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At least 127 records · Page 7

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗

Non-spectroscopic surface plasmon sensor with a tunable sensitivity

We demonstrate a non-spectroscopic surface plasmon sensor with a tunable sensitivity which is based on the relationship between the wave number of surface plasmon polaritons (SPPs) on metal film and the refractive index of the specimen in contact with the metal film. A change in the wave number of the SPPs results in a variation in the propagation angle of the leakage radiation of the SPPs. A reference light is used to interfere with the leakage radiation, and the refractive index of the specimen can be obtained by measuring the period of the interference fringes. The sensitivity of the sensor can be tuned by changing the incident direction of the reference light and this cannot be realized by conventional surface plasmon sensors. For a reference angle of 1.007°, the sensitivity and resolution of the sensor are 4629 μm/RIU (RIU stands for refractive index unit) and 3.6 × 10{sup −4} RIU, respectively. In addition, the sensor only needs a monochromatic light source, which simplifies the measurement setup and reduces the cost.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Response of large area avalanche photodiodes to low energy x rays

For an experiment to study neutron radiative beta-decay, we operated large area avalanche photodiodes (APDs) near liquid nitrogen temperature to detect x rays with energies between 0.2 keV and 20 keV. Whereas there are numerous reports of x ray spectrometry using APDs at energies above 1 keV, operation near liquid nitrogen temperature allowed us to reach a nominal threshold of 0.1 keV. However, due to the short penetration depth of x rays below 1 keV, the pulse height spectrum of the APD become complex. We studied the response using monochromatic x ray beams and employed phenomenological fits of the pulse height spectrum to model the measurement of a continuum spectrum from a synchrotron. In addition, the measured pulse height spectrum was modelled using a profile for the variation in efficiency of collection of photoelectrons with depth into the APD. The best results are obtained with the collection efficiency model.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quantitative electron density characterization of soft tissue substitute plastic materials using grating-based x-ray phase-contrast imaging

Many scientific research areas rely on accurate electron density characterization of various materials. For instance in X-ray optics and radiation therapy, there is a need for a fast and reliable technique to quantitatively characterize samples for electron density. We present how a precise measurement of electron density can be performed using an X-ray phase-contrast grating interferometer in a radiographic mode of a homogenous sample in a controlled geometry. A batch of various plastic materials was characterized quantitatively and compared with calculated results. We found that the measured electron densities closely match theoretical values. The technique yields comparable results between a monochromatic and a polychromatic X-ray source. Measured electron densities can be further used to design dedicated X-ray phase contrast phantoms and the additional information on small angle scattering should be taken into account in order to exclude unsuitable materials.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Reflection of a TE-polarised Gaussian beam from a layered structure under conditions of resonance excitation of waveguide modes

The problem of reflection of a TE-polarised Gaussian light beam from a layered structure under conditions of resonance excitation of waveguide modes using a total internal reflection prism is considered. Using the spectral approach we have derived the analytic expressions for the mode propagation lengths, widths and depths of m-lines (sharp and narrow dips in the angular dependence of the specular reflection coefficient), depending on the structure parameters. It is shown that in the case of weak coupling, when the propagation lengths l{sub m} of the waveguide modes are mainly determined by the extinction coefficient in the film, the depth of m-lines grows with the mode number m. In the case of strong coupling, when l{sub m} is determined mainly by the radiation of modes into the prism, the depth of m-lines decreases with increasing m. The change in the TE-polarised Gaussian beam shape after its reflection from the layered structure is studied, which is determined by the energy transfer from the incident beam into waveguide modes that propagate along the structure by the distance l{sub m}, are radiated in the direction of specular reflection and interfere with a part of the beam reflected from the working face of the prism. It is shown that this interference can lead to the field intensity oscillations near m-lines. The analysis of different methods for determining the parameters of thin-film structures is presented, including the measurement of mode angles θ{sub m} and the reflected beam shape. The methods are based on simultaneous excitation of a few waveguide modes in the film with a strongly focused monochromatic Gaussian beam, the waist width of which is much smaller than the propagation length of the modes. As an example of using these methods, the refractive index and the thickness of silicon monoxide film on silica substrate at the wavelength 633 nm are determined. (fibre and integrated-optical structures)

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Gamma-ray burst polarization via Compton scattering process

Synchrotron radiation and Compton scattering are widely accepted as the most likely emission mechanisms of some astrophysical phenomena, such as gamma-ray bursts (GRBs) and active galactic nuclei. The measurement of the polarization of photons provides a useful tool to distinguish different emission mechanisms and structures of the emission region. Based on the differential cross section of a polarized photon scattered by an unpolarized electron of any initial momentum, we derive an analytical formula of polarization for beamed photons scattered by isotropic electrons with a power-law distribution. Numerical calculations are carried out in four special cases: electrons at rest, Thomson limit, head-on collision, and monochromatic electrons. It is found that the maximum polarization can be as high as 100% for low energy photons, if the electrons are at rest. Although polarization is highly suppressed due to the isotropic electrons, a maximum value of ∼10%-20% can still be achieved. The Compton scattering process can be used to explain the polarization of GRB 041219A and GRB 100826A.

79 ASTRONOMY AND ASTROPHYSICS↗

X-ray background at high redshifts from pop III remnants: results from pop III star formation rates in the renaissance simulations

Due to their long mean free paths, X-rays are expected to have global impacts on the properties of the intergalactic medium (IGM) by their large-scale heating and ionizing processes. At high redshifts, X-rays from Population (Pop) III binaries might have important effects on cosmic reionization and the Lyα forest. As a continuation of our previous work on Pop III binary X-rays, we use the Pop III distribution and evolution from the Renaissance Simulations, a suite of self-consistent cosmological radiation hydrodynamics simulations of the formation of the first galaxies, to calculate the X-ray luminosity density and background over the redshift range 20⩾z⩾7.6. As we find that Pop III star formation continues at a low, nearly constant rate to the end of reionization, X-rays are being continuously produced at significant rates compared to other possible X-ray sources, such as AGNs and normal X-ray binaries during the same period of time. We estimate that Pop III binaries produce approximately 6 eV of energy in the X-rays per hydrogen atom. We calculate the X-ray background for different monochromatic photon energies. KeV X-rays redshift and accumulate to produce a strong X-ray background spectrum extending to roughly 500 eV. The X-ray background is strong enough to heat the IGM to ∼1000 K and to ionize a few percent of the neutral hydrogen. These effects are important for an understanding of the neutral hydrogen hyperfine transition 21 cm line signatures, the Lyα forest, and the Thomson optical depth to the CMB.

79 ASTRONOMY AND ASTROPHYSICS↗

A Practical Guide to Writing a Radiative Transfer Code

Using our decades-long experience in radiative transfer (RT) code development for Earth science, we endeavor to reduce the knowledge gap of bringing RT from theory to code quickly. Despite numerous classic and recent literature, it is still hard to develop anRT code from scratch within a few weeks. It is equally hard to understand, not to mention modify, an existing “monster” RT code, for which the developer is either located remotely or has retired. Following the format of “Numerical Recipes” by Press et al., we collocate in this paper small pieces of necessary theory with corresponding small pieces of RT code. These are arranged in an order that is natural for code development, which is often opposite of the natural order for laying out the theoretical basis. We focus on the transfer of unpolarized monochromatic solar radiation in a plane-parallel atmosphere over a reflecting surface. Both the surface and the atmosphere are homogeneous (uniform) at all directions. The multiple scattering is numerically solved using the deterministic method of Gauss-Seidel iterations. Except for the presented Python-Numba open-source RT code gsit, the paper does not report any new scientific results, but rather serves as an academic demonstration. If development time is an issue or the reader is familiar with basic concepts of RT theory, we recommend proceeding directly to Sec.3 “RT code development.

multiple light scattering↗

Wire number dependence of the implosion dynamics, stagnation, and radiation output of tungsten wire arrays at Z driver

We report results of the experimental campaign, which studied the initiation, implosion dynamics, and radiation yield of tungsten wire arrays as a function of the wire number. The wire array dimensions and mass were those of interest for the Z-pinch driven Inertial Confinement Fusion (ICF) program. An optimization study of the x-ray emitted peak power, rise time, and full width at half maximum was effectuated by varying the wire number while keeping the total array mass constant and equal to {approx}5.8 mg. The driver utilized was the {approx}20-MA Z accelerator before refurbishment in its usual short pulse mode of 100 ns. We studied single arrays of 20-mm diameter and 1-cm height. The smaller wire number studied was 30 and the largest 600. It appears that 600 is the highest achievable wire number with present day's technology. Radial and axial diagnostics were utilized including crystal monochromatic x-ray backlighter. An optimum wire number of {approx}375 was observed which was very close to the routinely utilized 300 for the ICF program in Sandia.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

System of laser pump and synchrotron radiation probe microdiffraction to investigate optical recording process

We have developed a system of laser-pump and synchrotron radiation probe microdiffraction to investigate the phase-change process on a nanosecond time scale of Ge{sub 2}Sb{sub 2}Te{sub 5} film embedded in multi-layer structures, which corresponds to real optical recording media. The measurements were achieved by combining (i) the pump-laser system with a pulse width of 300 ps, (ii) a highly brilliant focused microbeam with wide peak-energy width ({Delta}E/E {approx} 2%) made by focusing helical undulator radiation without monochromatization, and (iii) a precise sample rotation stage to make repetitive measurements. We successfully detected a very weak time-resolved diffraction signal by using this system from 100-nm-thick Ge{sub 2}Sb{sub 2}Te{sub 5} phase-change layers. This enabled us to find the dependence of the crystal-amorphous phase change process of the Ge{sub 2}Sb{sub 2}Te{sub 5} layers on laser power.

36 MATERIALS SCIENCE↗

CITIUS: An infrared-extreme ultraviolet light source for fundamental and applied ultrafast science

We present the main features of CITIUS, a new light source for ultrafast science, generating tunable, intense, femtosecond pulses in the spectral range from infrared to extreme ultraviolet (XUV). The XUV pulses (about 10{sup 5}-10{sup 8} photons/pulse in the range 14-80 eV) are produced by laser-induced high-order harmonic generation in gas. This radiation is monochromatized by a time-preserving monochromator, also allowing one to work with high-resolution bandwidth selection. The tunable IR-UV pulses (10{sup 12}-10{sup 15} photons/pulse in the range 0.4-5.6 eV) are generated by an optical parametric amplifier, which is driven by a fraction of the same laser pulse that generates high order harmonics. The IR-UV and XUV pulses follow different optical paths and are eventually recombined on the sample for pump-probe experiments. We also present the results of two pump-probe experiments: with the first one, we fully characterized the temporal duration of harmonic pulses in the time-preserving configuration; with the second one, we demonstrated the possibility of using CITIUS for selective investigation of the ultra-fast dynamics of different elements in a magnetic compound.

74 ATOMIC AND MOLECULAR PHYSICS↗

Gastrointestinal stromal tumor risk classification: spectral CT quantitative parameters

Purpose: To examine the value of spectral CT quantitative parameters in gastrointestinal stromal tumor (GIST) risk classification. Materials and methods: This retrospective study was approved by the institutional review board. The requirement for informed consent was signed. The authors evaluated 86 patients (30 high risk, 22 medium risk, 28 low risk, and 6 very low risk; mean age: 59 years [range 19–83 years]) with pathologically confirmed GIST who underwent plain and triple-phase contrast-enhanced CT with spectral CT imaging mode from March 2015 through September 2017, with manual follow-up. Quantitative parameters including the CT value of 70 keV monochromatic images, the slope of spectral curves, and the normalized iodine concentration (NIC) and water (iodine) concentrations were measured and calculated, and conducted a power analysis of the above data. Results: (1) The CT values at 70 keV of the high-risk group were higher than the intermediate and low groups in each of the enhanced phases (P ≤ 0.001), no significant differences in the intermediate-risk and low-risk groups were noted (P = 0.874, 0.871, 0.831, respectively). (2) The slope of the spectral curve of the high-risk group was higher than those of the intermediate and low groups in each of the enhanced phases (P ≤ 0.001), and there were no significant differences between the intermediate- and low-risk groups (P = 0.069, 0.466, 0.840, respectively). (3) The NIC of the high-risk group significantly differed from the lower risk groups (P ≤ 0.001). There was also no significant difference observed between the intermediate- and low-risk groups (P = 0.671, 0.457, 0.833, respectively). (4) The power analysis results show that only the low-risk group with delay period is 0.530, the rest groups are all greater than 0.999. Conclusion: Dual-energy spectral CT with quantitative analysis may help to increase the accuracy in differentiating the pathological risk classification of GIST between high risk and non-high risk, preoperatively. There were limitations for distinguishing the intermediate- and low-risk groups.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Nonlinear Second Harmonics of Localized Shear Waves in an Anisotropic Layer Between Anisotropic Half Spaces Under the Conditions of Imperfect Contact

We construct a numerical-analytic solution of the problem of generation of the nonlinear second harmonics in the course of propagation of elastic symmetric localized shear waves in the crystalline layer of cubic system of the m3m class located between the crystalline half spaces of the same type and the same class of anisotropy under the conditions of imperfect sliding contact of components of the waveguide. We determine the analytic form of the functions of wave motions for nonlinear anharmonic perturbations in the form of longitudinal-shear-type waves. We also perform the numerical investigations of the amplitude-frequency characteristics of the second harmonics for monochromatic localized waves in a layer of a single crystal of germanium between the half spaces from the single crystal of silicon.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Near-Edge Soft X-ray Absorption Mass Spectrometry of Protonated Melittin

We have investigated the photoionization and photofragmentation yields of gas-phase multiply protonated melittin cations for photon energies at the K-shell absorption edges of carbon, nitrogen, and oxygen. Two similar experimental approaches were employed. In both experiments, mass selected [melittin+qH]{sup q+} (q=2–4) ions were accumulated in radiofrequency ion traps. The trap content was exposed to intense beams of monochromatic soft X-ray photons from synchrotron beamlines and photoproducts were analyzed by means of time-of-flight mass spectrometry. Mass spectra were recorded for fixed photon energies, and partial ion yield spectra were recorded as a function of photon energy. The combination of mass spectrometry and soft X-ray spectroscopy allows for a direct correlation of protein electronic structure with various photoionization channels. Non-dissociative single and double ionization are used as a reference. The contribution of both channels to various backbone scission channels is quantified and related to activation energies and protonation sites. Soft X-ray absorption mass spectrometry combines fast energy deposition with single and double ionization and could complement established activation techniques. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Vacuum pair-production in a classical electric field and an electromagnetic wave

Using semiclassical WKB-methods, we calculate the rate of electron–positron pair-production from the vacuum in the presence of two external fields, a strong (space- or time-dependent) classical field and a monochromatic electromagnetic wave. We discuss the possible medium effects on the rate in the presence of thermal electrons, bosons, and neutral plasma of electrons and protons at a given temperature and chemical potential. Using our rate formula, we calculate the rate enhancement due to a laser beam, and discuss the possibility that a significant enhancement may appear in a plasma of electrons and protons with self-focusing properties. -- Highlights: •The electron–positron pair-production rate in an electric field and an electromagnetic wave. •The pair-production rate enhanced by the amplitude of the electromagnetic wave. •Its application for the superposition of the static electric field and laser beams. •Medium effects on the pair-production rate. •The enhancement of the pair-production rate by the self-focusing property of laser beams.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Light beams with general direction and polarization: Global description and geometric phase

We construct the manifold describing the family of plane monochromatic light waves with all directions, polarizations, phases and intensities. A smooth description of polarization, valid over the entire sphere S{sup 2} of directions, is given through the construction of an orthogonal basis pair of complex polarization vectors for each direction; any light beam is then uniquely and smoothly specified by giving its direction and two complex amplitudes. This implies that the space of all light beams is the six dimensional manifold S{sup 2}×C{sup 2}∖(0), the (untwisted) Cartesian product of a sphere and a two dimensional complex vector space minus the origin. A Hopf map (i.e. mapping the two complex amplitudes to the Stokes parameters) then leads to the four dimensional manifold S{sup 2}×S{sup 2} which describes beams with all directions and polarization states. This product of two spheres can be viewed as an ordered pair of two points on a single sphere, in contrast to earlier work in which the same system was represented using Majorana’s mapping of the states of a spin one quantum system to an unordered pair of points on a sphere. This is a different manifold, CP{sup 2}, two dimensional complex projective space, which does not faithfully represent the full space of all directions and polarizations. Following the now-standard framework, we exhibit the fibre bundle whose total space is the set of all light beams of non-zero intensity, and base space S{sup 2}×S{sup 2}. We give the U(1) connection which determines the geometric phase as the line integral of a one-form along a closed curve in the total space. Bases are classified as globally smooth, global but singular, and local, with the last type of basis being defined only when the curve traversed by the system is given. Existing as well as new formulae for the geometric phase are presented in this overall framework. -- Highlights: • We construct a polarization basis for light which is smooth in all directions. • Proof that the manifold of all polarizations and directions is S{sup 2}×S{sup 2}. • Formula for the geometric phase for paths in S{sup 2}×S{sup 2}, generalizing earlier work.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Theoretical study on optical response in nanostructures in the Born–Markov regime: The role of spontaneous emission and dephasing

We theoretically study the linear and nonlinear optical susceptibility in a nanostructure that interacts with a classical monochromatic optical field, by means of the solution of a Born–Markov master equation in the Lindblad form, considering as environment for the system the quantum vacuum of the continuum of modes of the external electromagnetic field. The processes of spontaneous emission and dephasing between two levels of the nanostructured quantum system are studied formally, within the framework of the quantum theory of open systems. It was found that the phenomenological master equation corresponds to a Born–Markov master equation in the Lindblad form that considers only the dissipative terms of spontaneous emission and dephasing, provided that the transverse coherence time T{sub 2} is smaller than spontaneous emission time T{sub 1}. Finally, comparative results are presented between the proposed methodology and the conventional method for: optical rectification, optical absorption, generation of second harmonic and generation of third harmonic in a cylindrical quantum dot (CQD) of AsGa∕AsGaAl with a hydrogen-like impurity inside it and under the action of a uniform magnetic field.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Characterization of morphology and hydration products of high-volume fly ash paste by monochromatic scanning x-ray micro-diffraction (μ-SXRD)

The present study focuses on identification and micro-structural characterization of the hydration products formed in high-volume fly ash (HVFA)/portland cement (PC) systems using monochromatic scanning x-ray micro-diffraction (μ-SXRD) and SEM-EDS. Pastes with up to 80% fly ash replacement were studied. Phase maps for HVFA samples using μ-SXRD patterns prove that μ-SXRD is an effective method to identify and visualize the distribution of phases in the matrix. μ-SXRD and SEM-EDS analysis shows that the C-S-H formed in HVFA system containing 50% or more of fly ash has a similar structure as C-S-H(I) with comparatively lower Ca/Si ratio than the one produced in PC system. Moreover, coexistence of C-S-H(I) and strätlingite is observed in the system containing 80% of fly ash, confirming that the amount of alumina and silicate phases provided by the fly ash is a major factor for the formation of C-S-H(I) and strätlingite in HVFA system. - Highlights: • High-volume fly ash (HVFA) paste was studied by scanning x-ray micro-diffraction. • Coexistence of C-S-H(I) and strätlingite in the HVFA system is clearly shown. • The distribution of minor phases in the HVFA system is shown. • Differences between inner and outer products of fly ash are observed by SEM-EDS.

36 MATERIALS SCIENCE↗