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DOE OSTI2023

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure–function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Finally, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Ab initio calculation of X-ray and related core-level spectroscopies: Green's function approaches

X-Ray and related spectroscopies are powerful probes of atomic, vibrational, and electronic structure. In order to unlock the full potential of such experimental techniques, accurate and efficient theoretical and computational approaches are essential. Here we review the status of a variety of first-principles and nearly first principles techniques for X-ray spectroscopies such as X-ray absorption, X-ray emission, and X-ray photoemission, with a focus on Green's function based methods. In particular, we describe the current state of multiple scattering Green's function techniques available in the FEFF10 code and cumulant Green's function techniques for including the effects of many-body electronic excitations. Furthermore, illustrative examples are shown for a variety of materials and compared with other theoretical and experimental results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1989

Reflected fluxes for broken clouds over a Lambertian surface

Reflected fluxes are calculated for broken cloudiness (i.e., nonplane parallel) as a function of cloud cover, cloud optical depth, solar zenith angle and surface albedo. These calculations extend previous results for broken cloud reflected fluxes over a black surface. The present study demonstrates that not only radiances but also radiative fluxes over high albedo surfaces may be decreased by the presence of broken cloudiness. Conventional wisdom states that cloud radiances (brightnesses) are always greater than the background. While most cloud retrieval schemes are built around this assumption, it is incorrect for clouds over high albedo surfaces such as found in polar regions. However, the most startling and counterintuitive conclusion of this study is that nonabsorbing finite clouds over a highly reflecting surface will decrease the system albedo. As a result, surface absorption is increased, the result of multiple scattering between surface and cloud layer, controlled by cloud morphology and cloud optical thickness. A simple parameterization of the effects of cloud contamination upon retrieved albedo is given in terms of solar zenith angle, cloud optical depth, surface albedo, cloud cover, and plane-parallel cloud albedo. In this way, the effects of broken cloudiness are modeled in terms of easily computed plane-parallel values.

Welch, Ronald M.↗

NASA NTRS1992

The limitations of resonant Compton scattering as a gamma-ray burst model

Resonant Compton upscattering is commended as a mechanism that produces a hard gamma-ray spectrum while suppressing X-rays. This model, however, has severe physical and observational limitations. Effective X-ray suppression places a lower limit on the electron density; above this limit X-rays scatter multiple times, so the single-scattering approximation of this mechanism is invalid. Multiple scattering produces a spectrum that is much harder than the single-scattering spectrum. As the Thomson optical depth of a power-law electron beam approaches unity, photon spawning commences at a high rate and physically invalidates the underlying electron distribution. The Compton upscattering model is therefore only valid over a narrow range of electron densities. An observational consequence of this model is the absence of the third cyclotron resonance. Resonant scattering produces gamma-rays that propagate nearly along the magnetic field. The resonant cross section of the third harmonic, which is strongly angle dependent, falls below the Compton continuum for these gamma rays. The observation of a third cyclotron resonance in a gamma-ray burst spectrum would eliminate resonant Compton scattering as a gamma-ray burst process.

Brainerd, J. J.↗

NASA NTRS1995

An analytic radiative transfer model for a coupled atmosphere and leaf canopy

A new analytical radiative transfer model of a leaf canopy is developed that approximates multiple-scattering radiance by a four-stream formulation. The canopy model is coupled to a homogeneous atmospheric model as well as a non-Lambertian lower boundary soil surface. The same four-stream formulation is also used for the calculation of multiple scattering in the atmosphere. Comparisons of radiance derived from the four-stream model with those calculated by an iterative numerical solution of the radiative transfer equation show that the analytic model has a very high accuracy, even with a turbid atmosphere and a very dense canopy in which multiple scattering dominates. Because the coupling of canopy and atmospheric models fully accommodates anisotropic surface reflectance and atmospheric scattering and its effect on directional radiance, the model is especially useful for application to directional radiance and measurements obtained by remote sensing. Retrieval of biophysical parameters using this model is under investigation.

Liang, Shunlin↗

NASA NTRS2011

Towards Simulating a Realistic Planetary Seismic Wavefield: The Contribution of the Megaregolith and Low-Velocity Waveguides

Lunar seismograms are distinctly different from their terrestrial counterparts. The Apollo lunar seismometers recorded moonquakes without distinct P- or S-wave arrivals; instead waves arrive as a diffuse coda that decays over several hours making the identification of body waves difficult. The unusual character of the lunar seismic wavefield is generally tied to properties of the megaregolith: it consists of highly fractured and broken crustal rock, the result of extensive bombardment of the Moon. The megaregolith extends several kilometers into the lunar crust, possibly into the mantle in some regions, and is covered by a thin coating of fine-scale dust. These materials possess very low seismic velocities that strongly scatter the seismic wavefield at high frequencies. Directly modeling the effects of the megaregolith to simulate an accurate lunar seismic wavefield is a challenging computational problem, owing to the inherent 3-D nature of the problem and the high frequencies (greater than 1 Hz) required. Here we focus on modeling the long duration code, studying the effects of the low velocities found in the megaregolith. We produce synthetic seismograms using 1-D slowness integration methodologies, GEMINI and reflectivity, and a 3-D Cartesian finite difference code, Wave Propagation Program, to study the effect of thin layers of low velocity on the surface of a planet. These codes allow us generate seismograms with dominant frequencies of approximately 1 Hz. For background lunar seismic structure we explore several models, including the recent model of Weber et al., Science, 2011. We also investigate variations in megaregolithic thickness, velocity, attenuation, and seismogram frequency content. Our results are compared to the Apollo seismic dataset, using both a cross correlation technique and integrated envelope approach to investigate coda decay. We find our new high frequency results strongly support the hypothesis that the long duration of the lunar seismic codes is generated by the presence of the low velocity megaregolith, and that the diffuse arrivals are a combination of scattered energy and multiple reverberations within this layer. The 3-D modeling indicates the extreme surface topography of the Moon adds only a small contribution to scattering effects, though local geology may play a larger role. We also study the effects of the megaregolith on core reflected and converted phases and other body waves. Our analysis indicates detection of core interacting arrivals with a polarization filter technique is robust and lends the possibility of detecting other body waves from the Moon.

Schmerr, Nicholas C.↗

DOE OSTI2022

Ab initio nucleon-nucleus elastic scattering with chiral effective field theory uncertainties

Effective interactions for nucleon-nucleus elastic scattering from first principles require the use of the same nucleon-nucleon interaction in the structure and reaction calculations and a consistent treatment of the relevant operators at each order. Systematic investigations of the effect of truncation uncertainties of chiral nucleon-nucleon ( N N ) forces have been carried out for scattering observables in the two- and three-nucleons system as well as for bound-state properties of light nuclei. Here we extend this type of study to proton and neutron elastic scattering for 16 O and 12 C. Using the frameworks of the spectator expansion of multiple scattering theory as well as the no-core shell model, we employ one specific chiral interaction from the LENPIC collaboration and consistently calculate the leading-order effective nucleon-nucleus interaction up to the third chiral order, from which we extract elastic scattering observables. Then we apply pointwise as well as correlated uncertainty quantification for the estimation of the chiral truncation error. We calculate and analyze proton elastic scattering observables for 16 O and 12 C as well as neutron elastic scattering observables for 12 C between 65 and 185 MeV projectile kinetic energy. We find in all cases qualitatively similar results for the chiral truncation uncertainties as in few-body systems and assess them using similar diagnostic tools. The order-by-order convergence of the scattering observables for 16 O and 12 C is very reasonable around 100 MeV, while for higher energies the chiral expansion parameter becomes too large for convergence. Comparing proton and neutron differential cross sections reveals that their description is comparable up to around 100 MeV. Here, we also find a nearly perfect correlation between the differential cross section for neutron scattering and the N N Wolfenstein amplitudes for small momentum transfers. The diagnostic tools for studying order-by-order convergence in observables in few-body systems can be employed for observables in nucleon-nucleus scattering with only minor modifications provided the momentum scale in the problems is not too large. We also find that the chiral N N interaction on which our study is based gives a very good description of differential cross sections for 16 O and 12 C as low as 65-MeV projectile energy, particularly in the forward direction. In addition, the very forward direction of the neutron differential cross section mirrors the behavior of the N N interaction amazingly well.

6 ≤ A ≤ 19↗

DOE OSTI2022

Observation of Azimuth-Dependent Suppression of Hadron Pairs in Electron Scattering off Nuclei

Here, we present the first measurement of dihadron angular correlations in electron-nucleus scattering. The data were taken with the CLAS detector and a 5.0 GeV electron beam incident on deuterium, carbon, iron, and lead targets. Relative to deuterium, the nuclear yields of charged-pion pairs show a strong suppression for azimuthally opposite pairs, no suppression for azimuthally nearby pairs, and an enhancement of pairs with large invariant mass. These effects grow with increased nuclear size. The data are qualitatively described by the GIBUU model, which suggests that hadrons form near the nuclear surface and undergo multiple scattering in nuclei. These results show that angular correlation studies can open a new way to elucidate how hadrons form and interact inside nuclei.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1981

Stochastic treatment of electron multiplication without scattering in dielectrics

By treating the emission of optical phonons as a Markov process, a simple analytic method is developed for calculating the electronic ionization rate per unit length for dielectrics. The effects of scattering from acoustic and optical phonons are neglected. The treatment obtains universal functions in recursive form, the theory depending on only two dimensionless energy ratios. A comparison of the present work with other numerical approaches indicates that the effect of scattering becomes important only when the electric potential energy drop in a mean free path for optical-phonon emission is less than about 25% of the ionization potential. A comparison with Monte Carlo results is also given for Teflon.

Lin, D. L.↗

DOE OSTI2024

Light-flavor particle production in high-multiplicity pp collisions at $\sqrt{\textrm{s}}$ = 13 TeV as a function of transverse spherocity

Results on the transverse spherocity dependence of light-flavor particle production (π, K, p, ϕ, K *0 , K$^{0}_{S}$, Λ, Ξ) at midrapidity in high-multiplicity pp collisions at $\sqrt{\textrm{s}}$ = 13 TeV were obtained with the ALICE apparatus. The transverse spherocity estimator ($S$$^{p_T=1}_{O}$) categorizes events by their azimuthal topology. Utilizing narrow selections on $S$$^{p_T=1}_{O}$, it is possible to contrast particle production in collisions dominated by many soft initial interactions with that observed in collisions dominated by one or more hard scatterings. Results are reported for two multiplicity estimators covering different pseudorapidity regions. The $S$$^{p_T=1}_{O}$ estimator is found to effectively constrain the hardness of the events when the midrapidity (|η| < 0.8) estimator is used.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS2005

Ion Engine Plume Interaction Calculations for Prototypical Prometheus 1

Prometheus 1 is a conceptual mission to demonstrate the use of atomic energy for distant space missions. The hypothetical spacecraft design considered in this paper calls for multiple ion thrusters, each with considerably higher beam energy and beam current than have previously flown in space. The engineering challenges posed by such powerful thrusters relate not only to the thrusters themselves, but also to designing the spacecraft to avoid potentially deleterious effects of the thruster plumes. Accommodation of these thrusters requires good prediction of the highest angle portions of the main beam, as well as knowledge of clastically scattered and charge exchange ions, predictions for grid erosion and contamination of surfaces by eroded grid material, and effects of the plasma plume on radio transmissions. Nonlinear interactions of multiple thrusters are also of concern. In this paper we describe two- and three-dimensional calculations for plume structure and effects of conceptual Prometheus 1 ion engines. Many of the techniques used have been validated by application to ground test data for the NSTAR and NEXT ion engines. Predictions for plume structure and possible sputtering and contamination effects will be presented.

Mandell, Myron J.↗

DOE OSTI2025

Multipositivity bounds for scattering amplitudes

Lorentz invariance, unitarity, and causality enforce powerful constraints on the theory space of physical scattering amplitudes. However, virtually all efforts in this direction have centered on the very simplest case of four-point scattering. In this work, we derive an infinite web of “multipositivity bounds” that nonlinearly constrain all tree-level higher-point scattering amplitudes under similarly minimal assumptions. Our construction rules out several deformations of the string and implies mixed-multiplicity bounds on the Wilson coefficients of planar effective field theories. Curiously, an infinite class of multipositivity bounds is exactly saturated by the amplitudes of the open string.

effective field theory↗

DOE OSTI2024

Electron Radiation-Induced Nickel Nanoparticle Formation in KCl-ZnCl 2 Eutectic Molten Salt Using X-ray Absorption Spectroscopy

Understanding the speciation and local structure of metal solutes in molten salts is essential for predicting thermal properties and the redox and corrosion potentials of molten salts for next-generation nuclear reactors and concentrated solar power plant applications. Here, we employ X-ray absorption spectroscopy combined with electron paramagnetic resonance (EPR) measurements to investigate the effects of electron irradiation on 0.1 wt % NiCl 2 dissolved in molten eutectic KCl-ZnCl 2 salt. Radiation-driven reduction of Ni 2+ leading to nucleation and growth of Ni nanoparticles is studied as a function of electron dose (3–15 MGy) and temperature. Quantitative X-ray absorption near edge structure and linear combination fitting are utilized to investigate the extent of reduction as a function of the electron dose and temperature. A multiple-scattering (MS) approach is used for extended X-ray absorption fine structure analysis to deduce the size of the Ni nanoparticles formed and to understand the effect of the dose on the local structure of the nanoparticles. EPR studies on solidified NiCl 2 dissolved in molten eutectic KCl-ZnCl 2 salt show the formation of magnetic Ni nanoparticles.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Constraints on Intrinsic Charm from the SeaQuest Experiment

A nonperturbative charm production contribution, known as intrinsic charm, has long been speculated but has never been satisfactorily proven. The SeaQuest experiment at FNAL is in an ideal kinematic region to provide evidence of $J/\psi$ production by intrinsic charm. Here, $J/\psi$ production in the SeaQuest kinematics is calculated with a combination of perturbative QCD and intrinsic charm to see whether the SeaQuest data can put limits on an intrinsic charm contribution. $J/\psi$ production in perturbative QCD is calculated to next-to-leading order in the cross section. Cold nuclear matter effects included in this component are nuclear modification of the parton densities, absorption by nucleons, and $p_T$ broadening by multiple scattering. The $J/\psi$ contribution from intrinsic charm is calculated assuming production from a $|uud c \overline c \rangle$ Fock state. The nuclear modification factor, $R_{pA}$, is calculated as a function of $x_F$ and $p_T$ for $p+{\rm C}$, $p+{\rm Fe}$, and $p+{\rm W}$ interactions relative to $p+{\rm d}$. It is shown that the SeaQuest kinematic acceptance is ideal for setting limits on intrinsic charm in the proton.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1987

The role of photographic parameters in laser speckle or particle image displacement velocimetry

The parameters involved in obtaining the multiple exposure photographs in the laser speckle velocimetry method (to record the light scattering by the seeding particles) were optimized. The effects of the type, concentration, and dimensions of the tracer, the exposure conditions (time between exposures, exposure time, and number of exposures), and the sensitivity and resolution of the film on the quality of the final results were investigated, photographing an experimental flow behind an impulsively started circular cylinder. The velocity data were acquired by digital processing of Young's fringes, produced by point-by-point scanning of a photographic negative. Using the optimal photographing conditions, the errors involved in the estimation of the fringe angle and spacing were of the order of 1 percent for the spacing and +/1 deg for the fringe orientation. The resulting accuracy in the velocity was of the order of 2-3 percent of the maximum velocity in the field.

Lourenco, L.↗

NASA NTRS2022

Full-Wave Simulations of Scattering by Corn Fields at L-Band

In this paper, the Numerical Maxwell Model of 3D (NMM3D) full-wave simulation is performed over a corn field using a hybrid method to study the vegetation effect on the microwave. The commercial software of FEKO is used to extract T-matrix of single corn in the first step. Then the calculated T-matrix is combined with Wave Multiple Scattering Theory (W-MST) in the second step to consider the multiple scattering among different plants. The hybrid method is validated with HFSS by solving scattering from 2 corns. A corn field of 25 corn is simulated using the hybrid method and the transmission is calculated and compared with those obtained from the classical radiative transfer model.

Yueh, Simon↗

DOE OSTI2021

A parameterization of sub-grid topographical effects on solar radiation in the E3SM Land Model (version 1.0): implementation and evaluation over the Tibetan Plateau

Abstract. Topography exerts significant influences on the incoming solar radiation at the land surface. A few stand-alone regional and global atmospheric models have included parameterizations for sub-grid topographic effects on solar radiation. However, nearly all Earth system models (ESMs) that participated in the Coupled Model Intercomparison Project (CMIP6) use a plane-parallel (PP) radiative transfer scheme that assumes that the terrain is flat. In this study, we incorporated a well-validated sub-grid topographic (TOP) parameterization in the Energy Exascale Earth System Model (E3SM) Land Model (ELM) version 1.0 to quantify the effects of sub-grid topography on solar radiation flux, including the shadow effects and multi-scattering between adjacent terrain. We studied the role of sub-grid topography by performing ELM simulations with the PP and TOP schemes over the Tibetan Plateau (TP). Additional ELM simulations were performed at multiple spatial resolutions to investigate the role of spatial scale on sub-grid topographic effects on solar radiation. The Moderate Resolution Imaging Spectroradiometer (MODIS) data was used to compare with the ELM simulations. The results show that topography has non-negligible effects on surface energy budget, snow cover, snow depth, and surface temperature over the TP. The absolute differences in surface energy fluxes for net solar radiation, latent heat flux, and sensible heat flux between TOP and PP exceed 20, 10, and 5 W m−2, respectively. The differences in land surface albedo, snow cover fraction, snow depth, and surface temperature between TOP and PP exceed 0.1, 0.1, 10 cm, and 1 K, respectively. The magnitude of the sub-grid topographic effects is dependent on seasons and elevations and is also sensitive to the spatial scales. Although the sub-grid topographic effects on solar radiation are larger with more spatial details at finer spatial scales, they cannot be simply neglected at coarse spatial scales. When compared to MODIS data, incorporating the sub-grid topographic effects overall reduces the biases of ELM in simulating surface energy balance, snow cover, and surface temperature, especially in the high-elevation and snow-covered regions over the TP. The inclusion of sub-grid topographic effects on solar radiation parameterization in ELM will contribute to advancing our understanding of the role of the surface topography on terrestrial processes over complex terrain.

Hao, Dalei (ORCID:0000000334979774)↗

DOE OSTI2022

A quantitative model of charge injection by ruthenium chromophores connecting femtosecond to continuous irradiance conditions

A kinetic framework for the ultrafast photophysics of tris(2,2-bipyridine)ruthenium(II) phosphonated and methyl-phosphonated derivatives is used as a basis for modeling charge injection by ruthenium dyes into a semiconductor substrate. By including the effects of light scattering, dye diffusion, and adsorption kinetics during sample preparation and the optical response of oxidized dyes, quantitative agreement with multiple transient absorption datasets is achieved on timescales spanning femtoseconds to nanoseconds. In particular, quantitative agreement with important spectroscopic handles—the decay of an excited state absorption signal component associated with charge injection in the UV region of the spectrum and the dynamical redshift of a ~500 nm isosbestic point—validates our kinetic model. Pseudo-first-order rate coefficients for charge injection are estimated in this work, with an order of magnitude ranging from 10 11 to 10 12 s –1 . The model makes the minimalist assumption that all excited states of a particular dye have the same charge injection coefficient, an assumption that would benefit from additional theoretical and experimental exploration. Here, we have adapted this kinetic model to predict charge injection under continuous solar irradiation and find that as many as 68 electron transfer events per dye per second take place, significantly more than prior estimates in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗