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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↗

NASA NTRS2002

Interchange Method in Compressible Magnetized Couette Flow: Magnetorotational and Magnetoconvective Instabilities

We obtain the general forms of the axisymmetric stability criteria in a magnetized compressible Couette flow using an energy variational principle, the so-called interchange or Chandrasekhar s met hod, which we applied successfully in the incompressible case. This formulation accounts for the simultaneous presence of gravity, rotation, a toroidal magnetic field, a weak axial magnetic field, entropy gradients, and density gradients in the initial equilibrium state. The power of the method lies in its simplicity which allows us to derive extremely compact and physically clear expressions for the relevant stability criteria despite the inclusion of so many physical effects. In the implementation of the method, all the applicable conservation laws are explicitly taken into account during the variations of a quantity with dimensions of energy which we call the free energy function. As in the incompressible case, the presence of an axial field invalidates the conservation laws of angular momentum and azimuthal magnetic flux and introduces instead isorotation and axial current conservation along field lines. Our results are therefore markedly different depending on whether an axial magnetic field is present, and generalize in two simple expressions all previously known, partial stability criteria for the appearance of magnetorotational instability. Furthermore, the coupling between magnetic tension and buoyancy and its influence to the dynamics of nonhomoentropic magnetized flows becomes quite clear from our results. In the limits of plane-parallel atmospheres and homoentropic flows, our formulation easily recovers the stability criteria for suppression of convective and Parker instabilities, as well as some related special cases studied over 40 years ago by Newcomb and Tserkovnikov via laborious variational techniques.

Christodoulou, Dimitris M.↗

NASA NTRS2003

Radiative Heat Loss Measurements During Microgravity Droplet Combustion in a Slow Convective Flow

Radiative heat loss from burning droplets in a slow convective flow under microgravity conditions is measured using a broad-band (0.6 to 40 microns) radiometer. In addition, backlit images of the droplet as well as color images of the flame were obtained using CCD cameras to estimate the burning rates and the flame dimensions, respectively. Tests were carried out in air at atmospheric pressure using n-heptane and methanol fuels with imposed forced flow velocities varied from 0 to 10 centimeters per second and initial droplet diameters varied from 1 to 3 millimeters. Slow convective flows were generated using three different experimental configurations in three different facilities in preparation for the proposed International Space Station droplet experiments. In the 2.2 Second Drop-Tower Facility a droplet supported on the leading edge of a quartz fiber is placed within a flow tunnel supplied by compressed air. In the Zero-Gravity Facility (five-second drop tower) a tethered droplet is translated in a quiescent ambient atmosphere to establish a uniform flow field around the droplet. In the KC 135 aircraft an electric fan was used to draw a uniform flow past a tethered droplet. Experimental results show that the burn rate increases and the overall flame size decreases with increases in forced-flow velocities over the range of flow velocities and droplet sizes tested. The total radiative heat loss rate, Q(sub r), decreases as the imposed flow velocity increases with the spherically symmetric combustion having the highest values. These observations are in contrast to the trends observed for gas-jet flames in microgravity, but consistent with the observations during flame spread over solid fuels where the burning rate is coupled to the forced flow as here.

Hicks, Michael C.↗

NASA NTRS2009

Device for Measuring Low Flow Speed in a Duct

A multiple-throat venturi system has been invented for measuring laminar flow of air or other gas at low speed (1 to 30 cm/s) in a duct while preserving the laminar nature of the flow and keeping the velocity profile across the duct as nearly flat as possible. While means for measuring flows at higher speeds are well established, heretofore, there have been no reliable means for making consistent, accurate measurements in this speed range. In the original application for which this system was invented, the duct leads into the test section of a low-speed wind tunnel wherein uniform, low-speed, laminar flow is required for scientific experiments. The system could also be used to monitor a slow flow of gas in an industrial process like chemical vapor deposition. In the original application, the multiple- throat venturi system is mounted at the inlet end of the duct having a rectangular cross section of 19 by 14 cm, just upstream of an assembly of inlet screens and flow straighteners that help to suppress undesired flow fluctuations (see Figure 1). The basic venturi measurement principle is well established: One measures the difference in pressure between (1) a point just outside the inlet, where the pressure is highest and the kinetic energy lowest; and (2) the narrowest part (the throat) of the venturi passage, where the kinetic energy is highest and the pressure is lowest. Then by use of Bernoulli s equation for the relationship between pressure and kinetic energy, the volumetric flow speed in the duct can be calculated from the pressure difference and the inlet and throat widths. The design of this system represents a compromise among length, pressure recovery, uniformity of flow, and complexity of assembly. Traditionally, venturis are used to measure faster flows in narrower cross sections, with longer upstream and downstream passages to maintain accuracy. The dimensions of the passages of the present venturi system are sized to provide a readily measurable pressure drop. Multiple throats are used to minimize the length needed to recover internal energy and enable the velocity profile to recover to near flatness.

Quinn, Frank↗

NASA NTRS2009

Measuring Thermal Conductivity of a Small Insulation Sample

Miller, Robert A.↗

NASA NTRS2020

Inter-species molecular attraction effect in the development of a two-species mixing layer

Simulations of fluid mixing occurring at high-pressures mandate the use of real-fluid equations of state to capture the effect of boh intermolecular repulsive forces and attractive forces which are neglected in perfect gases. Dedicated mixing rules account for these forces by providing a generic mapping of the mixture state-space onto a pure fluid domain. However, the specific inter-species molecular forces depend on the particular characteristics of the molecular pairs under consideration, and typically require the knowledge of binary interaction coefficients k_{αβ}. The impact of k_{αβ} on a flow field is as of now unclear; further, k_{αβ} is unknown for many molecular pairs and when unknown, set to be null. This study addresses the impact of k_{αβ} on the temporal evolution of a real-fluid mixing layer and uses Direct Numerical Simulation (DNS) to explore this impact. The results show differences between augmented attraction (k_{αβ}<0) and diminished attraction (k_{αβ}>0), affecting both fluid dynamics and diffusion processes. Specifically, in a binary mixing layer, it is observed that augmented attraction leads to delayed transition and mixing layer growth, manifested in the momentum layer thickness. The fractal dimension, which is a manifestation of interface corrugation, is calculated. These results provide an hitherto undocumented mechanism affecting the development of mixing layers.

Banuti, Daniel↗

NASA NTRS2007

Microfossils of Cyanobacteria in Carbonaceous Meteorites

During the past decade, Environmental and Field Emission Scanning Electron Microscopes have been used at the NASA/Marshall Space Flight Center to investigate freshly fractured interior surfaces of a large number of different types of meteorites. Large, complex, microfossils with clearly recognizable biological affinities have been found embedded in several carbonaceous meteorites. Similar forms were notably absent in all stony and nickel-iron meteorites investigated. The forms encountered are consistent in size and morphology with morphotypes of known genera of Cyanobacteria and microorganisms that are typically encountered in associated benthic prokaryotic mats. Even though many coccoidal and isodiametric filamentous cyanobacteria have a strong morphological convergence with some other spherical and filamentous bacteria and algae, many genera of heteropolar cyanobacteria have distinctive apical and basal regions and cellular differentiation that makes it possible to unambiguously recognize the forms based entirely upon cellular dimensions, filament size and distinctive morphological characteristics. For almost two centuries, these morphological characteristics have historically provided the basis for the systematics and taxonomy of cyanobacteria. This paper presents ESEM and FESEM images of embedded filaments and thick mats found in-situ in the Murchison CM2 and Orgueil cn carbonaceous meteorites. Comparative images are also provided for known genera and species of cyanobacteria and other microbial extremophiles. Energy Dispersive X-ray Spectroscopy (EDS) studies indicate that the meteorite filaments typically exhibit dramatic chemical differentiation with distinctive difference between the possible microfossil and the meteorite matrix in the immediate proximity. Chemical differentiation is also observed within these microstructures with many of the permineralized filaments enveloped within electron transparent carbonaceous sheaths. Elemental distributions of these embedded filaments are not consistent with recent cyanobacteria or other living or preserved microbial extremophiles that have been investigated during this research. The meteorite filaments often have nitrogen content below the sensitivity level of the EDS detector. Carbon, Sulphur, Iron or Silicon are often highly enriched and hence anomalous C/N and CIS ratios when compared with modem cyanobacteria. The meteorite forms that are unambiguously recognizable as biological filaments are interpreted as indigenous microfossils analogous to several known genera of modem cyanobacteria and associated trichomic filamentous prokaryotes.

Hoover, Richard B.↗

DOE OSTI2021

Searching for gauge theories with the conformal bootstrap

Infrared fixed points of gauge theories provide intriguing targets for the modern conformal bootstrap program. In this work we provide some preliminary evidence that a family of gauged fermionic CFTs saturate bootstrap bounds and can potentially be solved with the conformal bootstrap. We start by considering the bootstrap for SO( N ) vector 4-point functions in general dimension D . In the large N limit, upper bounds on the scaling dimensions of the lowest SO( N ) singlet and traceless symmetric scalars interpolate between two solutions at Δ = D/ 2 – 1 and Δ = D – 1 via generalized free field theory. In 3D the critical O ( N ) vector models are known to saturate the bootstrap bounds and correspond to the kinks approaching Δ = 1 / 2 at large N . We show that the bootstrap bounds also admit another infinite family of kinks \( {\mathcal{T}}_D \) , which at large N approach solutions containing free fermion bilinears at Δ = D – 1 from below. The kinks \( {\mathcal{T}}_D \) appear in general dimensions with a D -dependent critical N * below which the kink disappears. We also study relations between the bounds obtained from the bootstrap with SO( N ) vectors, SU( N ) fundamentals, and SU( N ) × SU( N ) bi-fundamentals. We provide a proof for the coincidence between bootstrap bounds with different global symmetries. We show evidence that the proper symmetries of the underlying theories of \( {\mathcal{T}}_D \) are subgroups of SO( N ), and we speculate that the kinks \( {\mathcal{T}}_D \) relate to the fixed points of gauge theories coupled to fermions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Fractal breakage of porous carbonate sand particles: Microstructures and mechanisms

In situ, three-dimensional (3D) characterizations of particle breakage in porous carbonate sands are presented, for the first time, with synchrotron-based micro computed tomography. Evolution of grain-scale characteristics are identified and quantified via elaborate image processing and topology analyses. The sequential 3D images reveal distinctly different fracture mechanisms for carbonate sands from silica sands. The angular shape of carbonate sand particles facilitates bending fracture, and particles with a lower sphericity and a higher porosity are more prone to break. 3D crack networks extracted from fractured particles imply considerable cleavage along initial pores. The fractal dimension of crack networks increases with external loading due to crack branching via cleavage. The resultant fragment size distribution also appears fractal and the fractal feature is valid down to the breakage limit of calcium carbonate. Crack propagation along the initial pores reduces the energy barrier for particle breakage and thus fracture strength of particles

Carbonate sands↗

DOE OSTI2022

Spectroscopy-based isotopic (δ 13 C) analysis for high spatial resolution of carbon exchange in the rhizosphere

The rhizosphere is a highly dynamic zone bridging plant roots with needed nutrient resources in soil. While the rhizosphere may be small, it has a disproportionally large impact on plant success and biomass production. A suite of rhizosphere-hosted microbial and geochemical interactions facilitate nutrient acquisition by plant roots, and, in turn, the roots stimulate these processes by supplying organic carbon into the rhizosphere. The small physical dimensions of the rhizosphere, however, can constrain efforts to elucidate key carbon exchange processes and their spatial extent and localization. We present a method for spatially resolved δ 13 C analysis of rhizosphere samples by coupling laser ablation (LA) sampling with isotopic analysis using capillary absorption spectroscopy (CAS) which differs from conventional mass spectrometer (MS) approaches. The CAS system has high sensitivity (requires fewer nanomoles of CO 2 per analysis) than comparable MS systems, which enables reduced sample size requirements to thereby improve spatial resolution (from 25 μm to as low as a projected 5 μm spatial resolution). We demonstrate the utility of CAS using rhizosphere samples from switchgrass plants exposed to 13 CO 2 . As a result, this technique will provide a capability for tracking the extent and spatial distribution of root exudate into the rhizosphere at highly detailed spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Anatomy of Protein Electrospray Ionization Mass Spectra by Superconducting Tunnel Junction Mass and Energy Spectrometry

Cryogenic superconducting tunnel junction (STJ) detectors have the advantage of single-particle sensitivity, high quantum efficiency, low noise, and the ability to detect the time and relative impact energy of deposited ions. This makes them attractive for use in mass spectrometry (MS) and as a form of energy spectrometry. STJ cryodetectors have been coupled to time-offlight (TOF) mass spectrometers equipped with a matrix-assisted laser desorption ionization (MALDI) source and to an electrospray ionization (ESI) TOF mass spectrometer. Here, a lab-made linear ion trap (LIT) mass spectrometer system was coupled to an ESI source and a 16-channel Nb-STJ array with improved readout electronics. The goal was to investigate fundamentals of ESI-generated protein ions by further exploiting the advantage of resolving these ions in a third dimension of the relative energy deposited into the STJs. The proteins equine cytochrome c, bovine carbonic anhydrase, bovine serum albumin, and murine immunoglobulin G were studied using this ESI-LIT-STJ-MS instrument. Multiply charged monomers, multimers, and fragments from metastable ions were resolved from monomer peaks by differences in ion deposition energy even when these ions have the same mass-to-charge ratio as the corresponding monomer. The determination of fragment mass from metastable decomposition is accomplished without knowing the charge state of the fragment. The average charge state of the multimers is reduced with each addition of a protein which is a direct reflection of the surface area available for charging. Multiply charged in-source fragments have also been observed and distinguished in the mass spectrum of carbonic anhydrase by using the differences in the energy deposited in the STJs.

42 ENGINEERING↗

DOE OSTI2022

Synergistic Enhancement of Lead and Selenate Uptake at the Barite (001)–Water Interface

The interactions of heavy metals with minerals influence the mobility and bioavailability of toxic elements in natural aqueous environments. The sorption of heavy metals on covalently bonded minerals is generally well described by surface complexation models (SCMs). However, understanding sorption on sparingly soluble minerals is challenging because of the dynamically evolving chemistry of sorbent surfaces. The interpretation can be even more complicated when multiple metal ions compete for sorption. In the present study, we observed synergistically enhanced uptake of lead and selenate on the barite (001) surface through two sorption mechanisms: lattice incorporation that dominates at lower coverages and two-dimensional monolayer growth that dominates at higher coverages. Further, we also observed a systematic increase in the sorption affinity with increasing co-sorbed ion coverages, different from the assumption of invariant binding constants for individual adsorption processes in classical SCMs. Computational simulations showed thermodynamically favorable co-incorporation of lead and selenate by simultaneously substituting for barium and sulfate in neighboring sites, resulting in the formation of molecular clusters that locally match the net dimension of the substrate lattice. These results emphasize the importance of ion–ion interactions at mineral–water interfaces that control the fate and transport of contaminants in the environment.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

The interplay between laser focusing conditions, expansion dynamics, ablation mechanisms, and emission intensity in ultrafast laser-produced plasmas

The interplay between ultrafast laser focusing conditions, emission intensity, expansion dynamics, and ablation mechanisms is critical to the detection of light isotopes relevant to nuclear energy, forensics, and geochemistry applications. Here, we study deuterium (2Hα) emission in plasmas generated from femtosecond laser ablation of a Zircaloy-4 target with a deuterium concentration of ≈37 at. %. Changes in emission intensity, plume morphology, crater dimensions, and surface modifications were investigated for varying focusing lens positions, where the laser was focused behind, at, and in front of the target. Spatially resolved optical emission spectroscopy and spectrally integrated plasma imaging were performed to investigate emission spectral features and plume morphology. Laser ablation crater dimensions and morphology were analyzed via optical profilometry and scanning electron microscopy. The 2Hα emission intensity showed significant reduction at the geometrical focal point or when the focal point is in front of the target. For all laser spot sizes, a two-component plume was observed but with different temporal histories. At the best focal point, the plume was spherical. When the laser was focused behind the target, the plume was elongated and propagated to farther distances than for the best focal position. In contrast, when the laser was focused in front of the target, filaments were generated in the beam path, and filament-plasma coupling occurred. By focusing the laser behind the target, the amount of material removal in the laser ablation process can be significantly reduced while still generating a plasma with a sufficient 2Hα emission signal for analysis.

Kautz, Elizabeth J. (ORCID:0000000263389223)↗

DOE OSTI2024

A three-point velocity estimation method for two-dimensional coarse-grained imaging data

Time delay and velocity estimation methods have been widely studied subjects in the context of signal processing, with applications in many different fields of physics. The velocity of waves or coherent fluctuation structures is commonly estimated as the distance between two measurement points divided by the time lag that maximizes the cross correlation function between the measured signals, but this is demonstrated to result in erroneous estimates for two spatial dimensions. We present an improved method to accurately estimate both components of the velocity vector, relying on three non-aligned measurement points. We introduce a stochastic process describing the fluctuations as a superposition of uncorrelated pulses moving in two dimensions. Using this model, we show that the three-point velocity estimation method, using time delays calculated through cross correlations, yields the exact velocity components when all pulses have the same velocity. The two- and three-point methods are tested on synthetic data generated from realizations of such processes for which the underlying velocity components are known. The results reveal the superiority of the three-point technique. Finally, we demonstrate the applicability of the velocity estimation on gas puff imaging data of strongly intermittent plasma fluctuations due to the radial motion of coherent, blob-like structures at the boundary of the Alcator C-Mod tokamak.

Materials Science↗

NASA NTRS1976

Lightcurves and the axis of rotation of 433 Eros

Ten lightcurves and UBV photometry of 433 Eros were obtained between August 1972 and May 1975. The absolute magnitude of the lightcurve maximum is 10.75 and the phase coefficient is 0.025 mag/deg. There may be a small difference in B-V color between the northern and southern hemispheres. The pole of the axis of rotation is directed toward 16 deg, ecliptic longitude and 12 deg ecliptic latitude, respectively, and the rotation is direct with a sidereal period of 5 hr 16 min 13.4 sec. The dimensions derived from the polarimetric albedo and the lightcurve amplitudes are 12 km by 12 km by 31 km for a smooth cylinder with hemispherical ends.

Dunlap, J. L.↗

NASA NTRS1981

An explicit mixed numerical method for mesoscale model

A mixed numerical method has been developed for mesoscale models. The technique consists of a forward difference scheme for time tendency terms, an upstream scheme for advective terms, and a central scheme for the other terms in a physical system. It is shown that the mixed method is conditionally stable and highly accurate for approximating the system of either shallow-water equations in one dimension or primitive equations in three dimensions. Since the technique is explicit and two time level, it conserves computer and programming resources.

Hsu, H.-M.↗

NASA NTRS1988

Accurate solutions, parameter studies and comparisons for the Euler and potential flow equations

Parameter studies are conducted using the Euler and potential flow equation models for unsteady and steady flows in both two and three dimensions. The Euler code is an implicit, upwind, finite volume code which uses the Van Leer method of flux-vector-splitting which has been recently extended for use on dynamic meshes and maintain all the properties of the original splitting. The potential flow code is an implicit, finite difference method for solving the transonic small disturbance equations and incorporates both entropy and vorticity corrections into the solution procedures thereby extending its applicability into regimes where shock strength normally precludes its use. Parameter studies resulting in benchmark type calculations include the effects of spatial and temporal refinement, spatial order of accuracy, far field boundary conditions for steady flow, frequency of oscillation, and the use of subiterations at each time step to reduce linearization and factorization errors. Comparisons between Euler and potential flows results are made as well as with experimental data where available.

Anderson, W. Kyle↗

NASA NTRS1990

Obtaining an equivalent beam

In modeling a complex structure the researcher was faced with a component that would have logical appeal if it were modeled as a beam. The structure was a mast of a robot controlled gantry crane. The structure up to this point already had a large number of degrees of freedom, so the idea of conserving grid points by modeling the mast as a beam was attractive. The researcher decided to make a separate problem of of the mast and model it in three dimensions with plates, then extract the equivalent beam properties by setting up the loading to simulate beam-like deformation and constraints. The results could then be used to represent the mast as a beam in the full model. A comparison was made of properties derived from models of different constraints versus manual calculations. The researcher shows that the three-dimensional model is ineffective in trying to conform to the requirements of an equivalent beam representation. If a full 3-D plate model were used in the complete representation of the crane structure, good results would be obtained. Since the attempt is to economize on the size of the model, a better way to achieve the same results is to use substructuring and condense the mast to equivalent end boundary and intermediate mass points.

Butler, Thomas G.↗