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All sourcesNASA NTRSDOE OSTI
NASA NTRS2005

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1 %, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. Preliminary experiments show that the presence of the fluorescent probe does not affect the nucleation process or the quality of the X-ray data obtained.

Pusey, Marc L.↗
NASA NTRS1983

Experiments with phase transitions at very high pressure

Diamond cells were constructed for use to 1 Mbar. A refrigerator for cooling diamond cells was adapted for studies between 15 and 300 K. A cryostat for superconductivity studies between 1.5 to 300 K was constructed. Optical equipment was constructed for fluorescence, transmission, and reflectance studies. X-ray equipment was adapted for use with diamond cells. Experimental techniques were developed for X-ray diffraction studies using synchrotron radiation. AC susceptibility techniques were developed for detecting superconducting transitions. The following materials were studied: compressed solidified gases (Xe, Ar), semiconductors (Ge, Si, GaAs), superconductors (Nb3Ge, Nb3Si, Nb3As, CuCl), molecular crystals (I).

Spain, I. L.↗
NASA NTRS1978

X-ray observations of a flare in NGC4151 from OSO-8

The 2-60 keV flux from NGC4151 changed by a factor of two on a timescale of 1.5 days. No fluctuations were detected in excess of a factor of three on timescales less than four hours. During a total observation of approximately 11 days there were no statistically significant changes in spectral shape. The spectrum was fitted by a power law with photon index alpha approximately 1.42 + or - 0.06 and column density N sub H approximately 7.5 + or - 0.5 x 10 to the 22d power at/cu cm. A 2 sigma residual to this fit implies fluorescent Fe line emission with E. W. approximately 240 eV. Both synchrotron self-Compton and thermal Compton models are consistent with the X-ray data.

Mushotzky, R. F.↗
NASA NTRS1978

X-ray observations of a flare in NGC 4151 from OSO 8

The 2-60-keV flux from NGC 4151 has been observed to change by a factor of 2 on a time scale of 1.5 days. No fluctuations in excess of a factor of 3 are detected on time scales less than 4 hours. During a total observation of approximately 11 days there were no statistically significant changes in spectral shape. The spectrum can be fitted by a power law with photon index of about 1.42 + or - 0.06 and a hydrogen column density of approximately 7.5 + or - 0.5 x 10 to the 22nd power atoms/sq cm. A 2-sigma residual to this fit implies fluorescent Fe line emission with an equivalent width of about 240 eV. Both synchrotron self-Compton and thermal Compton models are consistent with the X-ray data.

Mushotzky, R. F.↗
NASA NTRS1984

Experiments with phase transitions at very high pressure

A diamond anvil cell is described which was developed for studying hydrogen and other materials to pressure above 100 PGa, including measurements at low temperature. The benefits of X-ray diffraction using synchrotron radiation and using a fixed anode source are examined as well as the optimization of X-ray diffraction at low temperature. A Ge diode detector was incorporated into apparatus for measuring optical absorption, reflectance, and fluorescence in order to enable luminescence studies and Raman spectra were obtained. Results of experiments on Si, Ge, GaP, InAs, hydrogen, benzene, nitrogen, graphite, and the superconductor CeCu2Si2 are given.

Spain, I. L.↗
NASA NTRS1978

The X-ray emitting galaxy Centaurus A

OSO-8 X-ray observations of Cen A in 1975 and 1976 are reported. The source spectrum can be well fitted in both years by a power law of number index 1.66 and absorption due to 1.3 by 10 to the 23rd power atoms/sq cm. The total flux varied by a factor of 2 between 1975 and 1976. In 1976 there were flux variations of approximately 40% on a time scale of days. Measurements of the 6.4-keV Fe fluorescent line and the 7.1-keV absorption edge imply Fe/H of approximately 0.000016. Simultaneous radio measurements show variation in phase with X-ray variability. Consideration of radio, millimeter, infrared, and X-ray data shows that all the data can be accounted for by a model in which the X-rays are due to a synchrotron self-Compton source embedded in a cold H2 cloud.

Mushotzky, R. F.↗
NASA NTRS1977

The X-ray emitting galaxy Cen-A

OSO-8 X-ray observations of Cen-A in 1975 and 1976 are reported. The source spectrum is well fit in both years by a power law of number index 1.62 and absorption due to 1.3 x 10 to the 23rd power at/sq cm. The total flux varied by a factor 2 between 1975 and 1976. In 1976 there were approximately 40% flux variations on a time scale of days. The 6.4 keV Fe fluorescent line and the 7.1 keV absorption edge were measured implying Fe/H approximately equals .000016. Simultaneous radio measurements show variation in phase with X-ray variability. Models considering radio, milimeter, IR and X-ray data show that all the data can be accounted for by a model in which the X-rays are due to a synchrotron self-Compton source embedded in a cold H(2) cloud.

Mushotzky, R. F.↗
NASA NTRS2017

Recent Developments in X-Ray Diagnostics for Cryogenic and Optically Dense Coaxial Rocket Sprays

The mixing and atomization of propellants is often characterized by optically dense flow fields and complex breakup dynamics. In the development of propulsion systems, the complexity of relevant physics and the range of spatio-temporal scales often makes computational simulation impractical for full scale injector elements; consequently, continued research into improved systems for experimental flow diagnostics is ongoing. One area of non-invasive flow diagnostics which has seen widespread growth is using synchrotron based x-ray diagostics. Over the past 3 years, a series of water and cryogenic based experiments were performed at the Advanced Photon Source, Argonne National Lab, on a NASA in-house designed swirl co-axial rocket injector, designed for operation using liquid oxygen and liquid methane in support of Project Morpheus. A range of techniques, such as x-ray fluorescence and time-averaged radiography were performed providing qualitative and quantitative mass and phase distributions, and were complemented by investigations using time-resolved radiography and white beam imaging, which provided information on breakup and mixing dynamics. Results of these investigations are presented, and conclusions regarding the viability of x-ray based diagnostics are discussed.

Radke, Christopher D.↗
NASA NTRSDate not supplied

Initial analysis of “stone” size Ryugu samples: current status

As a part of the initial analysis of the Ryugu samples, we perform a variety of analyses of millimeter-sized "stones". Our goals are to elucidate the entire formation process of C-type asteroid Ryugu from the viewpoint of petrology and mineralogy ande obtain necessary information by sample analysis, and then simulate the formation of Ryugu based on the evidencef obtained rom sample analysis. Eighteen stones (8 from Room A and 10 from Room C) were received from the ISAS curation facility on June 1, 2021, and brought into a fully nitrogen-displaced glove box at Tohoku University. At the same time, we also received the powder samples from Room A and Room C. To completely block the atmosphere from leaking into the container, all samples were put in the sample transport containers prepared by ISAS, transferred from the main chamber to the glovebox at ISAS, and then all containers were completely sealed in plastic bags with moisture and oxygen absorbers. No moisture or oxygen was detected when the bags were opened in the glove box at Tohoku University, so it was confirmed that there was no exposure to the atmosphere during transport. To date, a number of analyses have been carried out successfully and almost on schedule. The analysis started with the measurement of reflectance spectra, which are sensitive to atmospheric oxidation, hydroxylation, and adsorbed water. The visible, near-infrared, and mid-infrared reflectance spectra were measured while the samples were kept airtight. The spectra of powder samples and stone samples (as aggregates and as single stone) were successfully obtained. A major feature of the stone team's analysis is the use of synchrotron radiation facilities around the world. Since this analysis is non-destructive, stone samples whose reflectance spectra were measured were sent to KEK, SPring-8, ESRF (France), SOLEIL (France), DESY (Germany), and APS (USA). Using these synchrotron radiation facilities, high spatial resolution and sensitivity XRD, STXM, XANES, CT [1], IR-CT, FT-IR [2, 3], XRF, and Mössbauer analyses were performed. Most of the analyses were carried out under air-tight conditions on the stone samples and the particulates separated from the stone samples. These analyses allowed us to determine the three-dimensional distribution of minerals and elements, redox state, density and porosity of the stone samples. Furthermore, as a characteristic analysis of the stone team, light elemental analysis using negative Muon was performed at the MLF facility of J-PARC with an exceptionally long allocation of machine time. This is the only non-destructive method to measure the concentration of light elements in the whole (not the surface) of stone samples. Because the characteristic X-rays produced by muon irradiation are much higher in energy than the fluorescent X-rays produced by X-ray irradiation, there is little effect of self-absorption by the sample, and therefore, the concentration of light elements such as carbon, oxygen, and Na in the entire "stone" sample can be determined. Some stone samples are currently being measured for heat and strength physical properties in order to understand the physical properties of asteroid Ryugu. The data obtained from these measurements are useful for interpreting the remote-sensing data data taken from the surface layer of the asteroid Ryugu [4-7]. It is also important for understanding the behavior of the Ryugu material during impact events. The surfaces of many stone samples were observed by electron microscopy and other techniques, especially on natural “flat” surfaces formed on 5 stomes. As a result, characteristric mineral aggregates formed by the reactions with water and characteiristic impact features were observed on some of the samples. Based on the observations of surfaces and the synchrotron measurements of the whole stones, important objects such as characteristic structures and specific crystal aggregates for understanding the formation history of the asteroid were identified, and these parts were separated from the stone samples using an Xe beam (pFIB) and analyzed by various methods including transmission electron microscopy and synchrotron radiation analysis. Many stone samples, from which important objects have been separated, are embedded in epoxy resin and cut to produce many polished sections. Electron microscopy and spectroscopic measurements of the polished surfaces are being carried out to reveal the detailed mineralogical properties and elemental distribution inside the stone samples. In the fall, machine time for synchrotron radiation will begin, and we plan to analyze single crystals and characteristic objects separated from the stone samples.

Tomoki Nakamura↗
NASA NTRS2015

Examining Volcanic Terrains Using In Situ Geochemical Technologies; Implications for Planetary Field Geology

Regardless of the target destination for the next manned planetary mission, the crew will require technology with which to select samples for return to Earth. The six Apollo lunar surface missions crews had only the tools to enable them to physically pick samples up off the surface or from a boulder and store those samples for return to the Lunar Module and eventually to Earth. Sample characterization was dependent upon visual inspection and relied upon their extensive geology training. In the four decades since Apollo however, great advances have been made in traditionally laboratory-based instrument technologies that enable miniaturization to a field-portable configuration. The implications of these advancements extend past traditional terrestrial field geology and into planetary surface exploration. With tools that will allow for real-time geochemical analysis, an astronaut can better develop a series of working hypotheses that are testable during surface science operations. One such technology is x-ray fluorescence (XRF). Traditionally used in a laboratory configuration, these instruments have now been developed and marketed commercially in a field-portable mode. We examine this technology in the context of geologic sample analysis and discuss current and future plans for instrument deployment. We also discuss the development of the Chromatic Mineral Identification and Surface Texture (CMIST) instrument at the NASA Goddard Space Flight Center (GSFC). Testing is taking place in conjunction with the RIS4E (Remote, In Situ, and Synchrotron Studies for Science and Exploration) SSERVI (Solar System Exploration and Research Virtual Institute) team activities, including field testing at Kilauea Volcano, HI..

Young, K. E.↗
NASA NTRS2016

NuSTAR and XMM-Newton Observations of the Hard X- Ray Spectrum of Centaurus A

We present simultaneous XMM-Newton and Nuclear Spectroscopic Telescope Array (NuSTAR) observations spanning 3-78 keV of the nearest radio galaxy, Centaurus A (Cen A). The accretion geometry around the central engine in Cen A is still debated, and we investigate possible configurations using detailed X-ray spectral modeling. NuSTAR imaged the central region of Cen A with subarcminute resolution at X-ray energies above 10 keV for the first time, but found no evidence for an extended source or other off-nuclear point sources. The XMM-Newton and NuSTAR spectra agree well and can be described with an absorbed power law with a photon index Gamma = 1.8150 +/- 0.005 and a fluorescent Fe Kaline in good agreement with literature values. The spectrum is greater than 1 MeV. A thermal Comptonization continuum describes the data well, with parameters that agree with values measured by INTEGRAL, in particular an electron temperature kTe between approximately 100-300 keV and seed photon input temperatures between 5 and 50 eV. We do not find evidence for reflection or a broad iron line and put stringent upper limits of R is less than 0.01 on the reflection fraction and accretion disk illumination. We use archival Chandra data to estimate the contribution from diffuse emission, extra-nuclear point sources, and the outer X-ray jet to the observed NuSTAR and XMM-Newton X-ray spectra and find the contribution to be negligible. We discuss different scenarios for the physical origin of the observed hard X-ray spectrum and conclude that the inner disk is replaced by an advection-dominated accretion flow or that the X-rays are dominated by synchrotron self-Compton emission from the inner regions of the radio jet or a combination thereof.

Galaxies: active - galaxies: individual (Centaurus↗
NASA NTRS2006

Fluorescent Applications to Crystallization

By covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and tests with model proteins have shown that labeling u to 5 percent of the protein molecules does not affect the X-ray data quality obtained . The presence of the trace fluorescent label gives a number of advantages. Since the label is covalently attached to the protein molecules, it "tracks" the protein s response to the crystallization conditions. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a darker background. Non-protein structures, such as salt crystals, do not show up under fluorescent illumination. Crystals have the highest protein concentration and are readily observed against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. Preliminary tests, using model proteins, indicates that we can use high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that more rapid amorphous precipitation kinetics may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Experiments are now being carried out to test this approach using a wider range, of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons.

Pusey, Marc L.↗
NASA NTRS2006

Fluorescent Approaches to High Throughput Crystallography

We have shown that by covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and the presence of the probe at low concentrations does not affect the X-ray data quality or the crystallization behavior. The presence of the trace fluorescent label gives a number of advantages when used with high throughput crystallizations. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a dark background. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Brightly fluorescent crystals are readily found against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. We are now testing the use of high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that kinetics leading to non-structured phases may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Preliminary experiments with test proteins have resulted in the extraction of a number of crystallization conditions from screening outcomes based solely on the presence of bright fluorescent regions. Subsequent experiments will test this approach using a wider range of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons.

Pusey, Marc L.↗
NASA NTRS2005

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, 51%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear hits. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Pusey, Marc L.↗
NASA NTRS2004

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically can not reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Pusey, Marc L.↗
NASA NTRS2004

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of a macromolecules purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals will show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "bits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Minamitani, Elizabeth Forsythe↗
NASA NTRS2016

The Mapping X-Ray Fluorescence Spectrometer (MAPX)

MapX will provide elemental imaging at ≤100 micron spatial resolution over 2.5 X 2.5 centimeter areas, yielding elemental chemistry at or below the scale length where many relict physical, chemical, and biological features can be imaged and interpreted in ancient rocks. MapX is a full-frame spectroscopic imager positioned on soil or regolith with touch sensors. During an analysis, an X-ray source (tube or radioisotope) bombards the sample surface with X-rays or αlpha-particles / gamma rays, resulting in sample X-ray Fluorescence (XRF). Fluoresced X-rays pass through an X-ray lens (X-ray μ-Pore Optic, "MPO") that projects a spatially resolved image of the X-rays onto a CCD. The CCD is operated in single photon counting mode so that the positions and energies of individual photons are retained. In a single analysis, several thousand frames are stored and processed. A MapX experiment provides elemental maps having a spatial resolution of ≤100 micron and quantitative XRF spectra from Regions of Interest (ROI) 2 centimers ≤ x ≤ 100 micron. ROI are compared with known rock and mineral compositions to extrapolate the data to rock types and putative mineralogies. The MapX geometry is being refined with ray-tracing simulations and with synchrotron experiments at SLAC. Source requirements are being determined through Monte Carlo modeling and experiment using XMIMSIM [1], GEANT4 [2] and PyMca [3] and a dedicated XRF test fixture. A flow-down of requirements for both tube and radioisotope sources is being developed from these experiments. In addition to Mars lander and rover missions, MapX could be used for landed science on other airless bodies (Phobos/Deimos, Comet nucleus, asteroids, the Earth's moon, and the icy satellites of the outer planets, including Europa.

Blake, David↗