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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
NASA NTRS1998

New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces. Measuring these units was not attempted before and most studies have assumed that the growth unit consisted of individual protein molecules. The linescan mode of AFM instruments allows the crystal surface to be scanned along a single line. By scanning across a growth step an image showing the motion of the step is obtained. Normally such an image shows a straight line for continuous and constant step velocity. In this study by increasing the scan rate and by decreasing the step velocity (by decreasing the supersaturation), we were able to capture images of individual growth events, shown by jump discontinuities in the step line. By suitable integration of the image the growth unit dimension in the scanned direction can be obtained. Since multiple units can be involved in the growth process it is necessary to collect a statistically relevant sample before drawing conclusions about the growth mechanism. This technique was successfully employed to obtain the dimensions of growth units for the (110) face, showing that they consisted of various aggregates corresponding to the 43 helices in the crystal structure.

Li, Huayu↗
DOE OSTI2022

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs

One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Simultaneous measurements of velocity and pressure fields in subsonic and supersonic flows through image-intensified detection of laser-induced fluorescence

An optical technique is presented for combined, spatially resolved measurements of two-dimensional velocity and pressure fields in compressible flows. The single-mode frequency of an argon laser is fixed in the wing of an absorption line of iodine molecules, seeded in an underexpanded round jet of nitrogen gas. The emitted fluorescence, being proportional to the amount of absorbed radiation and hence the absorption line-shape function, is detected with an intensified 100 x 100 photodiode array camera. A single-microchannel-plate image intensifier is fiber-optically coupled to the array in order to improve time resolution and SNR. Three components of the velocity vector in a cross-sectional plane are sequentially probed with four laser sheets from three different directions. By shifting the laser frequency in one of the sheets with a piezo-tuned intra-cavity etalon, the slope of the absorption line can be measured in situ in order to provide the required scaling factor for the velocity measurement. With its short measurement times of less than 250 ms, this method is well suited for blow-down wind tunnel experiments.

Hiller, B.↗
NASA NTRS2004

Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen

Atomic oxygen is one of the predominant constituents of Earth's upper atmosphere. It is created by the photodissociation of molecular oxygen (O2) into single O atoms by ultraviolet radiation. It is chemically very reactive because a single O atom readily combines with another O atom or with other atoms or molecules that can form a stable oxide. The effects of atomic oxygen on the external surfaces of spacecraft in low Earth orbit can have dire consequences for spacecraft life, and this is a well-known and much studied problem. Much less information is known about the effects of atomic oxygen on the internal surfaces of spacecraft. This degradation can occur when openings in components of the spacecraft exterior exist that allow the entry of atomic oxygen into regions that may not have direct atomic oxygen attack but rather scattered attack. Openings can exist because of spacecraft venting, microwave cavities, and apertures for Earth viewing, Sun sensors, or star trackers. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft were simulated at the NASA Glenn Research Center by using Monte Carlo computational techniques. A two-dimensional model was used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of the distance into a parallel-walled cavity. The model allows the atomic oxygen arrival direction, the Maxwell Boltzman temperature, and the ram energy to be varied along with the interaction parameters of the degree of recombination upon impact with polymer or nonreactive surfaces, the initial reaction probability, the reaction probability dependence upon energy and angle of attack, degree of specularity of scattering of reactive and nonreactive surfaces, and the degree of thermal accommodation upon impact with reactive and non-reactive surfaces to be varied to allow the model to produce atomic oxygen erosion geometries that replicate actual experimental results from space. The degree of erosion of various interior locations was compared with the erosion that would occur external to the spacecraft. Results of one cavity model indicate that, at depths into a two-dimensional cavity that are equal to 10 cavity widths, the erosion on the walls of the cavity is less than that on the top surface by over 2 orders of magnitude. Wall erosion near the surface of a cavity depends on which wall is receiving direct atomic oxygen attack. However, deep in the cavity little difference is present. Testing of various cavity models such as these gives spacecraft designers an indication of the level of threat to sensitive interior surfaces for different geometries. Even though the Monte Carlo model is two-dimensional, it can be used to provide qualitative information about spacecraft openings that are three-dimensional by offering reasonable insight as to the nature of the attenuation of damage that occurs within a spacecraft in low Earth orbit. As shown, there is more erosion on the side seeing direct atomic oxygen attack until a depth of approximately 5 times the width of the opening, where the erosion is the same on both sides.

Banks, Bruce A.↗
NASA NTRS2012

Compound-Specific Isotopic Analysis of Meteoritic Amino Acids as a Tool for Evaluating Potential Formation Pathways

Measurements of stable hydrogen, carbon, and nitrogen isotopic ratios (delta D, delta C-13, delta N-15) of organic compounds can reveal information about their origin and formation pathways. Several formation mechanisms and environments have been postulated for the amino acids detected in carbonaceous chondrites. As each proposed mechanism utilizes different precursor molecules, the isotopic signatures of the resulting amino acids may point towards the most likely of these proposed pathways. The technique of gas chromatography coupled with mass spectrometry and isotope ratio mass spectrometry provides compound-specific structural and isotopic information from a single splitless injection, enhancing the amount of information gained from small amounts of precious samples such as carbonaceous chondrites. We have applied this technique to measure the compound-specific C, N, and H isotopic ratios of amino acids from seven CM and CR carbonaceous chondrites. We are using these measurements to evaluate predictions of expected isotopic enrichments from potential formation pathways and environments, leading to a better understanding of the origin of these compounds.

Elsila, Jamie E.↗
DOE OSTI2022

Methods to Calculate Electronic Excited-State Dynamics for Molecules on Large Metal Clusters with Many States: Ensuring Fast Overlap Calculations and a Robust Choice of Phase

Here, we present an efficient set of methods for propagating excited-state dynamics involving a large number of configuration interaction singles (CIS) or Tamm-Dancoff approximation (TDA) single-reference excited states. Specifically, (i) following Head-Gordon et al., we implement an exact evaluation of the overlap of singly-excited CIS/TDA electronic states at different nuclear geometries using a biorthogonal basis and (ii) we employ a unified protocol for choosing the correct phase for each adiabat at each geometry. For many-electron systems, the combination of these techniques significantly reduces the computational cost of integrating the electronic Schrodinger equation and imposes minimal overhead on top of the underlying electronic structure calculation. As a demonstration, we calculate the electronic excited-state dynamics for a hydrogen molecule scattering off a silver metal cluster, focusing on high-lying excited states, where many electrons can be excited collectively and crossings are plentiful. Interestingly, we find that the high-lying, plasmon-like collective excitation spectrum changes with nuclear dynamics, highlighting the need to simulate non-adiabatic nuclear dynamics and plasmonic excitations simultaneously. In the future, the combination of methods presented here should help theorists build a mechanistic understanding of plasmon-assisted charge transfer and excitation energy relaxation processes near a nanoparticle or metal surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Quantum interferometry and pathway selectivity in the nonlinear response of photosynthetic excitons

We propose a time–frequency resolved spectroscopic technique which employs nonlinear interferometers to study exciton–exciton scattering in molecular aggregates. A higher degree of control over the contributing Liouville pathways is obtained as compared to classical light. We show how the nonlinear response can be isolated from the orders-of-magnitude stronger linear background by either phase matching or polarization filtering. Both arise due to averaging the signal over a large number of noninteracting, randomly oriented molecules. We apply our technique to the Frenkel exciton model which excludes charge separation for the photosystem II reaction center. We show how the sum of the entangled photon frequencies can be used to select two-exciton resonances, while their delay times reveal the single-exciton levels involved in the optical process.

Science & Technology - Other Topics↗
NASA NTRS1990

Simultaneous measurements of velocity, temperature, and pressure using rapid CW wavelength-modulation laser-induced fluorescence of OH

In high speed flows, laser induced fluorescence (LIF) on Doppler shifted transitions is an attractive technique for velocity measurement. LIF velocimetry was applied to combined single-point measurements of velocity, temperature, and pressure and 2-D imaging of velocity and pressure. Prior to recent research using NO, LIF velocimetry in combustion related flows relied largely on the use of seed molecules. Simultaneous, single-point LIF measurements is reported of velocity, temperature, and pressure using the naturally occurring combustion species OH. This experiment is an extension of earlier research in which a modified ring dye laser was used to make time resolved temperature measurements behind reflected shock waves by using OH absorption an in postflame gases by using OH LIF. A pair of fused-silica rhombs mounted on a single galvanonmeter in an intracavity-doubled Spectra-Physics 380 ring laser permit the UV output to be swept continuously over a few wave numbers at an effective frequency of 3kHz.

Chang, A. Y.↗
NASA NTRSDate not supplied

Demonstration of Frequency-Scanning Burst-mode Filtered Rayleigh Scattering for Multi-Parameter Gas-Phase Measurements

Filtered Rayleigh scattering (FRS) is a diagnostic technique used for measurements of macroscopic properties of a gas. The FRS signal is passed through a narrow bandwidth molecular filter, commonly gaseous iodine, to measure the broadening and Doppler-shift of the scattering light from the molecules of the gas flow. However, in single-frequency, intensity-based approaches, the effects of pressure, temperature, and velocity can be difficult to deconvolve. To overcome this challenge, frequency-scanning FRS has been used to quasi-spectrally resolve the signal. In this work, a frequency-scanned, burst-mode laser was used to perform scanning FRS in an underexpanded jet to measure temperature, pressure, and radial velocity at measurement rates up to 1 kHz which is ~100,000 times faster than prior implementations of scanning FRS.

filtered Rayleigh scattering↗
NASA NTRS1972

Preferential orientation of CO adsorption on Ni as determined by extended Hueckel calculations.

The adsorption of CO on the nickel surface has been calculated using a modified extended Hueckel technique for a number of different orientations of the CO with respect to the nickel surface. The calculations show that double site adsorption with the CO molecule normal to the surface and the carbon atom closest to the metal gives the most stable configuration (2.57 eV). The single site absorbs with an energy of 2.39 eV. However, other configurations also give fairly large bonding energies. The CO normal to the surface with oxygen closest to the metal gives a heat of adsorption of 0.37 eV. Two-center adsorption with the CO axis parallel to the surface and the molecule symmetrically placed between the nearest neighbors gives a chemisorption energy of 1.34 eV. These values compare with an experimental value of 1.98 eV.

Robertson, J. C.↗
NASA NTRS1990

New parameter-free polarization potentials in low-energy positron collisions

The polarization potential plays a decisive role in shaping up the cross sections in low energy positron collisions with atoms and molecules. However, its inclusion without involving any adjustable parameter, is still a challenge. Various other techniques employed so far for positron collisions are summarized, and a new, nonadjustable and very simple form of the polarization potential for positron-atom (molecule) collisions below the threshold of positronium formation is discussed. This new recently proposed potential is based on the correlation energy of a single positron in a homogeneous electron gas. The correlation energy was calculated by solving the Schrodinger equation of the positron-electron system and fitted to an analytical form in various ranges of the density parameter. In the outside region, the correlation energy is joined smoothly with the correct asymptotic form. This new positron correlation polarization (PCOP) potential was tested on several atomic and molecular targets such as the Ar, CO, and CH4. The results on the total and differential cross sections on these targets are shown along with the experimental data where available.

Jain, Ashok↗
NASA NTRS2008

NASA Tech Briefs, May 2008

Topics covered inclde: Deployable Wireless Camera Penetrators; Hand-Held Units for Short-Range Wireless Biotelemetry; Wearable Wireless Telemetry System for Implantable BioMEMS Sensors; Electronic Escape Trails for Firefighters; Architecture for a High-to-Medium-Voltage Power Converter; 24-Way Radial Power Combiner/Divider for 31 to 36 GHz; Three-Stage InP Submillimeter-Wave MMIC Amplifier; Fast Electromechanical Switches Based on Carbon Nanotubes; Solid-State High-Temperature Power Cells; Fast Offset Laser Phase-Locking System; Fabricating High-Resolution X-Ray Collimators; Embossed Teflon AF Laminate Membrane Microfluidic Diaphragm Valves; Flipperons for Improved Aerodynamic Performance; System Estimates Radius of Curvature of a Segmented Mirror; Refractory Ceramic Foams for Novel Applications; Self-Deploying Trusses Containing Shape-Memory Polymers; Fuel-Cell Electrolytes Based on Organosilica Hybrid Proton Conductors; Molecules for Fluorescence Detection of Specific Chemicals; Cell-Detection Technique for Automated Patch Clamping; Redesigned Human Metabolic Simulator; Compact, Highly Stable Ion Atomic Clock; LiGa(OTf)(sub 4) as an Electrolyte Salt for Li-Ion Cells; Compact Dielectric-Rod White-Light Delay Lines; Single-Mode WGM Resonators Fabricated by Diamond Turning; Mitigating Photon Jitter in Optical PPM Communication; MACOS Version 3.31; Fiber-Optic Determination of N2, O2, and Fuel Vapor in the Ullage of Liquid-Fuel Tanks; Spiking Neurons for Analysis of Patterns; Symmetric Phase-Only Filtering in Particle-Image Velocimetry; Efficient Coupler for a Bessel Beam Dispersive Element; and Attitude and Translation Control of a Solar Sail Vehicle.

Source record↗
NASA NTRS2021

ICESat-2 Atmospheric Channel Description, Data Processing and First Results

The Advanced Topographic Laser Altimeter System (ATLAS) was launched aboard the Ice Cloud and land-Elevation Satellite-2 (ICESat-2) satellite in September 2018. ATLAS is a single wavelength (532 nm) lidar system designed to acquire high resolution measurements of the earth's surface while also obtaining atmospheric backscatter from molecules, clouds, and aerosols. Because ATLAS is optimized for altimetry, the atmospheric data acquired is unique in many respects and requires non-standard analysis techniques. For example, the high repetition rate laser limits the vertical extent of the profiles to just 14 km and causes atmospheric scattering from above 15 km to be added to the scattering in the lower 0–14 km profile. In addition, the limited vertical range of the acquired profiles renders it difficult to compute the magnitude of the solar background and hinders the application of standard calibration techniques. Despite these limitations, methods have been developed to successfully produce data products that have value to the atmospheric community for cloud and aerosol research and are currently available at the National Snow and Ice Data Center (NSIDC). In this paper we describe the ICESat-2 atmospheric channel and the methods used to process the ATLAS raw photon count data to obtain calibrated backscatter and higher level products such as layer heights and type, blowing snow, column optical depth and apparent surface reflectance.

Stephen P Palm↗
NASA NTRS2007

Antibodies Against Three Forms of Urokinase

Antibodies that bind to preselected regions of the urokinase molecule have been developed. These antibodies can be used to measure small quantities of each of three molecular forms of urokinase that could be contained in microsamples or conditioned media harvested from cultures of mammalian cells. Previously available antibodies and assay techniques do not yield both clear distinctions among, and measurements of, all three forms. Urokinase is a zymogen that is synthesized in a single-chain form, called ScuPA, which is composed of 411 amino acid residues (see figure). ScuPA has very little enzyme activity, but it can be activated in two ways: (1) by cleavage of the peptide bond lysine 158/isoleucine 159 and the loss of lysine 158 to obtain the high molecular-weight (HMW) form of the enzyme or (2) by cleavage of the bond lysine 135/lysine 136 to obtain the low-molecular-weight (LMW) form of the enzyme. The antibodies in question were produced in mice and rabbits by use of peptides as immunogens. The peptides were selected to obtain antibodies that bind to regions of ScuPA that include the lysine 158/isoleucine 159 and the lysine 135/lysine 136 bonds. The antibodies include monoclonal and polyclonal ones that yield indications as to whether either of these bonds is intact. The polyclonal antibodies include ones that preferentially bind to the HMW or LMW forms of the urokinase molecule. The monoclonal antibodies include ones that discriminate between the ScuPA and the HMW form. A combination of these molecular-specific antibodies will enable simultaneous assays of the ScuPA, HMW, and LMW forms in the same specimen of culture medium.

Morrison, Dennis R.↗
NASA NTRS1984

Experimental techniques for cross-section measurements

Attention is given to electron collision phenomena which can be studied under single-collision conditions at low and intermediate electron impact energies, ranging from threshold to a few hundred eV, using gas phase molecular targets. Several of the experimental methods discussed were first developed and applied to atoms, but are equally applicable to molecules with minor modifications in the interpretation of the data, due to the greater complexity of molecular systems.

Trajmar, S.↗
DOE OSTI2023

Mid-infrared spectroscopy with a broadly tunable thin-film lithium niobate optical parametric oscillator

Mid-infrared spectroscopy, an important technique for sensing molecules, has encountered barriers from sources either limited in tuning range or excessively bulky for widespread use. We present a compact, efficient, and broadly tunable optical parametric oscillator surmounting these challenges. Leveraging dispersion-engineered thin-film lithium niobate-on-sapphire photonics and a singly resonant cavity allows broad, controlled tuning over an octave from 1.5–3.3 µm. The device generates >25mW of mid-infrared light at 3.2 µm with 15% conversion efficiency. The ability to precisely control the device’s mid-infrared emission enables spectroscopy of methane and ammonia, demonstrating our approach’s relevance for sensing. Our work signifies an important advance in nonlinear photonics miniaturization, bringing practical field applications of high-speed, broadband mid-infrared spectroscopy closer to reality.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS2003

Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

Vercoutere, Wenonah↗
NASA NTRS1983

Quantitative measurement of density and velocity in compressible flows using laser-induced iodine fluorescence

A nonintrusive optical technique for the quantitative measurement of molecular density and velocity at a point or in an entire cross-sectional plane of a compressible flowfield is reported. Iodine molecules, seeded into the flowfield reservoir, are excited by a tunable narrow-bandwidth laser and the resulting spatially-resolved fluorescence is collected by a single- or multiple-element detector. A theoretical model for the iodine laser-induced fluorescence process is essential for quantitative measurements and is developed using a rate-equation approach. Density measurements using laser-induced fluorescence are normally complicated by collisional quenching; however, the theory predicts that the off-resonant fluorescent signal is directly proportional to density. Velocity is directly related to the Doppler shift of the iodine absorption line, determined by monitoring the broadband fluorescent signal as the laser is tuned in frequency. Experiments in a steady supersonic flowfield are compared with numerical calculations to demonstrate the accuracy of the approach for density and velocity measurement and the lack of perturbation to the flowfield by the iodine seeding. Extensions of the current approach to density and velocity measurement in lower Mach number flows, to the measurement of pressure and temperature, and to temporally-resolved measurements are discussed.

Mcdaniel, J. C.↗