measurement of viscous flow velocity and flow visualization using two magnetic resonance imagers

NASA Astrophysics Data System (ADS)

Boiko, A. V.; Akulov, A. E.; Chupakhin, A. P.; Cherevko, A. A.; Denisenko, N. S.; Savelov, A. A.; Stankevich, Yu. A.; Khe, A. K.; Yanchenko, A. A.; Tulupov, A. A.

2017-03-01

The accuracies of measuring the velocity field using clinical and research magnetic resonance imagers are compared. The flow velocity of a fluid simulating blood in a carotid artery model connected to a programmable pump was measured. Using phase-contrast magnetic resonance tomography, the velocity distributions in the carotid artery model were obtained and compared with the analytical solution for viscous liquid flow in a cylindrical tube (Poiseuille flow). It is found that the accuracy of the velocity measurement does not depend on the field induction and spatial resolution of the imagers.

Moiré deflectometry using the Talbot-Lau interferometer as refraction diagnostic for High Energy Density plasmas at energies below 10 keV

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

Valdivia, M. P.; Stutman, D.; Finkenthal, M.

2014-07-15

The highly localized density gradients expected in High Energy Density (HED) plasma experiments can be characterized by x-ray phase-contrast imaging in addition to conventional attenuation radiography. Moiré deflectometry using the Talbot-Lau grating interferometer setup is an attractive HED diagnostic due to its high sensitivity to refraction induced phase shifts. We report on the adaptation of such a system for operation in the sub-10 keV range by using a combination of free standing and ultrathin Talbot gratings. This new x-ray energy explored matches well the current x-ray backlighters used for HED experiments, while also enhancing phase effects at lower electron densities.more » We studied the performance of the high magnification, low energy Talbot-Lau interferometer, for single image phase retrieval using Moiré fringe deflectometry. Our laboratory and simulation studies indicate that such a device is able to retrieve object electron densities from phase shift measurements. Using laboratory x-ray sources from 7 to 15 μm size we obtained accurate simultaneous measurements of refraction and attenuation for both sharp and mild electron density gradients.« less

Moiré deflectometry using the Talbot-Lau interferometer as refraction diagnostic for high energy density plasmas at energies below 10 keV.

PubMed

Valdivia, M P; Stutman, D; Finkenthal, M

2014-07-01

The highly localized density gradients expected in High Energy Density (HED) plasma experiments can be characterized by x-ray phase-contrast imaging in addition to conventional attenuation radiography. Moiré deflectometry using the Talbot-Lau grating interferometer setup is an attractive HED diagnostic due to its high sensitivity to refraction induced phase shifts. We report on the adaptation of such a system for operation in the sub-10 keV range by using a combination of free standing and ultrathin Talbot gratings. This new x-ray energy explored matches well the current x-ray backlighters used for HED experiments, while also enhancing phase effects at lower electron densities. We studied the performance of the high magnification, low energy Talbot-Lau interferometer, for single image phase retrieval using Moiré fringe deflectometry. Our laboratory and simulation studies indicate that such a device is able to retrieve object electron densities from phase shift measurements. Using laboratory x-ray sources from 7 to 15 μm size we obtained accurate simultaneous measurements of refraction and attenuation for both sharp and mild electron density gradients.

The Physics of Traffic

NASA Astrophysics Data System (ADS)

Davis, L. Craig

2006-03-01

Congestion in freeway traffic is an example of self-organization in the language of complexity theory. Nonequilibrium, first-order phase transitions from free flow cause complex spatiotemporal patterns. Two distinct phases of congestion are observed in empirical traffic data--wide moving jams and synchronous flow. Wide moving jams are characterized by stopped or slowly moving vehicles within the jammed region, which widens and moves upstream at 15-20 km/h. Above a critical density of vehicles, a sudden decrease in the velocity of a lead vehicle can initiate a transition from metastable states to this phase. Human behaviors, especially delayed reactions, are implicated in the formation of jams. The synchronous flow phase results from a bottleneck such as an on-ramp. Thus, in contrast to a jam, the downstream front is pinned at a fixed location. The name of the phase comes from the equilibration (or synchronization) of speed and flow rate across all lanes caused by frequent vehicle lane changes. Synchronous flow occurs when the mainline flow and the rate of merging from an on-ramp are sufficiently large. Large-scale simulations using car-following models reproduce the physical phenomena occurring in traffic and suggest methods to improve flow and mediate congestion.

An Examination of Strategy Implementation During Abstract Nonlinguistic Category Learning in Aphasia.

PubMed

Vallila-Rohter, Sofia; Kiran, Swathi

2015-08-01

Our purpose was to study strategy use during nonlinguistic category learning in aphasia. Twelve control participants without aphasia and 53 participants with aphasia (PWA) completed a computerized feedback-based category learning task consisting of training and testing phases. Accuracy rates of categorization in testing phases were calculated. To evaluate strategy use, strategy analyses were conducted over training and testing phases. Participant data were compared with model data that simulated complex multi-cue, single feature, and random pattern strategies. Learning success and strategy use were evaluated within the context of standardized cognitive-linguistic assessments. Categorization accuracy was higher among control participants than among PWA. The majority of control participants implemented suboptimal or optimal multi-cue and single-feature strategies by testing phases of the experiment. In contrast, a large subgroup of PWA implemented random patterns, or no strategy, during both training and testing phases of the experiment. Person-to-person variability arises not only in category learning ability but also in the strategies implemented to complete category learning tasks. PWA less frequently developed effective strategies during category learning tasks than control participants. Certain PWA may have impairments of strategy development or feedback processing not captured by language and currently probed cognitive abilities.

A table-top monochromator for tunable femtosecond XUV pulses generated in a semi-infinite gas cell: Experiment and simulations

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

Conta, A. von; Huppert, M.; Wörner, H. J.

2016-07-15

We present a new design of a time-preserving extreme-ultraviolet (XUV) monochromator using a semi-infinite gas cell as a source. The performance of this beamline in the photon-energy range of 20 eV–42 eV has been characterized. We have measured the order-dependent XUV pulse durations as well as the flux and the spectral contrast. XUV pulse durations of ≤40 fs using 32 fs, 800 nm driving pulses were measured on the target. The spectral contrast was better than 100 over the entire energy range. A simple model based on the strong-field approximation is presented to estimate different contributions to the measured XUVmore » pulse duration. On-axis phase-matching calculations are used to rationalize the variation of the photon flux with pressure and intensity.« less

Rapid distortion analysis of high speed homogeneous turbulence subject to periodic shear

DOE PAGES

Bertsch, Rebecca L.; Girimaji, Sharath S.

2015-12-30

The effect of unsteady shear forcing on small perturbation growth in compressible flow is investigated. In particular, flow-thermodynamic field interaction and the resulting effect on the phase-lag between applied shear and Reynolds stress are examined. Simplified linear analysis of the perturbation pressure equation reveals crucial differences between steady and unsteady shear effects. The analytical findings are validated with numerical simulations of inviscid rapid distortion theory (RDT) equations. In contrast to steadily sheared compressible flows, perturbations in the unsteady (periodic) forcing case do not experience an asymptotic growth phase. Further, the resonance growth phenomenon found in incompressible unsteady shear turbulence ismore » absent in the compressible case. Overall, the stabilizing influence of both unsteadiness and compressibility is compounded leading to suppression of all small perturbations. As a result, the underlying mechanisms are explained.« less

Functional Near Infrared Spectroscopy: Watching the Brain in Flight

NASA Technical Reports Server (NTRS)

Harrivel, Angela; Hearn, Tristan

2012-01-01

Functional Near Infrared Spectroscopy (fNIRS) is an emerging neurological sensing technique applicable to optimizing human performance in transportation operations, such as commercial aviation. Cognitive state can be determined via pattern classification of functional activations measured with fNIRS. Operational application calls for further development of algorithms and filters for dynamic artifact removal. The concept of using the frequency domain phase shift signal to tune a Kalman filter is introduced to improve the quality of fNIRS signals in realtime. Hemoglobin concentration and phase shift traces were simulated for four different types of motion artifact to demonstrate the filter. Unwanted signal was reduced by at least 43%, and the contrast of the filtered oxygenated hemoglobin signal was increased by more than 100% overall. This filtering method is a good candidate for qualifying fNIRS signals in real time without auxiliary sensors

Functional Near Infrared Spectroscopy: Watching the Brain in Flight

NASA Technical Reports Server (NTRS)

Harrivel, Angela; Hearn, Tristan A.

2012-01-01

Functional Near Infrared Spectroscopy (fNIRS) is an emerging neurological sensing technique applicable to optimizing human performance in transportation operations, such as commercial aviation. Cognitive state can be determined via pattern classification of functional activations measured with fNIRS. Operational application calls for further development of algorithms and filters for dynamic artifact removal. The concept of using the frequency domain phase shift signal to tune a Kalman filter is introduced to improve the quality of fNIRS signals in real-time. Hemoglobin concentration and phase shift traces were simulated for four different types of motion artifact to demonstrate the filter. Unwanted signal was reduced by at least 43%, and the contrast of the filtered oxygenated hemoglobin signal was increased by more than 100% overall. This filtering method is a good candidate for qualifying fNIRS signals in real time without auxiliary sensors.

Rapid distortion analysis of high speed homogeneous turbulence subject to periodic shear

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

Bertsch, Rebecca L., E-mail: rlb@lanl.gov; Girimaji, Sharath S., E-mail: girimaji@aero.tamu.edu

2015-12-15

The effect of unsteady shear forcing on small perturbation growth in compressible flow is investigated. In particular, flow-thermodynamic field interaction and the resulting effect on the phase-lag between applied shear and Reynolds stress are examined. Simplified linear analysis of the perturbation pressure equation reveals crucial differences between steady and unsteady shear effects. The analytical findings are validated with numerical simulations of inviscid rapid distortion theory (RDT) equations. In contrast to steadily sheared compressible flows, perturbations in the unsteady (periodic) forcing case do not experience an asymptotic growth phase. Further, the resonance growth phenomenon found in incompressible unsteady shear turbulence ismore » absent in the compressible case. Overall, the stabilizing influence of both unsteadiness and compressibility is compounded leading to suppression of all small perturbations. The underlying mechanisms are explained.« less

The Extraterrestrial Materials Simulation Laboratory

NASA Technical Reports Server (NTRS)

Green, J. R.

2001-01-01

In contrast to fly-by and orbital missions, in situ missions face an incredible array of challenges in near-target navigation, landing site selection, descent, landing, science operations, sample collection and handling, drilling, anchoring, subsurface descent, communications, and contamination. The wide range of materials characteristics and environments threaten mission safety and success. For example, many physical properties are poorly characterized, including strength, composition, heterogeneity, phase change, texture, thermal properties, terrain features, atmospheric interaction, and stratigraphy. Examples of the range of materials properties include, for example: (1) Comets, with a possible compressive strength ranging from a light fluff to harder than concrete: 10(exp 2) to 10 (exp 8) Pa; (2) Europa, including a possible phase change at the surface, unknown strength and terrain roughness; and (3) Titan, with a completely unknown surface and possible liquid ocean. Additional information is contained in the original extended abstract.

Zernike phase contrast cryo-electron tomography of whole bacterial cells

PubMed Central

Guerrero-Ferreira, Ricardo C.; Wright, Elizabeth R.

2014-01-01

Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution. PMID:24075950

Detectability index of differential phase contrast CT compared with conventional CT: a preliminary channelized Hotelling observer study

NASA Astrophysics Data System (ADS)

Tang, Xiangyang; Yang, Yi; Tang, Shaojie

2013-03-01

Under the framework of model observer with signal and background exactly known (SKE/BKE), we investigate the detectability of differential phase contrast CT compared with that of the conventional attenuation-based CT. Using the channelized Hotelling observer and the radially symmetric difference-of-Gaussians channel template , we investigate the detectability index and its variation over the dimension of object and detector cells. The preliminary data show that the differential phase contrast CT outperforms the conventional attenuation-based CT significantly in the detectability index while both the object to be detected and the cell of detector used for data acquisition are relatively small. However, the differential phase contrast CT's dominance in the detectability index diminishes with increasing dimension of either object or detector cell, and virtually disappears while the dimension of object or detector cell approaches a threshold, respectively. It is hoped that the preliminary data reported in this paper may provide insightful understanding of the differential phase contrast CT's characteristic in the detectability index and its comparison with that of the conventional attenuation-based CT.

Ultrasound imaging based on nonlinear pressure field properties

NASA Astrophysics Data System (ADS)

Bouakaz, Ayache; Frinking, Peter J. A.; de Jong, Nico

2000-07-01

Ultrasound image quality has experienced a significant improvement over the past years with the utilization of harmonic frequencies. This brings the need to understand the physical processes involved in the propagation of finite amplitude sound beams, and the issues for redesigning and optimizing the phased array transducers. New arrays with higher imaging performances are essential for tissue imaging and contrast imaging as well. This study presents measurements and simulations on a 4.6 MHz square transducer. The numerical scheme used solves the KZK equation in the time domain. Comparison of measured and computed data showed good agreement for low and high excitation levels. In a similar way, a numerical simulation was performed on a linear array with five elements. The simulation showed that the second harmonic beam is narrower than the fundamental with less energy in the near field. In addition, the grating lobes are significantly lower. Accordingly, selective harmonic imaging shows less near field artifacts and will lower the clutter, resulting in much cleaner images.

Simulation-Based Evaluation of Light Posts and Street Signs as 3-D Geolocation Targets in SAR Images

NASA Astrophysics Data System (ADS)

Auer, S.; Balss, U.

2017-05-01

The assignment of phase center positions (in 2D or 3D) derived from SAR data to physical object is challenging for many man-made structures such as buildings or bridges. In contrast, light poles and traffic signs are promising targets for tasks based on 3-D geolocation as they often show a prominent and spatially isolated appearance. For a detailed understanding of the nature of both targets, this paper presents results of a dedicated simulation case study, which is based on ray tracing methods (simulator RaySAR). For the first time, the appearance of the targets is analyzed in 2D (image plane) and 3D space (world coordinates of scene model) and reflecting surfaces are identified for related dominant image pixels. The case studies confirms the crucial impact of spatial resolution in the context of light poles and traffic signs and the appropriateness of light poles as target for 3-D geolocation in case of horizontal ground surfaces beneath.

Evidence for link between modelled trends in Antarctic sea ice and underestimated westerly wind changes

PubMed Central

Purich, Ariaan; Cai, Wenju; England, Matthew H.; Cowan, Tim

2016-01-01

Despite global warming, total Antarctic sea ice coverage increased over 1979–2013. However, the majority of Coupled Model Intercomparison Project phase 5 models simulate a decline. Mechanisms causing this discrepancy have so far remained elusive. Here we show that weaker trends in the intensification of the Southern Hemisphere westerly wind jet simulated by the models may contribute to this disparity. During austral summer, a strengthened jet leads to increased upwelling of cooler subsurface water and strengthened equatorward transport, conducive to increased sea ice. As the majority of models underestimate summer jet trends, this cooling process is underestimated compared with observations and is insufficient to offset warming in the models. Through the sea ice-albedo feedback, models produce a high-latitude surface ocean warming and sea ice decline, contrasting the observed net cooling and sea ice increase. A realistic simulation of observed wind changes may be crucial for reproducing the recent observed sea ice increase. PMID:26842498

Evidence for link between modelled trends in Antarctic sea ice and underestimated westerly wind changes.

PubMed

Purich, Ariaan; Cai, Wenju; England, Matthew H; Cowan, Tim

2016-02-04

Despite global warming, total Antarctic sea ice coverage increased over 1979-2013. However, the majority of Coupled Model Intercomparison Project phase 5 models simulate a decline. Mechanisms causing this discrepancy have so far remained elusive. Here we show that weaker trends in the intensification of the Southern Hemisphere westerly wind jet simulated by the models may contribute to this disparity. During austral summer, a strengthened jet leads to increased upwelling of cooler subsurface water and strengthened equatorward transport, conducive to increased sea ice. As the majority of models underestimate summer jet trends, this cooling process is underestimated compared with observations and is insufficient to offset warming in the models. Through the sea ice-albedo feedback, models produce a high-latitude surface ocean warming and sea ice decline, contrasting the observed net cooling and sea ice increase. A realistic simulation of observed wind changes may be crucial for reproducing the recent observed sea ice increase.

Modeling astronomical adaptive optics performance with temporally filtered Wiener reconstruction of slope data

NASA Astrophysics Data System (ADS)

Correia, Carlos M.; Bond, Charlotte Z.; Sauvage, Jean-François; Fusco, Thierry; Conan, Rodolphe; Wizinowich, Peter L.

2017-10-01

We build on a long-standing tradition in astronomical adaptive optics (AO) of specifying performance metrics and error budgets using linear systems modeling in the spatial-frequency domain. Our goal is to provide a comprehensive tool for the calculation of error budgets in terms of residual temporally filtered phase power spectral densities and variances. In addition, the fast simulation of AO-corrected point spread functions (PSFs) provided by this method can be used as inputs for simulations of science observations with next-generation instruments and telescopes, in particular to predict post-coronagraphic contrast improvements for planet finder systems. We extend the previous results and propose the synthesis of a distributed Kalman filter to mitigate both aniso-servo-lag and aliasing errors whilst minimizing the overall residual variance. We discuss applications to (i) analytic AO-corrected PSF modeling in the spatial-frequency domain, (ii) post-coronagraphic contrast enhancement, (iii) filter optimization for real-time wavefront reconstruction, and (iv) PSF reconstruction from system telemetry. Under perfect knowledge of wind velocities, we show that $\\sim$60 nm rms error reduction can be achieved with the distributed Kalman filter embodying anti- aliasing reconstructors on 10 m class high-order AO systems, leading to contrast improvement factors of up to three orders of magnitude at few ${\\lambda}/D$ separations ($\\sim1-5{\\lambda}/D$) for a 0 magnitude star and reaching close to one order of magnitude for a 12 magnitude star.

Quantitative phase imaging and complex field reconstruction by pupil modulation differential phase contrast

PubMed Central

Lu, Hangwen; Chung, Jaebum; Ou, Xiaoze; Yang, Changhuei

2016-01-01

Differential phase contrast (DPC) is a non-interferometric quantitative phase imaging method achieved by using an asymmetric imaging procedure. We report a pupil modulation differential phase contrast (PMDPC) imaging method by filtering a sample’s Fourier domain with half-circle pupils. A phase gradient image is captured with each half-circle pupil, and a quantitative high resolution phase image is obtained after a deconvolution process with a minimum of two phase gradient images. Here, we introduce PMDPC quantitative phase image reconstruction algorithm and realize it experimentally in a 4f system with an SLM placed at the pupil plane. In our current experimental setup with the numerical aperture of 0.36, we obtain a quantitative phase image with a resolution of 1.73μm after computationally removing system aberrations and refocusing. We also extend the depth of field digitally by 20 times to ±50μm with a resolution of 1.76μm. PMID:27828473

The curious case of cuprous chloride: Giant thermal resistance and anharmonic quasiparticle spectra driven by dispersion nesting

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Saikat; Bansal, Dipanshu; Delaire, Olivier; Perrodin, Didier; Bourret-Courchesne, Edith; Singh, David J.; Lindsay, Lucas

2017-09-01

Strongly anharmonic phonon properties of CuCl are investigated with inelastic neutron-scattering measurements and first-principles simulations. An unusual quasiparticle spectral peak emerges in the phonon density of states with increasing temperature, in both simulations and measurements, emanating from exceptionally strong coupling between conventional phonon modes. Associated with this strong anharmonicity, the lattice thermal conductivity of CuCl is extremely low and exhibits anomalous, nonmonotonic pressure dependence. We show how this behavior arises from the structure of the phonon dispersions augmenting the phase space available for anharmonic three-phonon scattering processes, and contrast this mechanism with common arguments based on negative Grüneisen parameters. These results demonstrate the importance of considering intrinsic phonon-dispersion structure toward understanding scattering processes and designing new ultralow thermal conductivity materials.

Dynamic Modeling and Simulation of a Rotational Inverted Pendulum

NASA Astrophysics Data System (ADS)

Duart, J. L.; Montero, B.; Ospina, P. A.; González, E.

2017-01-01

This paper presents an alternative way to the dynamic modeling of a rotational inverted pendulum using the classic mechanics known as Euler-Lagrange allows to find motion equations that describe our model. It also has a design of the basic model of the system in SolidWorks software, which based on the material and dimensions of the model provides some physical variables necessary for modeling. In order to verify the theoretical results, It was made a contrast between the solutions obtained by simulation SimMechanics-Matlab and the system of equations Euler-Lagrange, solved through ODE23tb method included in Matlab bookstores for solving equations systems of the type and order obtained. This article comprises a pendulum trajectory analysis by a phase space diagram that allows the identification of stable and unstable regions of the system.

Phase-contrast tomography of sciatic nerves: image quality and experimental parameters

NASA Astrophysics Data System (ADS)

Töpperwien, M.; Krenkel, M.; Ruhwedel, T.; Möbius, W.; Pacureanu, A.; Cloetens, P.; Salditt, T.

2017-06-01

We present propagation-based phase-contrast tomography of mouse sciatic nerves stained with osmium, leading to an enhanced contrast in the myelin sheath around the axons, in order to visualize the threedimensional (3D) structure of the nerve. We compare different experimental parameters and show that contrast and resolution are high enough to identify single axons in the nerve, including characteristic functional structures such as Schmidt-Lanterman incisures.

Mouse blood vessel imaging by in-line x-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Zhang, Xi; Liu, Xiao-Song; Yang, Xin-Rong; Chen, Shao-Liang; Zhu, Pei-Ping; Yuan, Qing-Xi

2008-10-01

It is virtually impossible to observe blood vessels by conventional x-ray imaging techniques without using contrast agents. In addition, such x-ray systems are typically incapable of detecting vessels with diameters less than 200 µm. Here we show that vessels as small as 30 µm could be detected using in-line phase-contrast x-ray imaging without the use of contrast agents. Image quality was greatly improved by replacing resident blood with physiological saline. Furthermore, an entire branch of the portal vein from the main axial portal vein to the eighth generation of branching could be captured in a single phase-contrast image. Prior to our work, detection of 30 µm diameter blood vessels could only be achieved using x-ray interferometry, which requires sophisticated x-ray optics. Our results thus demonstrate that in-line phase-contrast x-ray imaging, using physiological saline as a contrast agent, provides an alternative to the interferometric method that can be much more easily implemented and also offers the advantage of a larger field of view. A possible application of this methodology is in animal tumor models, where it can be used to observe tumor angiogenesis and the treatment effects of antineoplastic agents.

A simulation of T-wave alternans vectocardiographic representation performed by changing the ventricular heart cells action potential duration.

PubMed

Janusek, D; Kania, M; Zaczek, R; Zavala-Fernandez, H; Maniewski, R

2014-04-01

The presence of T wave alternans (TWA) in the surface ECG signals has been recognized as a marker of electrical instability, and is hypothesized to be related to patients at increased risk for ventricular arrhythmias. In this paper we present a TWA simulation study. The TWA phenomenon was simulated by changing the duration of the ventricular heart cells action potential. The magnitude was calculated in the surface ECG with the use of the time domain method. The spatially concordant TWA, where during one heart beat all ventricular cells display a short-duration action potential and during the next beat they exhibit a long-duration action potential, as well as the discordant TWA, where at least one region is out of phase, was simulated. The vectocardiographic representation was employed. The obtained results showed a high level of T-loop pattern and location disturbances connected to the discordant TWA simulation in contrast to the concordant one. This result may be explained by the spatial heterogeneity of the ventricular repolarization process, which could be higher for the discordant TWA than for the concordant TWA. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Quantitative X-ray Differential Interference Contrast Microscopy

NASA Astrophysics Data System (ADS)

Nakamura, Takashi

Full-field soft x-ray microscopes are widely used in many fields of sciences. Advances in nanofabrication technology enabled short wavelength focusing elements with significantly improved spatial resolution. In the soft x-ray spectral region, samples as small as 12 nm can be resolved using micro zone-plates as the objective lens. In addition to conventional x-ray microscopy in which x-ray absorption difference provides the image contrast, phase contrast mechanisms such as differential phase contrast (DIC) and Zernike phase contrast have also been demonstrated These phase contrast imaging mechanisms are especially attractive at the x-ray wavelengths where phase contrast of most materials is typically 10 times stronger than the absorption contrast. With recent progresses in plasma-based x- ray sources and increasing accessibility to synchrotron user facilities, x-ray microscopes are quickly becoming standard measurement equipment in the laboratory. To further the usefulness of x-ray DIC microscopy this thesis explicitly addresses three known issues with this imaging modality by introducing new techniques and devices First, as opposed to its visible-light counterpart, no quantitative phase imaging technique exists for x-ray DIC microscopy. To address this issue, two nanoscale x-ray quantitative phase imaging techniques, using exclusive OR (XOR) patterns and zone-plate doublets, respectively, are proposed. Unlike existing x-ray quantitative phase imaging techniques such as Talbot interferometry and ptychography, no dedicated experimental setups or stringent illumination coherence are needed for quantitative phase retrieval. Second, to the best of our knowledge, no quantitative performance characterization of DIC microscopy exists to date. Therefore the imaging system's response to sample's spatial frequency is not known In order to gain in-depth understanding of this imaging modality, performance of x-ray DIC microscopy is quantified using modulation transfer function. A new illumination apparatus required for the transfer function analysis under partially coherent illumination is also proposed. Such a characterization is essential for a proper selection of DIC optics for various transparent samples under study. Finally, optical elements used for x-ray DIC microscopy are highly absorptive and high brilliance x-ray sources such as synchrotrons are generally needed for image contrast. To extend the use of x-ray DIC microscopy to a wider variety of applications, a high efficiency large numerical aperture optical element consisting of high reflective Bragg reflectors is proposed. Using Bragg reflectors, which have 70% ˜99% reflectivity at extreme ultraviolet and soft x-rays for all angles of glancing incidence, the first order focusing efficiency is expected to increase by ˜ 8 times compared to that of a typical Fresnel zone-plate. This thesis contributes to current nanoscale x-ray phase contrast imaging research and provides new insights for biological, material, and magnetic sciences

Diffraction enhance x-ray imaging for quantitative phase contrast studies

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

Agrawal, A. K.; Singh, B., E-mail: balwants@rrcat.gov.in; Kashyap, Y. S.

2016-05-23

Conventional X-ray imaging based on absorption contrast permits limited visibility of feature having small density and thickness variations. For imaging of weakly absorbing material or materials possessing similar densities, a novel phase contrast imaging techniques called diffraction enhanced imaging has been designed and developed at imaging beamline Indus-2 RRCAT Indore. The technique provides improved visibility of the interfaces and show high contrast in the image forsmall density or thickness gradients in the bulk. This paper presents basic principle, instrumentation and analysis methods for this technique. Initial results of quantitative phase retrieval carried out on various samples have also been presented.

Optimization of propagation-based x-ray phase-contrast tomography for breast cancer imaging

NASA Astrophysics Data System (ADS)

Baran, P.; Pacile, S.; Nesterets, Y. I.; Mayo, S. C.; Dullin, C.; Dreossi, D.; Arfelli, F.; Thompson, D.; Lockie, D.; McCormack, M.; Taba, S. T.; Brun, F.; Pinamonti, M.; Nickson, C.; Hall, C.; Dimmock, M.; Zanconati, F.; Cholewa, M.; Quiney, H.; Brennan, P. C.; Tromba, G.; Gureyev, T. E.

2017-03-01

The aim of this study was to optimise the experimental protocol and data analysis for in-vivo breast cancer x-ray imaging. Results are presented of the experiment at the SYRMEP beamline of Elettra Synchrotron using the propagation-based phase-contrast mammographic tomography method, which incorporates not only absorption, but also x-ray phase information. In this study the images of breast tissue samples, of a size corresponding to a full human breast, with radiologically acceptable x-ray doses were obtained, and the degree of improvement of the image quality (from the diagnostic point of view) achievable using propagation-based phase-contrast image acquisition protocols with proper incorporation of x-ray phase retrieval into the reconstruction pipeline was investigated. Parameters such as the x-ray energy, sample-to-detector distance and data processing methods were tested, evaluated and optimized with respect to the estimated diagnostic value using a mastectomy sample with a malignant lesion. The results of quantitative evaluation of images were obtained by means of radiological assessment carried out by 13 experienced specialists. A comparative analysis was performed between the x-ray and the histological images of the specimen. The results of the analysis indicate that, within the investigated range of parameters, both the objective image quality characteristics and the subjective radiological scores of propagation-based phase-contrast images of breast tissues monotonically increase with the strength of phase contrast which in turn is directly proportional to the product of the radiation wavelength and the sample-to-detector distance. The outcomes of this study serve to define the practical imaging conditions and the CT reconstruction procedures appropriate for low-dose phase-contrast mammographic imaging of live patients at specially designed synchrotron beamlines.

Parallelization of TWOPORFLOW, a Cartesian Grid based Two-phase Porous Media Code for Transient Thermo-hydraulic Simulations

NASA Astrophysics Data System (ADS)

Trost, Nico; Jiménez, Javier; Imke, Uwe; Sanchez, Victor

2014-06-01

TWOPORFLOW is a thermo-hydraulic code based on a porous media approach to simulate single- and two-phase flow including boiling. It is under development at the Institute for Neutron Physics and Reactor Technology (INR) at KIT. The code features a 3D transient solution of the mass, momentum and energy conservation equations for two inter-penetrating fluids with a semi-implicit continuous Eulerian type solver. The application domain of TWOPORFLOW includes the flow in standard porous media and in structured porous media such as micro-channels and cores of nuclear power plants. In the latter case, the fluid domain is coupled to a fuel rod model, describing the heat flow inside the solid structure. In this work, detailed profiling tools have been utilized to determine the optimization potential of TWOPORFLOW. As a result, bottle-necks were identified and reduced in the most feasible way, leading for instance to an optimization of the water-steam property computation. Furthermore, an OpenMP implementation addressing the routines in charge of inter-phase momentum-, energy- and mass-coupling delivered good performance together with a high scalability on shared memory architectures. In contrast to that, the approach for distributed memory systems was to solve sub-problems resulting by the decomposition of the initial Cartesian geometry. Thread communication for the sub-problem boundary updates was accomplished by the Message Passing Interface (MPI) standard.

Facilitating atmosphere oxidation through mantle convection

NASA Astrophysics Data System (ADS)

Lee, K. K. M.; Gu, T.; Creasy, N.; Li, M.; McCammon, C. A.; Girard, J.

2017-12-01

Earth's mantle connects the surface with the deep interior through convection, and the evolution of its redox state will affect the distribution of siderophile elements, recycling of refractory isotopes, and the oxidation state of the atmosphere through volcanic outgassing. While the rise of oxygen in the atmosphere, i.e., the Great Oxidation Event (GOE) occurred 2.4 billion years ago (Ga), multiple lines of evidence point to oxygen production in the atmosphere well before 2.4 Ga. In contrast to the fluctuations of atmospheric oxygen, vanadium in Archean mantle lithosphere suggests that the mantle redox state has been constant for 3.5 Ga. Indeed, the connection between the redox state of the deep Earth and the atmosphere is enigmatic as is the effect of redox state on mantle dynamics. Here we show a redox-induced density contrast affects mantle convection and may potentially cause the oxidation of the upper mantle. We compressed two synthetic enstatite chondritic samples with identical bulk compositions but formed under different oxygen fugacities (fO2) to lower mantle pressures and temperatures and find Al2O3 forms its own phase separate from the dominant bridgmanite phase in the more reduced composition, in contrast to a more Al-rich, bridgmanite-dominated assemblage for a more oxidized starting composition. As a result, the reduced material is 1-1.5% denser than the oxidized material. Subsequent experiments on other plausible mantle compositions, which differ only in redox state of the starting glass materials, show similar results: distinct mineral assemblages and density contrasts up to 4%. Our geodynamic simulations suggest that such a density contrast causes a rapid ascent and accumulation of oxidized material in the upper mantle, with descent of the denser reduced material to the core-mantle boundary. The resulting heterogeneous redox conditions in Earth's interior may have contributed to the large low-shear velocity provinces in the lower mantle and the rise of oxygen in Earth's atmosphere.

System Characterizations and Optimized Reconstruction Methods for Novel X-ray Imaging Modalities

NASA Astrophysics Data System (ADS)

Guan, Huifeng

In the past decade there have been many new emerging X-ray based imaging technologies developed for different diagnostic purposes or imaging tasks. However, there exist one or more specific problems that prevent them from being effectively or efficiently employed. In this dissertation, four different novel X-ray based imaging technologies are discussed, including propagation-based phase-contrast (PB-XPC) tomosynthesis, differential X-ray phase-contrast tomography (D-XPCT), projection-based dual-energy computed radiography (DECR), and tetrahedron beam computed tomography (TBCT). System characteristics are analyzed or optimized reconstruction methods are proposed for these imaging modalities. In the first part, we investigated the unique properties of propagation-based phase-contrast imaging technique when combined with the X-ray tomosynthesis. Fourier slice theorem implies that the high frequency components collected in the tomosynthesis data can be more reliably reconstructed. It is observed that the fringes or boundary enhancement introduced by the phase-contrast effects can serve as an accurate indicator of the true depth position in the tomosynthesis in-plane image. In the second part, we derived a sub-space framework to reconstruct images from few-view D-XPCT data set. By introducing a proper mask, the high frequency contents of the image can be theoretically preserved in a certain region of interest. A two-step reconstruction strategy is developed to mitigate the risk of subtle structures being oversmoothed when the commonly used total-variation regularization is employed in the conventional iterative framework. In the thirt part, we proposed a practical method to improve the quantitative accuracy of the projection-based dual-energy material decomposition. It is demonstrated that applying a total-projection-length constraint along with the dual-energy measurements can achieve a stabilized numerical solution of the decomposition problem, thus overcoming the disadvantages of the conventional approach that was extremely sensitive to noise corruption. In the final part, we described the modified filtered backprojection and iterative image reconstruction algorithms specifically developed for TBCT. Special parallelization strategies are designed to facilitate the use of GPU computing, showing demonstrated capability of producing high quality reconstructed volumetric images with a super fast computational speed. For all the investigations mentioned above, both simulation and experimental studies have been conducted to demonstrate the feasibility and effectiveness of the proposed methodologies.

Design and validation of a mathematical breast phantom for contrast-enhanced digital mammography

NASA Astrophysics Data System (ADS)

Hill, Melissa L.; Mainprize, James G.; Jong, Roberta A.; Yaffe, Martin J.

2011-03-01

In contrast-enhanced digital mammography (CEDM) an iodinated contrast agent is employed to increase lesion contrast and to provide tissue functional information. Here, we present the details of a software phantom that can be used as a tool for the simulation of CEDM images, and compare the degree of anatomic noise present in images simulated using the phantom to that associated with breast parenchyma in clinical CEDM images. Such a phantom could be useful for multiparametric investigations including characterization of CEDM imaging performance and system optimization. The phantom has a realistic mammographic appearance based on a clustered lumpy background and models contrast agent uptake according to breast tissue physiology. Fifty unique phantoms were generated and used to simulate regions of interest (ROI) of pre-contrast images and logarithmically subtracted CEDM images using monoenergetic ray tracing. Power law exponents, β, were used as a measure of anatomic noise and were determined using a linear least-squares fit to log-log plots of the square of the modulus of radially averaged image power spectra versus spatial frequency. The power spectra for ROI selected from regions of normal parenchyma in 10 pairs of clinical CEDM pre-contrast and subtracted images were also measured for comparison with the simulated images. There was good agreement between the measured β in the simulated CEDM images and the clinical images. The values of β were consistently lower for the logarithmically subtracted CEDM images compared to the pre-contrast images, indicating that the subtraction process reduced anatomical noise.

Central and peripheral vision loss differentially affects contextual cueing in visual search.

PubMed

Geringswald, Franziska; Pollmann, Stefan

2015-09-01

Visual search for targets in repeated displays is more efficient than search for the same targets in random distractor layouts. Previous work has shown that this contextual cueing is severely impaired under central vision loss. Here, we investigated whether central vision loss, simulated with gaze-contingent displays, prevents the incidental learning of contextual cues or the expression of learning, that is, the guidance of search by learned target-distractor configurations. Visual search with a central scotoma reduced contextual cueing both with respect to search times and gaze parameters. However, when the scotoma was subsequently removed, contextual cueing was observed in a comparable magnitude as for controls who had searched without scotoma simulation throughout the experiment. This indicated that search with a central scotoma did not prevent incidental context learning, but interfered with search guidance by learned contexts. We discuss the role of visuospatial working memory load as source of this interference. In contrast to central vision loss, peripheral vision loss was expected to prevent spatial configuration learning itself, because the restricted search window did not allow the integration of invariant local configurations with the global display layout. This expectation was confirmed in that visual search with a simulated peripheral scotoma eliminated contextual cueing not only in the initial learning phase with scotoma, but also in the subsequent test phase without scotoma. (c) 2015 APA, all rights reserved).

Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations.

PubMed

Zeller, Fabian; Zacharias, Martin

2014-02-11

The accurate calculation of potentials of mean force for ligand-receptor binding is one of the most important applications of molecular simulation techniques. Typically, the separation distance between ligand and receptor is chosen as a reaction coordinate along which a PMF can be calculated with the aid of umbrella sampling (US) techniques. In addition, restraints can be applied on the relative position and orientation of the partner molecules to reduce accessible phase space. An approach combining such phase space reduction with flattening of the free energy landscape and configurational exchanges has been developed, which significantly improves the convergence of PMF calculations in comparison with standard umbrella sampling. The free energy surface along the reaction coordinate is smoothened by iteratively adapting biasing potentials corresponding to previously calculated PMFs. Configurations are allowed to exchange between the umbrella simulation windows via the Hamiltonian replica exchange method. The application to a DNA molecule in complex with a minor groove binding ligand indicates significantly improved convergence and complete reversibility of the sampling along the pathway. The calculated binding free energy is in excellent agreement with experimental results. In contrast, the application of standard US resulted in large differences between PMFs calculated for association and dissociation pathways. The approach could be a useful alternative to standard US for computational studies on biomolecular recognition processes.

Use of Caval Subtraction 2D Phase-Contrast MR Imaging to Measure Total Liver and Hepatic Arterial Blood Flow: Preclinical Validation and Initial Clinical Translation

PubMed Central

Walker-Samuel, Simon; Davies, Nathan; Halligan, Steve; Lythgoe, Mark F.

2016-01-01

Purpose To validate caval subtraction two-dimensional (2D) phase-contrast magnetic resonance (MR) imaging measurements of total liver blood flow (TLBF) and hepatic arterial fraction in an animal model and evaluate consistency and reproducibility in humans. Materials and Methods Approval from the institutional ethical committee for animal care and research ethics was obtained. Fifteen Sprague-Dawley rats underwent 2D phase-contrast MR imaging of the portal vein (PV) and infrahepatic and suprahepatic inferior vena cava (IVC). TLBF and hepatic arterial flow were estimated by subtracting infrahepatic from suprahepatic IVC flow and PV flow from estimated TLBF, respectively. Direct PV transit-time ultrasonography (US) and fluorescent microsphere measurements of hepatic arterial fraction were the standards of reference. Thereafter, consistency of caval subtraction phase-contrast MR imaging–derived TLBF and hepatic arterial flow was assessed in 13 volunteers (mean age, 28.3 years ± 1.4) against directly measured phase-contrast MR imaging PV and proper hepatic arterial inflow; reproducibility was measured after 7 days. Bland-Altman analysis of agreement and coefficient of variation comparisons were undertaken. Results There was good agreement between PV flow measured with phase-contrast MR imaging and that measured with transit-time US (mean difference, −3.5 mL/min/100 g; 95% limits of agreement [LOA], ±61.3 mL/min/100 g). Hepatic arterial fraction obtained with caval subtraction agreed well with those with fluorescent microspheres (mean difference, 4.2%; 95% LOA, ±20.5%). Good consistency was demonstrated between TLBF in humans measured with caval subtraction and direct inflow phase-contrast MR imaging (mean difference, −1.3 mL/min/100 g; 95% LOA, ±23.1 mL/min/100 g). TLBF reproducibility at 7 days was similar between the two methods (95% LOA, ±31.6 mL/min/100 g vs ±29.6 mL/min/100 g). Conclusion Caval subtraction phase-contrast MR imaging is a simple and clinically viable method for measuring TLBF and hepatic arterial flow. Online supplemental material is available for this article. PMID:27171018

Use of Caval Subtraction 2D Phase-Contrast MR Imaging to Measure Total Liver and Hepatic Arterial Blood Flow: Preclinical Validation and Initial Clinical Translation.

PubMed

Chouhan, Manil D; Mookerjee, Rajeshwar P; Bainbridge, Alan; Walker-Samuel, Simon; Davies, Nathan; Halligan, Steve; Lythgoe, Mark F; Taylor, Stuart A

2016-09-01

Purpose To validate caval subtraction two-dimensional (2D) phase-contrast magnetic resonance (MR) imaging measurements of total liver blood flow (TLBF) and hepatic arterial fraction in an animal model and evaluate consistency and reproducibility in humans. Materials and Methods Approval from the institutional ethical committee for animal care and research ethics was obtained. Fifteen Sprague-Dawley rats underwent 2D phase-contrast MR imaging of the portal vein (PV) and infrahepatic and suprahepatic inferior vena cava (IVC). TLBF and hepatic arterial flow were estimated by subtracting infrahepatic from suprahepatic IVC flow and PV flow from estimated TLBF, respectively. Direct PV transit-time ultrasonography (US) and fluorescent microsphere measurements of hepatic arterial fraction were the standards of reference. Thereafter, consistency of caval subtraction phase-contrast MR imaging-derived TLBF and hepatic arterial flow was assessed in 13 volunteers (mean age, 28.3 years ± 1.4) against directly measured phase-contrast MR imaging PV and proper hepatic arterial inflow; reproducibility was measured after 7 days. Bland-Altman analysis of agreement and coefficient of variation comparisons were undertaken. Results There was good agreement between PV flow measured with phase-contrast MR imaging and that measured with transit-time US (mean difference, -3.5 mL/min/100 g; 95% limits of agreement [LOA], ±61.3 mL/min/100 g). Hepatic arterial fraction obtained with caval subtraction agreed well with those with fluorescent microspheres (mean difference, 4.2%; 95% LOA, ±20.5%). Good consistency was demonstrated between TLBF in humans measured with caval subtraction and direct inflow phase-contrast MR imaging (mean difference, -1.3 mL/min/100 g; 95% LOA, ±23.1 mL/min/100 g). TLBF reproducibility at 7 days was similar between the two methods (95% LOA, ±31.6 mL/min/100 g vs ±29.6 mL/min/100 g). Conclusion Caval subtraction phase-contrast MR imaging is a simple and clinically viable method for measuring TLBF and hepatic arterial flow. Online supplemental material is available for this article.

Spatially encoded phase-contrast MRI-3D MRI movies of 1D and 2D structures at millisecond resolution.

PubMed

Merboldt, Klaus-Dietmar; Uecker, Martin; Voit, Dirk; Frahm, Jens

2011-10-01

This work demonstrates that the principles underlying phase-contrast MRI may be used to encode spatial rather than flow information along a perpendicular dimension, if this dimension contains an MRI-visible object at only one spatial location. In particular, the situation applies to 3D mapping of curved 2D structures which requires only two projection images with different spatial phase-encoding gradients. These phase-contrast gradients define the field of view and mean spin-density positions of the object in the perpendicular dimension by respective phase differences. When combined with highly undersampled radial fast low angle shot (FLASH) and image reconstruction by regularized nonlinear inversion, spatial phase-contrast MRI allows for dynamic 3D mapping of 2D structures in real time. First examples include 3D MRI movies of the acting human hand at a temporal resolution of 50 ms. With an even simpler technique, 3D maps of curved 1D structures may be obtained from only three acquisitions of a frequency-encoded MRI signal with two perpendicular phase encodings. Here, 3D MRI movies of a rapidly rotating banana were obtained at 5 ms resolution or 200 frames per second. In conclusion, spatial phase-contrast 3D MRI of 2D or 1D structures is respective two or four orders of magnitude faster than conventional 3D MRI. Copyright © 2011 Wiley-Liss, Inc.

Zernike phase contrast cryo-electron tomography of whole bacterial cells.

PubMed

Guerrero-Ferreira, Ricardo C; Wright, Elizabeth R

2014-01-01

Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Diffracting aperture based differential phase contrast for scanning X-ray microscopy.

PubMed

Kaulich, Burkhard; Polack, Francois; Neuhaeusler, Ulrich; Susini, Jean; di Fabrizio, Enzo; Wilhein, Thomas

2002-10-07

It is demonstrated that in a zone plate based scanning X-ray microscope, used to image low absorbing, heterogeneous matter at a mesoscopic scale, differential phase contrast (DPC) can be implemented without adding any additional optical component to the normal scheme of the microscope. The DPC mode is simply generated by an appropriate positioning and alignment of microscope apertures. Diffraction from the apertures produces a wave front with a non-uniform intensity. The signal recorded by a pinhole photo diode located in the intensity gradient is highly sensitive to phase changes introduced by the specimen to be recorded. The feasibility of this novel DPC technique was proven with the scanning X-ray microscope at the ID21 beamline of the European Synchrotron Radiation facility (ESRF) operated at 6 keV photon energy. We observe a differential phase contrast, similar to Nomarski's differential interference contrast for the light microscope, which results in a tremendous increase in image contrast of up to 20 % when imaging low absorbing specimen.

In search of the best match: probing a multi-dimensional cloud microphysical parameter space to better understand what controls cloud thermodynamic phase

NASA Astrophysics Data System (ADS)

Tan, Ivy; Storelvmo, Trude

2015-04-01

Substantial improvements have been made to the cloud microphysical schemes used in the latest generation of global climate models (GCMs), however, an outstanding weakness of these schemes lies in the arbitrariness of their tuning parameters, which are also notoriously fraught with uncertainties. Despite the growing effort in improving the cloud microphysical schemes in GCMs, most of this effort has neglected to focus on improving the ability of GCMs to accurately simulate the present-day global distribution of thermodynamic phase partitioning in mixed-phase clouds. Liquid droplets and ice crystals not only influence the Earth's radiative budget and hence climate sensitivity via their contrasting optical properties, but also through the effects of their lifetimes in the atmosphere. The current study employs NCAR's CAM5.1, and uses observations of cloud phase obtained by NASA's CALIOP lidar over a 79-month period (November 2007 to June 2014) guide the accurate simulation of the global distribution of mixed-phase clouds in 20∘ latitudinal bands at the -10∘ C, -20∘C and -30∘C isotherms, by adjusting six relevant cloud microphysical tuning parameters in the CAM5.1 via Quasi-Monte Carlo sampling. Among the parameters include those that control the Wegener-Bergeron-Findeisen (WBF) timescale for the conversion of supercooled liquid droplets to ice and snow in mixed-phase clouds, the fraction of ice nuclei that nucleate ice in the atmosphere, ice crystal sedimentation speed, and wet scavenging in stratiform and convective clouds. Using a Generalized Linear Model as a variance-based sensitivity analysis, the relative contributions of each of the six parameters are quantified to gain a better understanding of the importance of their individual and two-way interaction effects on the liquid to ice proportion in mixed-phase clouds. Thus, the methodology implemented in the current study aims to search for the combination of cloud microphysical parameters in a GCM that produce the most accurate reproduction of observations of cloud thermodynamic phase, while simultaneously assessing the weaknesses of the parameterizations in the model. We find that the simulated proportion of liquid to ice in mixed-phase clouds is dominated by the fraction of active ice nuclei in the atmosphere and the WBF timescale. In a follow-up to this study, we apply these results to a fully-coupled GCM, CESM, and find that cloud thermodynamic phase has profound ramifications for the uncertainty associated with climate sensitivity estimates.

Maskless EUV lithography: an already difficult technology made even more complicated?

NASA Astrophysics Data System (ADS)

Chen, Yijian

2012-03-01

In this paper, we present the research progress made in maskless EUV lithography and discuss the emerging opportunities for this disruptive technology. It will be shown nanomirrors based maskless approach is one path to costeffective and defect-free EUV lithography, rather than making it even more complicated. The focus of our work is to optimize the existing vertical comb process and scale down the mirror size from several microns to sub-micron regime. The nanomirror device scaling, system configuration, and design issues will be addressed. We also report our theoretical and simulation study of reflective EUV nanomirror based imaging behavior. Dense line/space patterns are formed with an EUV nanomirror array by assigning a phase shift of π to neighboring nanomirrors. Our simulation results show that phase/intensity imbalance is an inherent characteristic of maskless EUV lithography while it only poses a manageable challenge to CD control and process window. The wafer scan and EUV laser jitter induced image blur phenomenon is discussed and a blurred imaging theory is constructed. This blur effect is found to degrade the image contrast at a level that mainly depends on the wafer scan speed.

Fuelling decisions in migratory birds: geomagnetic cues override the seasonal effect.

PubMed

Kullberg, Cecilia; Henshaw, Ian; Jakobsson, Sven; Johansson, Patrik; Fransson, Thord

2007-09-07

Recent evaluations of both temporal and spatial precision in bird migration have called for external cues in addition to the inherited programme defining the migratory journey in terms of direction, distance and fuelling behaviour along the route. We used juvenile European robins (Erithacus rubecula) to study whether geomagnetic cues affect fuel deposition in a medium-distance migrant by simulating a migratory journey from southeast Sweden to the wintering area in southern Spain. In the late phase of the onset of autumn migration, robins exposed to the magnetic treatment attained a lower fuel load than control birds exposed to the ambient magnetic field of southeast Sweden. In contrast, robins captured in the early phase of the onset of autumn migration all showed low fuel deposition irrespective of experimental treatment. These results are, as expected, the inverse of what we have found in similar studies in a long-distance migrant, the thrush nightingale (Luscinia luscinia), indicating that the reaction in terms of fuelling behaviour to a simulated southward migration varies depending on the relevance for the species. Furthermore, we suggest that information from the geomagnetic field act as an important external cue overriding the seasonal effect on fuelling behaviour in migratory birds.

Adaptive windowing in contrast-enhanced intravascular ultrasound imaging.

PubMed

Lindsey, Brooks D; Martin, K Heath; Jiang, Xiaoning; Dayton, Paul A

2016-08-01

Intravascular ultrasound (IVUS) is one of the most commonly-used interventional imaging techniques and has seen recent innovations which attempt to characterize the risk posed by atherosclerotic plaques. One such development is the use of microbubble contrast agents to image vasa vasorum, fine vessels which supply oxygen and nutrients to the walls of coronary arteries and typically have diameters less than 200μm. The degree of vasa vasorum neovascularization within plaques is positively correlated with plaque vulnerability. Having recently presented a prototype dual-frequency transducer for contrast agent-specific intravascular imaging, here we describe signal processing approaches based on minimum variance (MV) beamforming and the phase coherence factor (PCF) for improving the spatial resolution and contrast-to-tissue ratio (CTR) in IVUS imaging. These approaches are examined through simulations, phantom studies, ex vivo studies in porcine arteries, and in vivo studies in chicken embryos. In phantom studies, PCF processing improved CTR by a mean of 4.2dB, while combined MV and PCF processing improved spatial resolution by 41.7%. Improvements of 2.2dB in CTR and 37.2% in resolution were observed in vivo. Applying these processing strategies can enhance image quality in conventional B-mode IVUS or in contrast-enhanced IVUS, where signal-to-noise ratio is relatively low and resolution is at a premium. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessing the Impact of Air Pollution on Grain Yield of Winter Wheat - A Case Study in the North China Plain.

PubMed

Liu, Xiuwei; Sun, Hongyong; Feike, Til; Zhang, Xiying; Shao, Liwei; Chen, Suying

2016-01-01

The major wheat production region of China the North China Plain (NCP) is seriously affected by air pollution. In this study, yield of winter wheat (Triticum aestivum L.) was analyzed with respect to the potential impact of air pollution index under conditions of optimal crop management in the NCP from 2001 to 2012. Results showed that air pollution was especially serious at the early phase of winter wheat growth significantly influencing various weather factors. However, no significant correlations were found between final grain yield and the weather factors during the early growth phase. In contrast, significant correlations were found between grain yield and total solar radiation gap, sunshine hour gap, diurnal temperature range and relative humidity during the late growing phase. To disentangle the confounding effects of various weather factors, and test the isolated effect of air pollution induced changes in incoming global solar radiation on yield under ceteris paribus conditions, crop model based scenario-analysis was conducted. The simulation results of the calibrated Agricultural Production Systems Simulator (APSIM) model indicated that a reduction in radiation by 10% might cause a yield reduction by more than 10%. Increasing incident radiation by 10% would lead to yield increases of (only) 7%, with the effects being much stronger during the late growing phase compared to the early growing phase. However, there is evidence that APSIM overestimates the effect of air pollution induced changes on radiation, as it does not consider the changes in radiative properties of solar insulation, i.e. the relative increase of diffuse over direct radiation, which may partly alleviate the negative effects of reduced total radiation by air pollution. Concluding, the present study could not detect a significantly negative effect of air pollution on wheat yields in the NCP.

Contrast-enhanced digital mammography (CEDM): imaging modeling, computer simulations, and phantom study

NASA Astrophysics Data System (ADS)

Chen, Biao; Jing, Zhenxue; Smith, Andrew

2005-04-01

Contrast enhanced digital mammography (CEDM), which is based upon the analysis of a series of x-ray projection images acquired before/after the administration of contrast agents, may provide physicians critical physiologic and morphologic information of breast lesions to determine the malignancy of lesions. This paper proposes to combine the kinetic analysis (KA) of contrast agent uptake/washout process and the dual-energy (DE) contrast enhancement together to formulate a hybrid contrast enhanced breast-imaging framework. The quantitative characteristics of materials and imaging components in the x-ray imaging chain, including x-ray tube (tungsten) spectrum, filter, breast tissues/lesions, contrast agents (non-ionized iodine solution), and selenium detector, were systematically modeled. The contrast-noise-ration (CNR) of iodinated lesions and mean absorbed glandular dose were estimated mathematically. The x-ray techniques optimization was conducted through a series of computer simulations to find the optimal tube voltage, filter thickness, and exposure levels for various breast thicknesses, breast density, and detectable contrast agent concentration levels in terms of detection efficiency (CNR2/dose). A phantom study was performed on a modified Selenia full field digital mammography system to verify the simulated results. The dose level was comparable to the dose in diagnostic mode (less than 4 mGy for an average 4.2 cm compressed breast). The results from the computer simulations and phantom study are being used to optimize an ongoing clinical study.

Validation of Microphysical Schemes in a CRM Using TRMM Satellite

NASA Astrophysics Data System (ADS)

Li, X.; Tao, W.; Matsui, T.; Liu, C.; Masunaga, H.

2007-12-01

The microphysical scheme in the Goddard Cumulus Ensemble (GCE) model has been the most heavily developed component in the past decade. The cloud-resolving model now has microphysical schemes ranging from the original Lin type bulk scheme, to improved bulk schemes, to a two-moment scheme, to a detailed bin spectral scheme. Even with the most sophisticated bin scheme, many uncertainties still exist, especially in ice phase microphysics. In this study, we take advantages of the long-term TRMM observations, especially the cloud profiles observed by the precipitation radar (PR), to validate microphysical schemes in the simulations of Mesoscale Convective Systems (MCSs). Two contrasting cases, a midlatitude summertime continental MCS with leading convection and trailing stratiform region, and an oceanic MCS in tropical western Pacific are studied. The simulated cloud structures and particle sizes are fed into a forward radiative transfer model to simulate the TRMM satellite sensors, i.e., the PR, the TRMM microwave imager (TMI) and the visible and infrared scanner (VIRS). MCS cases that match the structure and strength of the simulated systems over the 10-year period are used to construct statistics of different sensors. These statistics are then compared with the synthetic satellite data obtained from the forward radiative transfer calculations. It is found that the GCE model simulates the contrasts between the continental and oceanic case reasonably well, with less ice scattering in the oceanic case comparing with the continental case. However, the simulated ice scattering signals for both PR and TMI are generally stronger than the observations, especially for the bulk scheme and at the upper levels in the stratiform region. This indicates larger, denser snow/graupel particles at these levels. Adjusting microphysical schemes in the GCE model according the observations, especially the 3D cloud structure observed by TRMM PR, result in a much better agreement.

Comprehensive MRI simulation methodology using a dedicated MRI scanner in radiation oncology for external beam radiation treatment planning

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

Paulson, Eric S., E-mail: epaulson@mcw.edu; Erickson, Beth; Schultz, Chris

Purpose: The use of magnetic resonance imaging (MRI) in radiation oncology is expanding rapidly, and more clinics are integrating MRI into their radiation therapy workflows. However, radiation therapy presents a new set of challenges and places additional constraints on MRI compared to diagnostic radiology that, if not properly addressed, can undermine the advantages MRI offers for radiation treatment planning (RTP). The authors introduce here strategies to manage several challenges of using MRI for virtual simulation in external beam RTP. Methods: A total of 810 clinical MRI simulation exams were performed using a dedicated MRI scanner for external beam RTP ofmore » brain, breast, cervix, head and neck, liver, pancreas, prostate, and sarcoma cancers. Patients were imaged in treatment position using MRI-optimal immobilization devices. Radiofrequency (RF) coil configurations and scan protocols were optimized based on RTP constraints. Off-resonance and gradient nonlinearity-induced geometric distortions were minimized or corrected prior to using images for RTP. A multidisciplinary MRI simulation guide, along with window width and level presets, was created to standardize use of MR images during RTP. A quality assurance program was implemented to maintain accuracy and repeatability of MRI simulation exams. Results: The combination of a large bore scanner, high field strength, and circumferentially wrapped, flexible phased array RF receive coils permitted acquisition of thin slice images with high contrast-to-noise ratio (CNR) and image intensity uniformity, while simultaneously accommodating patient setup and immobilization devices. Postprocessing corrections and alternative acquisition methods were required to reduce or correct off-resonance and gradient nonlinearity induced geometric distortions. Conclusions: The methodology described herein contains practical strategies the authors have implemented through lessons learned performing clinical MRI simulation exams. In their experience, these strategies provide robust, high fidelity, high contrast MR images suitable for external beam RTP.« less

Soft-tissue and phase-contrast imaging at the Swiss Light Source

NASA Astrophysics Data System (ADS)

Schneider, Philipp; Mohan, Nishant; Stampanoni, Marco; Muller, Ralph

2004-05-01

Recent results show that bone vasculature is a major contributor to local tissue porosity, and therefore can be directly linked to the mechanical properties of bone tissue. With the advent of third generation synchrotron radiation (SR) sources, micro-computed tomography (μCT) with resolutions in the order of 1 μm and better has become feasible. This technique has been employed frequently to analyze trabecular architecture and local bone tissue properties, i.e. the hard or mineralized bone tissue. Nevertheless, less is known about the soft tissues in bone, mainly due to inadequate imaging capabilities. Here, we discuss three different methods and applications to visualize soft tissues. The first approach is referred to as negative imaging. In this case the material around the soft tissue provides the absorption contrast necessary for X-ray based tomography. Bone vasculature from two different mouse strains was investigated and compared qualitatively. Differences were observed in terms of local vessel number and vessel orientation. The second technique represents corrosion casting, which is principally adapted for imaging of vascular systems. The technique of corrosion casting has already been applied successfully at the Swiss Light Source. Using the technology we were able to show that pathological features reminiscent of Alzheimer"s disease could be distinguished in the brain vasculature of APP transgenic mice. The third technique discussed here is phase contrast imaging exploiting the high degree of coherence of third generation synchrotron light sources, which provide the necessary physical conditions for phase contrast. The in-line approach followed here for phase contrast retrieval is a modification of the Gerchberg-Saxton-Fienup type. Several measurements and theoretical thoughts concerning phase contrast imaging are presented, including mathematical phase retrieval. Although up-to-now only phase images have been computed, the approach is now ready to retrieve the phase for a large number of angular positions of the specimen allowing application of holotomography, which is the three-dimensional reconstruction of phase images.

Quantification of synthesized hydration products using synchrotron microtomography and spectral analysis

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

Deboodt, Tyler; Ideker, Jason H.; Isgor, O. Burkan

2017-12-01

The use of x-ray computed tomography (CT) as a standalone method has primarily been used to characterize pore structure, cracking and mechanical damage in cementitious systems due to low contrast in the hydrated phases. These limitations have resulted in the inability to extract quantifiable information on such phases. The goal of this research was to address the limitations caused by low contrast and improving the ability to distinguish the four primary hydrated phases in portland cement; C-S-H, calcium hydroxide, monosulfate, and ettringite. X-ray CT on individual layers, binary mixtures of phases, and quaternary mixtures of phases to represent a hydratedmore » portland cement paste were imaged with synchrotron radiation. Known masses of each phase were converted to a volume and compared to the segmented image volumes. It was observed that adequate contrast in binary mixing of phases allowed for segmentation, and subsequent image analysis indicated quantifiable volumes could be extracted from the tomographic volume. However, low contrast was observed when C-S-H and monosulfate were paired together leading to difficulties segmenting in an unbiased manner. Quantification of phases in quaternary mixtures included larger errors than binary mixes due to histogram overlaps of monosulfate, C-S-H, and calcium hydroxide.« less

Phase Contrast Microscopy Analysis of Breast Tissue

PubMed Central

Wells, Wendy A.; Wang, Xin; Daghlian, Charles P.; Paulsen, Keith D.; Pogue, Brian W.

2010-01-01

OBJECTIVE To assess how optical scatter properties in breast tissue, as measured by phase contrast microscopy and interpreted pathophysiologically, might be exploited as a diagnostic tool to differentiate cancer from benign tissue. STUDY DESIGN We evaluated frozen human breast tissue sections of adipose tissue, normal breast parenchyma, benign fibroadenoma tumors and noninvasive and invasive malignant cancers by phase contrast microscopy through quantification of grayscale values, using multiple regions of interest (ROI). Student’s t tests were performed on phase contrast measures across diagnostic categories testing data from individual cases; all ROI data were used as separate measures. RESULTS Stroma demonstrated significantly higher scatter intensity than did epithelium, with lower scattering in tumor-associated stroma as compared with normal or benign-associated stroma. Measures were comparable for invasive and noninvasive malignant tumors but were higher than those found in benign tumors and were lowest in adipose tissue. CONCLUSION Significant differences were found in scatter coefficient properties of epithelium and stroma across diagnostic categories of breast tissue, particularly between benign and malignant-associated stroma. Improved understanding of how scatter properties correlate with morphologic criteria used in routine pathologic diagnoses could have a significant clinical impact as developing optical technology allows macroscopic in situ phase contrast imaging. PMID:19736867

Radial Modulation Contrast Imaging Using a 20-MHz Single-Element Intravascular Ultrasound Catheter

PubMed Central

Yu, Francois T. H.; Villanueva, Flordeliza S.; Chen, Xucai

2014-01-01

Contrast-enhanced intravascular ultrasound imaging is a promising tool for the characterization of coronary vasa vasorum proliferation, which has been identified as a marker of, and possible etiologic factor in, the development of high-risk atherosclerotic plaques. Resonance-based nonlinear detection methods have required the development of prototype catheters which are not commercially available, thus limiting clinical translation. In this study, we investigated the performances of a radial modulation imaging approach (25/3 MHz combination) using simulations, implemented it on a clinical 20-MHz rotating catheter, and tested it in a wall-less tissue-mimicking flow phantom perfused with lipid-encapsulated microbubbles (MBs). The effects of the phase lag, low-frequency pressure, and MB concentration on the envelope subtracted radial modulation signals were investigated as a function of depth. Our dual-pulse dual-frequency approach produced contrast-specific images with contrast-to-tissue improvements over B-mode of 15.1 ± 2.1 dB at 2 mm and 6.8 ± 0.1 dB at 4 mm depths. Using this imaging strategy, 200-μm-diameter cellulose tubing perfused with MBs could be resolved while surrounding tissue scattering was suppressed. These results raise promise for the detection of coronary vasa vasorum and may ultimately facilitate the detection of plaque at risk for rupture. PMID:24803134

Simulation of the Indian Summer Monsoon Using Comprehensive Atmosphere-land Interactions, in the Absence of Two-way Air-sea Interactions

NASA Technical Reports Server (NTRS)

Lim, Young-Kwon; Shin, D. W.; Cocke, Steven; Kang, Sung-Dae; Kim, Hae-Dong

2011-01-01

Community Land Model version 2 (CLM2) as a comprehensive land surface model and a simple land surface model (SLM) were coupled to an atmospheric climate model to investigate the role of land surface processes in the development and the persistence of the South Asian summer monsoon. Two-way air-sea interactions were not considered in order to identify the reproducibility of the monsoon evolution by the comprehensive land model, which includes more realistic vertical soil moisture structures, vegetation and 2-way atmosphere-land interactions at hourly intervals. In the monsoon development phase (May and June). comprehensive land-surface treatment improves the representation of atmospheric circulations and the resulting convergence/divergence through the improvements in differential heating patterns and surface energy fluxes. Coupling with CLM2 also improves the timing and spatial distribution of rainfall maxima, reducing the seasonal rainfall overestimation by approx.60 % (1.8 mm/d for SLM, 0.7 mm/dI for CLM2). As for the interannual variation of the simulated rainfall, correlation coefficients of the Indian seasonal rainfall with observation increased from 0.21 (SLM) to 0.45 (CLM2). However, in the mature monsoon phase (July to September), coupling with the CLM2 does not exhibit a clear improvement. In contrast to the development phase, latent heat flux is underestimated and sensible heat flux and surface temperature over India are markedly overestimated. In addition, the moisture fluxes do not correlate well with lower-level atmospheric convergence, yielding correlation coefficients and root mean square errors worse than those produced by coupling with the SLM. A more realistic representation of the surface temperature and energy fluxes is needed to achieve an improved simulation for the mature monsoon period.

Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study.

PubMed

ManickamAchari, Vijayan; Bryce, Richard A; Hashim, Rauzah

2014-01-01

The rational design of a glycolipid application (e.g. drug delivery) with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20%) in the hydrophobic region of the lamellar crystal (LC) phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.

Pressure-induced transformations in computer simulations of glassy water.

PubMed

Chiu, Janet; Starr, Francis W; Giovambattista, Nicolas

2013-11-14

Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a "P-T phase diagram" for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water.

Pressure-induced transformations in computer simulations of glassy water

NASA Astrophysics Data System (ADS)

Chiu, Janet; Starr, Francis W.; Giovambattista, Nicolas

2013-11-01

Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a "P-T phase diagram" for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water.