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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

TMD program at JLab

Measurements of multiplicities and asymmetries of multiparticle final states in wide kinematics, including dihadrons and vector mesons, will be crucial for a separation of different structure functions, and different contributions to specific structure functions, used in phenomenological studies of Semi-Inclusive DIS (SIDIS). Measurements of various beam Single Spin Asymmetries are discussed as a possible tool to separate different kinematical regions as well as different dynamical contributions. Precision measurements in JLab, including detailed studies of the $Q^2$ dependences of observables, would also allow testing the impact of several theoretical assumptions used in phenomenological studies of generalized PDFs (GPDs, TMDs) , also providing a mechanism for validation of the extraction frameworks, which is critical for the proper evaluation of systematic uncertainties.

Avagyan, Harutyun↗
NASA NTRS2005

The Effects of Instrumental Elliptical Polarization on Stellar Point Spread Function Fine Structure

We present procedures and preliminary results from a study on the effects of instrumental polarization on the fine structure of the stellar point spread function (PSF). These effects are important to understand because the the aberration caused by instrumental polarization on an otherwise diffraction-limited will likely have have severe consequences for extreme high contrast imaging systems such as NASA's planned Terrestrial Planet Finder (TPF) mission and the proposed NASA Eclipse mission. The report here, describing our efforts to examine these effects, includes two parts: 1) a numerical analysis of the effect of metallic reflection, with some polarization-specific retardation, on a spherical wavefront; 2) an experimental approach for observing this effect, along with some preliminary laboratory results. While the experimental phase of this study requires more fine-tuning to produce meaningful results, the numerical analysis indicates that the inclusion of polarization-specific phase effects (retardation) results in a point spread function (PSF) aberration more severe than the amplitude (reflectivity) effects previously recorded in the literature.

high angular resolution↗
DOE OSTI2022

Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels

Engineered antibody fragments (Fabs) have made major impacts on structural biology research, particularly to aid structural determination of membrane proteins. Nonetheless, Fabs generated by traditional monoclonal technology suffer from challenges of routine production and storage. Starting from the known IgG paratopes of an antibody that binds to the “turret loop” of the KcsA K+ channel, we engineered a synthetic Fab (sFab) based upon the highly stable Herceptin Fab scaffold, which can be recombinantly expressed in Escherichia coli and purified with single-step affinity chromatography. This synthetic Fab was used as a crystallization chaperone to obtain crystals of the KcsA channel that diffracted to a resolution comparable to that from the parent Fab. Furthermore, we show that the turret loop can be grafted into the unrelated voltage-gated Kv1.2–Kv2.1 channel and still strongly bind the engineered sFab, in support of the loop grafting strategy. Macroscopic electrophysiology recordings show that the sFab affects the activation and conductance of the chimeric voltage-gated channel. These results suggest that straightforward engineering of antibodies using recombinant formats can facilitate the rapid and scalable production of Fabs as structural biology tools and functional probes. The impact of this approach is expanded significantly based on the potential portability of the turret loop to a myriad of other K+ channels.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2008

Arterial Structure and Function in Women and Men Following Long Duration Bed Rest

Orthostatic intolerance is a well-recognized consequence of space flight and bed rest (BR), with a greater incidence reported in women. We hypothesized that leg, but not arm, arterial structure and function would be altered following prolonged BR, as a model of space flight, and that women would be more susceptible to BR-induced deconditioning than men. METHODS: Ten volunteers (5 males, 5 females) completed 90 d of 6 head-down BR. Subjects participated in tests of brachial (BA) and anterior tibial (AT) artery endothelium-dependent (flow mediated dilation [FMD] following 5-7 min of arterial occlusion) and endothelium-independent (0.4 mg sublingual nitroglycerin [SN]) vasodilation before BR (PRE) and on days 7 (BR7), 21 (BR21), and 90 (BR90) of BR. Vessel diameter and intimal medial thickness (IMT) were measured by ultrasound. IMT, baseline diameter, and percent change in diameter from baseline during FMD and SN tests were compared across BR and between genders using repeated measures two-way ANOVA with Bonferroni post-hoc tests in which PRE and women were control conditions. RESULTS: Baseline vessel diameter was lower in women than in men in both the BA (p=0.005) and AT (p=0.01) across all days. Baseline AT diameter decreased during BR (p=0.01) and tended to be more profound in women (interaction, p=0.06). AT diameter was reduced in women at BR21 and BR90 (p<0.01) but not in men. In contrast, there was no BR effect on baseline BA diameter. IMT also decreased in the AT (p<0.001) but not in the BA during BR; AT IMT was reduced by BR21 (p<0.05). As a group, there was no effect of BR on AT FMD, BA FMD, and AT SN-dilation, although BA SN-dilation was significantly reduced on BR21 (p=0.01). Across all BR days, women exhibited higher AT FMD (p=0.03), BA FMD (p=0.02), and BA SN-dilation (p=0.01) and tended to demonstrate greater AT SN-dilation (p=0.11). CONCLUSIONS: These preliminary results suggest that arterial remodeling occurs during BR in the leg (decreased diameter and IMT), but not in the arm, and that women appear to be more responsive to BR than men. These changes in the leg, coupled with larger responses to direct and indirect stimulation of the arterial smooth muscle, may be related to the greater incidence of orthostatic intolerance in women after BR and space flight.

Lee, Stuart M. C.↗
NASA NTRS2016

ERRATUM: 'MAPPING THE GAS TURBULENCE IN THE COMA CLUSTER: PREDICTIONS FOR ASTRO-H'

The published version of this paper contained an error in Figure 5. This figure is intended to show the effect on the structure function of subtracting the bias induced by the statistical and systematic errors on the line shift. The filled circles show the bias-subtracted structure function. The positions of these points in the left panel of the original figure were calculated incorrectly. The figure is reproduced below (with the original caption) with the correct values for the bias-subtracted structure function. No other computations or figures in the original manuscript are affected.

galaxies: clusters: intracluster medium- methods: ↗
DOE OSTI2020

Similarities and Differences in the Effects of Toxic Concentrations of Cadmium and Chromium on the Structure and Functions of Thylakoid Membranes in Chlorella variabilis

Trace metal contaminations in natural waters, wetlands, and wastewaters pose serious threats to aquatic ecosystems—mainly via targeting microalgae. In this work, we investigated the effects of toxic amounts of chromium and cadmium ions on the structure and function of the photosynthetic machinery of Chlorella variabilis cells. To halt the propagation of cells, we used high concentrations of Cd and Cr, 50–50 mg L –1 , in the forms of CdCl 2 x 2.5 H 2 O and K 2 Cr 2 O 7 , respectively. Both treatments led to similar, about 50% gradual diminishment of the chlorophyll contents of the cells in 48 h, which was, however, accompanied by a small (~10%) but statistically significant enrichment (Cd) and loss (Cr) of ß-carotene. Both Cd and Cr inhibited the activity of photosystem II (PSII)—but with more severe inhibitions with Cr. On the contrary, the PsbA (D1) protein of PSII and the PsbO protein of the oxygen-evolving complex were retained more in Cr-treated cells than in the presence of Cd. These data and the higher susceptibility of P700 redox transients in Cr-treated cells suggest that, unlike with Cd, PSII is not the main target in the photochemical apparatus. These differences at the level of photochemistry also brought about dissimilarities at higher levels of the structural complexity of the photosynthetic apparatus. Circular dichroism (CD) spectroscopy measurements revealed moderate perturbations in the macro-organization of the protein complexes—with more pronounced decline in Cd-treated cells than in the cells with Cr. Also, as reflected by transmission electron microscopy and small-angle neutron scattering, the thylakoid membranes suffered shrinking and were largely fragmented in Cd-treated cells, whereas no changes could be discerned with Cr. The preservation of integrity of membranes in Cr-treated cells was most probably aided by high proportion of the de-epoxidized xanthophylls, which were absent with Cd. It can thus be concluded that beside strong similarities of the toxic effects of Cr and Cd, the response of the photosynthetic machinery of C. variabilis to these two trace metal ions substantially differ from each other—strongly suggesting different inhibitory and protective mechanisms following the primary toxic events.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1984

The influence of gravity on structure and function of animals

Gravity is the only environmental parameter that has remained constant during the period of evolution of living matter on earth. Thus, it must have been a major force in shaping living things. The influence of gravitational loading on evolution of the vertebrate skeleton is well recognized, and scale effects have been studied. This paper, however, considers in addition four pivotal events in early evolution that would seem to have been significant for the later success and diversifcation of animal life. These are evolution of the cytoskeleton, cell motility (flagellae and cilia), gravity detecting devices (accelerometers), and biomineralization. All are functionally calcium dependent in eukaryotes and all occurred or were foreshadowed in prokaryotes. A major question is why calcium was selected as an ion of great importance to the structure and function of living matter; another is whether gravity played a role in its selection.

Ross, M. D.↗
NASA NTRS2012

First-and Second-Order Displacement Transfer Functions for Structural Shape Calculations Using Analytically Predicted Surface Strains

New first- and second-order displacement transfer functions have been developed for deformed shape calculations of nonuniform cross-sectional beam structures such as aircraft wings. The displacement transfer functions are expressed explicitly in terms of beam geometrical parameters and surface strains (uniaxial bending strains) obtained at equally spaced strain stations along the surface of the beam structure. By inputting the measured or analytically calculated surface strains into the displacement transfer functions, one could calculate local slopes, deflections, and cross-sectional twist angles of the nonuniform beam structure for mapping the overall structural deformed shapes for visual display. The accuracy of deformed shape calculations by the first- and second-order displacement transfer functions are determined by comparing these values to the analytically predicted values obtained from finite element analyses. This comparison shows that the new displacement transfer functions could quite accurately calculate the deformed shapes of tapered cantilever tubular beams with different tapered angles. The accuracy of the present displacement transfer functions also are compared to those of the previously developed displacement transfer functions.

Ko, William L.↗
NASA NTRS1978

Structural and Functional Organization of the Vestibular Apparatus in Rats Subjected to Weightlessness for 19.5 Days Aboard the Kosmos-782 Satellite

The vestibular apparatus was investigated in rats subjected to weightlessness for 19.5 days. The vestibular apparatus was removed and its sections were fixed in a glutaraldehyde solution for investigation by light and electron microscopes. Structural and functional charges were noted in the otolith portions of the ear, with the otolith particles clinging to the utricular receptor surface and with the peripheral arrangement of the nucleolus in the nuclei of the receptor cells. It is possible that increased edema of the vestibular tissue resulted in the destruction of some receptor cells and in changes in the form and structure of the otolith. In the horizontal crista, the capula was separated.

Vinnikov, Y. A.↗
DOE OSTI2024

Cross Section Evaluation for Exclusive Channels of K+Λ and K+Σ0 Electroproduction off Protons Using CLAS Detector Data

In this work, a method for evaluating the cross sections of electroproduction of K+Λ0 and K+Σ0 off protons in the region of invariant masses of final hadrons MK + MY <W < 2.65 GeV (MK and MY being the masses of the kaon and hyperon, respectively) and squares of four-momentum transfers of virtual photons, i.e., photon virtualities 0 < Q2 < 5 GeV2, is developed based on experimental data of these exclusive channels’ cross sections measured by the CLAS detector in Hall B at Jefferson Lab. A set of algorithms has been implemented to evaluate the differential cross sections of these channels, along with their statistical and systematic uncertainties. A program was developed for the evaluation of differential cross sections and structure functions using C++ and Python libraries. An interactive website was created for working with the program, enabling the analysis of one-dimensional and two-dimensional dependences of structure functions and differential cross sections. The evaluation of differential cross sections for the K+Λ and K+Σ0 electroproduction channels is necessary for extracting the structure function σLT from the data on the polarization asymmetry of electroproduction reactions of these final states with longitudinally polarized electrons. The obtained results are also important for the development of realistic Monte Carlo event generators in planning future experiments and for evaluating the efficiency of detecting final particles when extracting reaction cross sections from experimental data.

Golda, A. V.↗
DOE OSTI2020

Neutron Valence Structure from Nuclear Deep Inelastic Scattering

Mechanisms of spin-flavor SU(6) symmetry breaking in Quantum Chromodynamics (QCD) are studied via an extraction of the free neutron structure function from a global analysis of deep inelastic scattering (DIS) data on the proton and on nuclei from $A = 2$ (deuterium) to 208 (lead). Modification of the structure function of nucleons bound in atomic nuclei (known as the EMC effect) are consistently accounted for within the framework of a universal modification of nucleons in short-range correlated (SRC) pairs. Our extracted neutron-to-proton structure function ratio $F_2^n/F_2^p$ becomes constant for $x_B \ge 0.6$, equalling $0.47 \pm 0.04$ as $x_B \rightarrow 1$, in agreement with theoretical predictions of perturbative QCD and the Dyson Schwinger equation, and in disagreement with predictions of the Scalar Diquark dominance model. Finally, we also predict $F_2^{^3\mathrm{He}}/F_2^{^3\mathrm{H}}$, recently measured, yet unpublished, by the MARATHON collaboration, the nuclear correction function that is needed to extract $F_2^n/F_2^p$ from $F_2^{^3\mathrm{He}}/F_2^{^3\mathrm{H}}$, and the theoretical uncertainty associated with this extraction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function

Computational biology is one of many scientific disciplines ripe for innovation and acceleration with the advent of high-performance computing (HPC). In recent years, the field of machine learning has also seen significant benefits from adopting HPC practices. In this work, we present a novel HPC pipeline that incorporates various machine-learning approaches for structure-based functional annotation of proteins on the scale of whole genomes. Our pipeline makes extensive use of deep learning and provides computational insights into best practices for training advanced deep-learning models for high-throughput data such as proteomics data. We showcase methodologies our pipeline currently supports and detail future tasks for our pipeline to envelop, including large-scale sequence comparison using SAdLSA and prediction of protein tertiary structures using AlphaFold2.

Gao, Mu↗
NASA NTRS1995

Intermittent turbulence in solar wind from the south polar hole

The magnetic fields measured by the Ulysses spacecraft are used to study solar wind turbulence in the fast solar wind from the south polar hole. The spacecraft was at about 46 deg south latitude and 3.9 AU. For a magnetic field with a Gaussian distribution the power spectrum (second-order structure function) is sufficient to completely characterize the turbulence. However, the actual distribution is non-Gaussian so that the effects of intermittency must be taken into account. The observed spectral exponents include effects of intermittency and cannot be directly compared with the standard second-order spectral theories such as the Kolmogorov and Kraichnan theories. To permit a better comparison of the observations with the theoretical models, we study the structure characteristics of the data. We find the exponents of the second-order structure functions (power spectra) and the higher-order normalized structure functions for the components of the magnetic fields. We show that these sets of exponents can be approximately described by two basic numbers: the spectral exponent and the intermittency exponent. The intermittency exponent characterizes correlation properties of the energy cascade from large to small scales. Before comparing the observations to the theoretically expected values, a reduction must be made to the observed spectral exponent. The amount of the reduction depends on both the intermittency exponent and the model of the energy cascade assumed in the turbulence theory. We reduce the measured spectral indices according to a simple model for Alfven turbulence that is described here. We then compare our reduced spectral indices with second-order spectral theory. The reduced spectral indices for the period range of 1 min to about a half hour are remarkably constant and in good agreement with the value of 3/2. Thus our treatment is self-consistent. Our tentative conclusion is that the high-frequency turbulence appears to agree with the model of random-phased Alfven waves. This tentative conclusion must be tested by further theoretical and observational work.

Ruzmaikin, A. A.↗
DOE OSTI2023

De novo design of protein structure and function with RFdiffusion

Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.

Science & Technology - Other Topics↗
DOE OSTI2024

Tagged DVCS on neutron with the CLAS12 Experiment and the detector BONuS12 at Jefferson Lab (USA)

Hadronic physics studies the properties of the proton and neutron. The theory of Quantum Chromodynamics (QCD) governs the structure of hadrons. Non-perturbative structure functions are used to describe the hadrons? structure. Generalized Parton Distributions (GPDs) are a set of structure functions providing access to a 3D view of the nucleon. GPDs contain information about the longitudinal momentum and transverse position of quarks and their correlation. They are related to the spin structure and play a role in solving the proton spin puzzle. They provide access to the quarks? orbital angular momentum, a crucial puzzle piece. For this, measurements on the proton, already present, and neutron are necessary. This thesis aims to explore Compton scattering on the neutron with a deuterium target by measuring the spectator proton with the CLAS12 detector and the BONuS12 RTPC at Jefferson Lab. This work first describes the implementation, which I carried out, of a Kalman filter to reconstruct spectator protons in the BONuS12 detector. The second part of the manuscript is dedicated to the work on the analysis of DVCS on the neutron with the subtraction of background noises. Two different methods for the subtraction of ?0 will be detailed. Finally, the obtained results are presented and discussed

Ouillon, Mathieu↗
NASA NTRS1986

Propagation of electromagnetic waves in a turbulent medium

Theoretical modeling of the wealth of experimental data on propagation of electromagnetic radiation through turbulent media has centered on the use of the Heisenberg-Kolmogorov (HK) model, which is, however, valid only for medium to small sized eddies. Ad hoc modifications of the HK model to encompass the large-scale region of the eddy spectrum have been widely used, but a sound physical basis has been lacking. A model for large-scale turbulence that was recently proposed is applied to the above problem. The spectral density of the temperature field is derived and used to calculate the structure function of the index of refraction N. The result is compared with available data, yielding a reasonably good fit. The variance of N is also in accord with the data. The model is also applied to propagation effects. The phase structure function, covariance of the log amplitude, and variance of the log intensity are calculated. The calculated phase structure function is in excellent agreement with available data.

Canuto, V. M.↗
DOE OSTI2022

Extraction of Deep Inelastic Cross Sections Using a 10.4 GeV Electron Beam and a Polarized Helium-3 Target

Experiment E12-06-121 at Jefferson Lab aims to do a precision measurement of the neutron spin structure function g2 using inclusive inelastic scattering of electrons over a large kinematic range of x and Q2. The third moment of the linear combination of the spin structure functions g1 and g2, d2, is one of the cleanest higher twist observables and contains information on quark-gluon correlations. It is connected to the \color polarizability or \color Lorentz force" of the nucleon. The experimental data taking was successfully conducted in Hall C using a longitudinally polarized electron beam with 10.4 GeV energy, and a polarized 3He gas target. The combination of the Super High Momentum Spectrometer (SHMS) and the High Momentum Spectrometer (HMS) allowed us to run the experiment for three constant Q2 values (3.0, 4.3, and 5.6 GeV2/c2) over a wide range of x (0:20 < x < 0:95) for the ?first time. To extract the neutron spin structure functions, precision determination of the unpolarized cross-sections and double spin asymmetries are required. The analysis of the deep inelastic scattering data and the results from the ?first measurements of unpolarized 3He cross-sections are reported in this work. The extracted cross-sections will be combined with the electron asymmetry results (ongoing work) to obtain the g2 and d2 of 3He. Finally, nuclear correction to the 3He results will have to be applied to extract g2 and d2 for the neutrons.

Roy, Murchhana↗
DOE OSTI2025

Effective field theory factorization for diffraction

We derive a factorization formula for coherent and incoherent ep diffraction using the soft collinear effective theory, utilizing multiple power expansion parameters to handle different kinematic regions. This goes beyond the known hard-collinear diffractive factorization to address the small-x Regge dynamics and Pomeron exchange from first principles. The effective field theory analysis also uncovers and factorizes an important irreducible incoherent background generated by color-nonsinglet exchange, dubbed “quasi-diffraction”, for which we calculate the associated Sudakov suppression. For unpolarized scattering we show that there are four diffractive structure functions at leading power, and point out the importance of studying ${F}_{3,4}^D$ through asymmetries, in addition to ${F}_{2,L}^D$. For the quasi-diffractive background, we make model independent predictions for ratios of the corresponding structure functions in a perturbative kinematic region. Our analysis also makes predictions for six leading-power spin-dependent structure functions. Finally, we provide connections to diffractive parton distributions, and assess the Ingelman-Schlein model. Our work lays a path for further QCD-based studies of diffraction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗