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DOE OSTI2020

Two-Nucleon Short-Range Correlations in Light Nuclei

Understanding the nucleon-nucleon interaction is a fundamental task in nuclear physics, as NN interaction models are a crucial input to modern nuclear structure calculations. While great progress has been made toward understanding this interaction, the available state-of-the-art models predict significantly different behaviors at short distances and high momenta (scale-and-scheme dependence), where two-nucleon Short-Range Correlations (SRCs) dominate the nuclear wave function. Thus, SRCs are a unique tool to constrain the NN interaction and vice versa. SRCs are naturallyoccurring high-local-density NN pairs that, as a result of their short-distance (approx. 0.1 fm) repulsive interaction, fly apart with high momenta, hence populating momentum states above the Fermi level. The study of SRCs also has significant implications for other fields, such as the astrophysics of neutron stars and the behavior of cold atomic gasses. This thesis describes experimental and phenomenological studies of the short-distance / high-momentum structure of the NN interaction through the study of SRCs and vice versa. Experimentally, I report the first measurement of the 3He and 3H(e,e'p) reactions in Hall A of the Thomas Jefferson National Accelerator Facility in kinematics in which the measured cross sections should be sensitive to the underlying nucleon momentum distributions in the range 40 to 500 MeV/c. The resulting cross-section ratios and absolute cross sections were compared to momentum-distribution ratios and precise cross-section calculations respectively. Phenomenologically, I report the generalization of the Contact Formalism (GCF) to nuclear systems, which exploits scale separation and universality to describe nucleons at short distances and high momenta.

Cruz Torres, Reynier↗

DOE OSTI2023

Evolution of the age-included nearest pair distribution in disperse multiphase flows

The age of the nearest particle pair is introduced as the difference between the current time and the most recent time when the nearest particle pair was formed. The evolution equation for the age-included nearest pair distribution function is derived. With the assumption of random destruction of the nearest particle pairs, the evolution equation predicts the exponential probability distribution of the ages of the nearest particle pairs. Particle-resolved numerical simulations with moving particles are performed to verify this prediction. The equation is then used to derive the evolution equation for the particle–fluid–particle (PFP) stress, which is known to be related to hyperbolicity of the two-fluid equations. It is found that the relaxation time of the age probability distribution is also the relaxation time for the PFP stress. Guided by the closure terms in the PFP stress evolution equation, we study kinematics of the nearest particle pairs in the particle-resolved simulations for flows caused by sedimentation of the particles with initially isotropic and homogeneous particle distributions. At the steady states, the particle Reynolds numbers are around 20. Anisotropy and inhomogeneity of particle distributions are seen to develop in these flows. The mean distances to the nearest particles and evolution of the distribution of the Voronoi cell volumes are studied. We also found the PFP stress is closely related to the changes in these inter-particle scale quantities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1991

Functional characteristics of the calcium modulated proteins seen from an evolutionary perspective

We have constructed dendrograms relating 173 EF-hand proteins of known amino acid sequence. We aligned all of these proteins by their EF-hand domains, omitting interdomain regions. Initial dendrograms were computed by minimum mutation distance methods. Using these as starting points, we determined the best dendrogram by the method of maximum parsimony, scored by minimum mutation distance. We identified 14 distinct subfamilies as well as 6 unique proteins that are perhaps the sole representatives of other subfamilies. This information is given in tabular form. Within subfamilies one can easily align interdomain regions. The resulting dendrograms are very similar to those computed using domains only. Dendrograms constructed using pairs of domains show general congruence. However, there are enough exceptions to caution against an overly simple scheme in which one pair of gene duplications leads from one domain precurser to a four domain prototype from which all other forms evolved. The ability to bind calcium was lost and acquired several times during evolution. The distribution of introns does not conform to the dendrogram based on amino acid sequences. The rates of evolution appear to be much slower within subfamilies, especially within calmodulin, than those prior to the definition of subfamily.

Kretsinger, R. H.↗

DOE OSTI2022

Node Distortion as a Tunable Mechanism for Negative Thermal Expansion in Metal–Organic Frameworks

Chemically functionalized series of metal–organic frameworks (MOFs), with subtle differences in local structure but divergent properties, provide a valuable opportunity to explore how local chemistry can be coupled to long-range structure and functionality. Using in situ synchrotron X-ray total scattering, with powder diffraction and pair distribution function (PDF) analysis, we investigate the temperature dependence of the local- and long-range structure of MOFs based on NU-1000, in which Zr 6 O 8 nodes are coordinated by different capping ligands (H 2 O/OH, Cl – ions, formate, acetylacetonate, and hexafluoroacetylacetonate). We show that the local distortion of the Zr 6 nodes depends on the lability of the ligand and contributes to a negative thermal expansion (NTE) of the extended framework. Using multivariate data analyses, involving non-negative matrix factorization (NMF), we demonstrate a new mechanism for NTE: progressive increase in the population of a smaller, distorted node state with increasing temperature leads to global contraction of the framework. The transformation between discrete node states is noncooperative and not ordered within the lattice, i.e., a solid solution of regular and distorted nodes. Density functional theory calculations show that removal of ligands from the node can lead to distortions consistent with the Zr···Zr distances observed in the experiment PDF data. Control of the node distortion imparted by the nonlinker ligand in turn controls the NTE behavior. Furthermore, these results reveal a mechanism to control the dynamic structure of MOFs based on local chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Atomic-Scale Imaging of Condensed Counterions

Here, the functioning of a wide variety of charged macromolecules, from DNA to fuel cell membranes, is dependent on how the counterions surrounding them are arranged. In order to decrease Coulombic repulsion, some of the fixed charges on these molecules are neutralized by a fraction of the counterions-this phenomenon is called counterion condensation. The nature of counterion condensation can be only be inferred indirectly from traditional experiments such as X-ray scattering and modern experiments such as single molecule electrometry. The prevalent conclusion in the literature, based on both theory and experiment, is that the distribution of counterions is peaked right next to the macromolecule, i.e., condensation results in the formation of contact ion pairs. In this study, cryogenic electron microscopy (cryo-EM) was used to study the arrangement of condensed halide counterions near a positively charged polypeptoid nanofiber. The locations of both condensed and fixed charges were determined directly from atomic-scale images. Our experimentally determined counterion distributions were peaked at distances of about 5 Å away from the fixed positive charge, indicating the presence of a layer of water molecules between condensed ion pairs. We posit that this distribution is driven by the entropy of the condensed ions.

36 MATERIALS SCIENCE↗

NASA NTRS2000

Fluorescence Studies of Protein Crystal Nucleation

We have postulated that, in the case of tetragonal chicken egg white lysozyme, crystal growth occurs by the addition of pre-critical nuclei sized n-mers that form in the bulk solution, and that the n-mer growth units were multiples of the tetrameric 4(sub 3) helical structure. These have the strongest intermolecular bonds in the crystal and are therefore likely to be the first species formed. High resolution AFM studies provide strong supporting evidence for this model, but the data also suggest that the actual species in solution may not be identical in structure to that found in the crystal. We are using fluorescence resonance energy transfer (FRET) to study the initial solution phase self-assembly process, using covalent fluorescent derivatives which crystallize in the characteristic P4(sub 3)2(sub 1)2(sub 1) space group. FRET studies are being carried out between the cascade blue (CB-lys, donor, Ex(sub max) 366 nm, Em 420 nm) and lucifer yellow (LY-lys, acceptor, Ex(sub max) 430 nm, Em 528 nm) asp101 derivatives. The estimated R(sub 0) for this probe pair, the distance where 50% of the donor energy is transferred to the acceptor, is approx. 1.2 nm, compared to 2.2 nm between the side chain carboxyls of adjacent asp101's in the crystalline 4(sub 3) helix. The short donor lifetime of 2.80 ns (chi(sup 2) = 0.644), coupled with the large average distances between the molecules (greater than or equal to 50 nm) in solution, ensure that any energy transfer observed is not due to random diffusive interactions. Lifetime data show that CB-lys has a single lifetime when it is the only species in solution. Similarly, LY-lys also exhibits a single lifetime of 4.63 ns (chi(sup 2) = 0.42) when alone in solution. Addition of LY-lys to CB-lys results in the appearance of a third lifetime component of 0.348ns for the CB-lys. The fractional intensities of the different species present can be used to estimate the distribution of monomer and n-mers in solution. The self-association process is a function of the protein concentration relative to the saturation concentration, and observing it in dilute solution (conc. less than or equal to 10(exp -5)M) requires that the experiments be performed under low solubility conditions, i.e., low temperatures and high salt concentrations. Data from preliminary steady state FRET studies with N-terminal bound pyrene acetic acid (PAA-lys, donor, Ex 340 nm, Em 376 nm) and asp101 LY-lys as an acceptor showed a consistent trend of decreasing donor fluorescence intensity with increasing total protein concentration. The FRET data have been obtained at pH 4.6, 0.1M NaAc buffer, at 5 and 7% NaCl, 4 C. The corresponding C(sub sat) values are 0.471 and 0.362 mg/ml (approx. 3.3 and approx. 2.5 x 10(exp -5)M respectively). The donor fluorescence decrease is more pronounced at7% NaCl, consistent with the expected increased intermolecular interactions at higher salt concentrations as reflected in the lower solubility. Results from these and other ongoing studies will be discussed in conjunction with an emerging model for how tetragonal lysozyme crystals nucleate and the relevance of that model to other proteins.

Pusey, Marc↗

DOE OSTI2025

Local structure of zinc–indium–tin oxide films via grazing-incidence x-ray pair-distribution functions and theoretical methods

A detailed experimental and theoretical study on the local (r ≤ 4.5 Å) atomic structure of amorphous and crystalline zinc–indium–tin oxide (ZITO) thin films using grazing-incidence x-ray Pair-Distribution Functions (PDFs), ab initio Molecular Dynamics (MD), and Empirical Potential Structure Refinement (EPSR) Monte Carlo simulations is presented. High-energy synchrotron x rays, a two-dimensional detector, and different incident angles were used to probe the depth uniformity of five (ZnO) 0.15 (In 2 O 3 ) 0.70 (SnO 2 ) 0.15 films that were deposited via pulsed-laser deposition at growth temperatures (T G ) ranging from 25 to 300 °C. Films deposited at T G ≤ 150 °C were amorphous. The partially crystalline (T G = 200 °C) and fully crystalline (T G = 300 °C) films were highly textured. Both crystalline and amorphous structures were investigated using ab initio MD and EPSR Monte Carlo simulations. The density of the amorphous films determined from the experimental data agreed with MD calculations. Coordination numbers, bond lengths, and distortion for metal–oxygen and for both the edge- and corner-shared In–metal shells up to 4.5 Å obtained from PDF analysis closely agreed with MD and EPSR simulations. There is a pronounced decrease in the edge- and corner-shared In–Zn distances arising from the shorter Zn–O bond length, Zn–O tetrahedral coordination, and In–O–Zn angle in amorphous ZITO compared to its crystalline counterpart. A maximum in electrical mobility was observed for the amorphous film just before crystallization occurred. While the peak is broad, consistent with nearly unchanged overall cation–oxygen coordination in the amorphous films, ESPR results indicate that the tetrahedral coordination follows the conductivity trend.

Grazing Incidence X-ray↗

NASA NTRS2015

Interphase Chromosome Conformation and Chromatin-Chromatin Interactions in Human Epithelial Cells Cultured Under Different Gravity Conditions

Microgravity has been shown to alter global gene expression patterns and protein levels both in cultured cells and animal models. It has been suggested that the packaging of chromatin fibers in the interphase nucleus is closely related to genome function, and the changes in transcriptional activity are tightly correlated with changes in chromatin folding. This study explores the changes of chromatin conformation and chromatin-chromatin interactions in the simulated microgravity environment, and investigates their correlation to the expression of genes located at different regions of the chromosome. To investigate the folding of chromatin in interphase under various culture conditions, human epithelial cells, fibroblasts, and lymphocytes were fixed in the G1 phase. Interphase chromosomes were hybridized with a multicolor banding in situ hybridization (mBAND) probe for chromosome 3 which distinguishes six regions of the chromosome as separate colors. After images were captured with a laser scanning confocal microscope, the 3-dimensional structure of interphase chromosome 3 was reconstructed at multi-mega base pair scale. In order to determine the effects of microgravity on chromosome conformation and orientation, measures such as distance between homologous pairs, relative orientation of chromosome arms about a shared midpoint, and orientation of arms within individual chromosomes were all considered as potentially impacted by simulated microgravity conditions. The studies revealed non-random folding of chromatin in interphase, and suggested an association of interphase chromatin folding with radiation-induced chromosome aberration hotspots. Interestingly, the distributions of genes with expression changes over chromosome 3 in cells cultured under microgravity environment are apparently clustered on specific loci and chromosomes. This data provides important insights into how mammalian cells respond to microgravity at molecular level.

International Space Station↗

DOE OSTI2022

Exclusive production of a pair of high transverse momentum photons in pion-nucleon collisions for extracting generalized parton distributions

We show that exclusive production of a pair of high transverse momentum photons in pion-nucleon collisions can be systematically studied in QCD factorization approach if the photon’s transverse momentum q T with respect to the colliding pion is much greater than Λ QCD . We demonstrate that the leading power non-perturbative contributions to the scattering amplitudes of this exclusive process are process-independent and can be systematically factorized into universal pion’s distribution amplitudes (DAs) and nucleon’s generalized parton distributions (GPDs), which are convoluted with corresponding infrared safe and perturbatively calculable short-distance hard parts. The correction to this factorized expression is suppressed by powers of 1/q T . We demonstrate quantitatively that this new type of exclusive processes is not only complementary to existing processes for extracting GPDs, but also capable of providing an enhanced sensitivity to the dependence of both DAs and GPDs on the active parton’s momentum fraction x. We also introduce additional, but the same type of exclusive observables to enhance our capability to explore GPDs, in particular, their x-dependence.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

The structure of CaO–MgO–Al 2 O 3 –SiO 2 melts and glasses doped with FeO X –NiO

Neutron and x-ray diffraction measurements have been performed on CaO–MgO–Al 2 O 3 –SiO 2 (CMAS) glasses doped with NiO–Fe X O at room temperature, along with x-ray measurements on aerodynamically levitated liquids at ≥2000 K. The disordered structures have been modeled using empirical potential structure refinement to investigate the relation between the aluminosilicate network and the modifying cations. The SiO 4 and AlO 4 tetrahedra are found to have wider Si–O and Al–O bond distance distributions in the glass, and the first Ca–O n coordination shell is highly distorted, redistributing different populations of long and short bonds between the liquid and the glass. The addition of Fe and Ni at low aluminosilicate content increases the number of free oxygens not bonded to AlO 4 or SiO 4 . Mg–O and Fe–O are both found to be predominantly fourfold and fivefold in the liquid and glassy states. Despite these low coordination numbers, their bond angle distributions indicate that they are predominantly in nontetrahedral-type geometries, with ferrous and ferric iron possessing similar coordination environments. The Ca–O and Mg–O average coordination numbers and enthalpies of solution are consistent with their higher reactivity within relatively acidic aluminosilicate melts.

36 MATERIALS SCIENCE↗

NASA NTRSDate not supplied

A Microphone Phased Array for Launch Acoustics Application

A new, portable, phased array of microphones is built at NASA Ames Research Center specifically for the harsh environment encountered in launch pads of rocket vehicles. It uses 70 rugged, piezo-electric, dynamic pressure sensors optimally distributed on a 10.5ft diameter open frame dome structure. The open frame is light yet robust to sustain the high wind load of typical seaside launch pads, and the blast and acoustic loads from the launch. A 200-ft long cable bundle carries the microphone signals to a weather-protected electronic cabinet containing the data acquisition system, computers, and other equipment. The array is equipped with an infra-red camera and a visible wavelength camera for imaging the launch site. The beamformed noise maps will be superimposed on the video footages collected by the cameras for correct identification of the noise sources. The array is tested with very loud noise sources to determine the beamforming ability. Multiple mathematical models, such as the conventional beamforming, orthogonal-functional beamforming, spectral element method etc. are used to determine the minimum spatial resolution of the sound sources that can be measured at different frequencies. Additionally, the array hardware is being tested for different environmental conditions and electro-magnetic compliance. The goal is to use the array for NASA’s Artemis/SLS vehicle that will be launched from a newly built Mobile Launch platform and a modified launch pad. Data from a couple of validation tests will be presented in this paper. The first test involves an outdoor setup where the array was placed on a crane at several different heights and distances from a pair of very loud noise sources. The second test from the static firing of the RS25 engines in an outdoor test stand.

Acoustics↗

NASA NTRS2004

Determining Sizes of Particles in a Flow from DPIV Data

A proposed method of measuring the size of particles entrained in a flow of a liquid or gas would involve utilization of data from digital particle-image velocimetry (DPIV) of the flow. That is to say, with proper design and operation of a DPIV system, the DPIV data could be processed according to the proposed method to obtain particle sizes in addition to particle velocities. As an additional benefit, one could then compute the mass flux of the entrained particles from the particle sizes and velocities. As in DPIV as practiced heretofore, a pulsed laser beam would be formed into a thin sheet to illuminate a plane of interest in a flow field and the illuminated plane would be observed by means of a charge-coupled device (CCD) camera aimed along a line perpendicular to the illuminated plane. Unlike in DPIV as practiced heretofore, care would be taken to polarize the laser beam so that its electric field would lie in the illuminated plane, for the reason explained in the next paragraph. The proposed method applies, more specifically, to transparent or semitransparent spherical particles that have an index of refraction different from that of the fluid in which they are entrained. The method is based on the established Mie theory, which describes the scattering of light by diffraction, refraction, and specular reflection of light by such particles. In the case of a particle illuminated by polarized light and observed in the arrangement described in the preceding paragraph, the Mie theory shows that the image of the particle on the focal plane of the CCD camera includes two glare spots: one attributable to light reflected toward the camera and one attributable to light refracted toward the camera. The distance between the glare spots is a known function of the size of the particle, the indices of refraction of the particle material, and design parameters of the camera optics. Hence, the size of a particle can be determined from the distance between the glare spots. The proposed method would be implemented in an algorithm that would automatically identify, and measure the distance between, the glare spots for each particle for which a suitable image has been captured in a DPIV image frame. The algorithm (see figure) would begin with thresholding of data from the entire image frame to reduce noise, thereby facilitating discrimination of particle images from the background and aiding in the separation of overlapping particles. It is important not to pick a threshold level so high that the light intensity between a given pair of glare spots does not fall below the threshold value, leaving the glare spots disconnected. The image would then be scanned in a sequence of rows and columns of pixels to identify groups of adjacent pixels that contain nonzero brightnesses and that are surrounded by pixels of zero brightness. Each such group would be assumed to constitute the image of one particle. Each such group would be further analyzed to determine whether the image was saturated; saturated particle images must be rejected because the locations of glare spots in saturated images cannot accurately be determined. Within each unsaturated particle image, the centroids (deemed to be the locations) of the glare spots would be determined by means of gradients of brightness distributions and three-point horizontal and three-point vertical Gaussian estimates based on the brightness values of the brightest pixels and the pixels adjacent to them. If the brightness of a given particle image contained only one peak, then it would be assumed that a second glare spot did not exist and that image would be rejected.

Wernet, M. P.↗