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DOE OSTI2022

Large-scale application of free energy perturbation calculations for antibody design

Abstract Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using the Amber software package, to facilitate antibody design and evaluation. In combination with Hamiltonian replica exchange, our FEP simulations aim to predict the effect of mutations on both the binding affinity and the structural stability. Importantly, we incorporate multiple strategies to faithfully estimate the statistical uncertainties in the FEP results. As a case study, we apply our protocols to systematically evaluate variants of the m396 antibody for their conformational stability and their binding affinity to the spike proteins of SARS-CoV-1 and SARS-CoV-2. By properly adjusting relevant parameters, the particle collapse problems in the FEP simulations are avoided. Furthermore, large statistical errors in a small fraction of the FEP calculations are effectively reduced by extending the sampling, such that acceptable statistical uncertainties are achieved for the vast majority of the cases with a modest total computational cost. Finally, our predicted conformational stability for the m396 variants is qualitatively consistent with the experimentally measured melting temperatures. Our work thus demonstrates the applicability of FEP in computational antibody design.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Study of Key 57 Ni ⁢(𝑝,𝛾)⁢ 58 Cu Resonances to Understand 44 Ti Nucleosynthesis in Supernovae

An important validation of nucleosynthesis models of core-collapse supernovae is the comparison of radioisotope predictions to abundances inferred from observations of 𝛾 rays emitted in remnants. One such isotope, 44 Ti, is especially sensitive to the 57 Ni ⁢(𝑝,𝛾)⁢ 58 Cu reaction rate. Despite this importance, no experimentally constrained rate exists for this reaction. It is thus crucial to determine this rate. GRETINA ORRUBA: Dual Detectors for Experimental Structure Studies (GODDESS) was used along with the first use of the Enge split-pole spectrograph at Notre Dame to measure structure properties of 58 Cu via the 58 Ni ⁢( 3 He,𝑡)⁢ 58 Cu reaction. Here, the combined analysis of these complementary data sets allows for precise determination of 58 Cu level energies, and spins are constrained from analysis of the 𝛾-ray decay. 44 Ti yields were found to change by over 25% compared to previous estimates in model calculations using the new experimentally constrained reaction rate.

energy levels↗

NASA NTRS1990

Virial theorem analysis of the structure and stability of magnetized clouds

The tensor virial theorem is used to analyze the structure and stability of self-gravitating, magnetized spheroids surrounded by a low-density medium with pressure and magnetic field. Analytical expressions are developed for the effect of a weak field and calculate critical states when the effect of the field is arbitrarily strong, comparing the results with full magnetohydrostatic calculations. This analysis suggests that a magnetic field may prevent gravitational collapse but may also be destabilizing, depending on its degree of concentration within the cloud.

Zweibel, Ellen G.↗

NASA NTRS1990

Virial theorem analysis of the structure and stability of magnetized clouds

Zweibel, Ellen G.↗

NASA NTRS1989

A two micron polarization survey toward dark clouds

A near infrared (2.2 micron) polarization survey of about 190 sources was conducted toward nearby dark clouds. The sample includes both background field stars and embedded young stellar objects. The aim is to determine the magnetic field structure in the densest regions of the dark clouds and study the role of magnetic fields in various phases of star formation processes, and to study the grain alignment efficiency in the dark cloud cores. From the polarization of background field stars and intrinsically unpolarized embedded sources, the magnetic field structure was determined in these clouds. From the intrinsic polarization of young stellar objects, the spatial distribution was determined of circumstellar dust around young stars. Combining the perpendicularity between the disks and magnetic fields with perpendicularity between the cloud elongation and magnetic fields, it is concluded that the magnetic fields might have dominated nearly all aspects of cloud dynamics, from the initial collapse of the clouds right through to the formation of disks/tori around young stars in these low to intermediate mass star forming clouds of the Taurus, Ophiuchus, and Perseus.

Tamura, M.↗

NASA NTRS2000

Reionization of the Universe and the Photoevaporation of Cosmological Minihalos

The first sources of ionizing radiation to condense out of the dark and neutral Intergalactic Medium (IGM) sent ionization fronts sweeping outward through their surroundings, overtaking other condensed objects and photoevaporating them. This feedback effect of universal reionization on cosmic structure formation is demonstrated here for the case of a cosmological minihalo of dark matter and baryons exposed to an external source of ionizing radiation with a quasar-like spectrum, just after the passage of the global ionization front created by the source. We model the pre-ionization minihalo as a truncated, nonsingular isothermal sphere in hydrostatic equilibrium following its collapse out of the expanding background universe and virialization. Results are presented of the first, gas dynamical simulations of this process, including radiative transfer. A sample of observational diagnostics is also presented, including the spatially-varying ionization levels of C, N, and O in the flow if a trace of heavy elements is present and the integrated column densities of H I, He I and He II, and C IV through the photoevaporating gas at different velocities, which would be measured in absorption against a background source like that responsible for the ionization.

Shapiro, Paul R.↗

NASA NTRS2023

Optimizing Surfactant Templating of Yttria-Stabilized Zirconia Aerogels for High-Temperature Applications: Effect of Anionic and Nonionic Surfactant

Aerogels, mesoporous materials with extreme material properties including high specific surface area, low density, and low thermal conductivity, can be useful for applications including catalysis, sorption media, and drug delivery. The low thermal conductivity and high surface area of aerogels makes them advantageous as thermal management systems, specifically for aerospace or aeronautics applications. However, the pore collapse and subsequent surface area decrease of aerogels following exposure to high temperatures must be mitigated to allow aerogels to be effectively used in thermal management applications. This work investigates the anionic surfactant sodium dodecyl sulfate (SDS) and the nonionic surfactant Pluronic® P-123 as surfactant templates in yttria-stabilized zirconia (YSZ) aerogels. By utilizing surfactant templates, known to influence pore structure, it is anticipated that sintering and densification of the aerogels following high-temperature exposure will be mitigated. It was determined that the addition of SDS and P-123 increased the surface area and pore volume of as-dried aerogels and suppressed crystallite growth at high temperatures. However, the impact of surfactant templates on the surface area and pore volume of heat-treated aerogels was negligible, potentially due to low concentrations of surfactant and the removal of the surfactant following high-temperature exposure.

Yttria-stabilized zirconia aerogels↗

DOE OSTI2026

Electron-doping-induced destabilization of the dimerized insulating state in monolayer IrTe 2

The ability to tune the electronic phases of two-dimensional (2D) materials through external perturbations provides a powerful route to engineer functional nanoscale systems. In particular, the ground state of monolayer (ML) 1T-IrTe 2 is highly sensitive to the interplay between local chemical bonding and global electronic topology, leading to a unique 2 × 1 dimerized insulating phase. Here, we present an angle-resolved photoemission study on the evolution of the electronic structure in ML IrTe 2 induced by in situ Rb adsorption. We find that Rb adsorption suppresses the 2 × 1 dimerized phase in ML IrTe 2 , inducing a clear insulator-to-metal transition. This transition is characterized by a reconstruction of the band topology toward a bilayer-like metallic configuration. Combined with first-principles calculations, our results demonstrate that the collapse of the insulating state originates from Ir valence change and suppression of Fermi surface nesting-driven instabilities. Our findings establish ML IrTe 2 as a model system for investigating instability-driven phase control in 2D materials and highlight its potential for tunable electronic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Contributions to the mechanistic understanding of the microstructural evolution in irradiated U-Mo dispersion fuel

Here, advanced microstructural characterization techniques, such as scanning electron microscopy (SEM) and scanning transmission electron microscopy - energy dispersive x-ray spectroscopy (STEM-EDS), were used to interpret the fuel microstructure evolution and fission products behavior in U-Mo dispersion fuel irradiated in the Advanced Test Reactor (ATR) as part of the European Mini-Plate Irradiation Experiment (EMPIrE) test. The larger as-fabricated fuel grain size achieved by heat-treating the U-Mo powder resulted in slower high burnup structure (HBS) development and reduced fission gas porosity. Slower HBS kinetics was observed at the fuel kernels’ periphery, which contained smaller and less fission gas bubbles at all fission densities (FDs) investigated and was attributed to a locally reduced damage density and fission products concentration, as corroborated with Monte Carlo simulations. The non-refined grains at the fuel kernel periphery hosted a perfectly ordered fission Gas Bubble Superlattice (GBS) up to 6.3 × 10 21 fissions/cm 3 . Nano-scale STEM-EDS analysis presented in this study provided useful information on the GBS characteristic morphology and evolution in U-Mo fuel. The concentration of fission gas in the GBS progressively increased with FD, pointing to an evolution of the nanobubble pressure status with irradiation. A possible connection between the GBS collapse and HBS onset is proposed for which there exists a threshold in the misorientation of the refined sub-grains above which the GBS stability during irradiation is no longer preserved, resulting in the GBS collapse.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Three-dimensional Core-collapse Supernova Simulations with 160 Isotopic Species Evolved to Shock Breakout

We present three-dimensional simulations of core-collapse supernovae using the FLASH code that follow the progression of the explosion to the stellar surface, starting from neutrino radiation hydrodynamic simulations of the neutrino-driven phase performed with the Chimera code. We consider a 9.6 M ⊙ zero-metallicity progenitor starting from both 2D and 3D Chimera models and a 10 M ⊙ solar-metallicity progenitor starting from a 2D Chimera model, all simulated until shock breakout in 3D while tracking 160 nuclear species. The relative velocity difference between the supernova shock and the metal-rich Rayleigh–Taylor (R-T) "bullets" determines how the metal-rich ejecta evolves as it propagates through the density profile of the progenitor and dictates the final morphology of the explosion. We find maximum 56 Ni velocities of ~1950 and ~1750 km s -1 at shock breakout from 2D and 3D 9.6 M ⊙ Chimera models, respectively, due to the bullets' ability to penetrate the He/H shell. When mapping from 2D, we find that the development of higher-velocity structures is suppressed when the 2D Chimera model and 3D FLASH model meshes are aligned. The development of faster-growing spherical-bubble structures, as opposed to the slower-growing toroidal structure imposed by axisymmetry, allows for interaction of the bullets with the shock and seeds further R-T instabilities at the He/H interface. We see similar effects in the 10 M ⊙ model, which achieves maximum 56 Ni velocities of ~2500 km s -1 at shock breakout.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Pahute Mesa-Oasis Valley Hydrostratigraphic Framework Model for Corrective Action Units 101 and 102: Central and Western Pahute Mesa, Nye County, Nevada (Rev. 0)

A new, revised three-dimensional (3-D) hydrostratigraphic framework model (HFM) for the Central and Western Pahute Mesa Corrective Action Units 101 and 102 was completed in 2019. The initial (Phase I) model was completed in 2002 and was documented in A Hydrostratigraphic Model and Alternatives for the Groundwater Flow and Contaminant Transport Model of Corrective Action Units 101 and 102: Central and Western Pahute Mesa, Nye County, Nevada (BN, 2002). Subsequent flow and transport modeling revealed the need to collect additional data to reduce uncertainties. The Phase II data collection and characterization effort included extensive well drilling and testing activities, and rebuilding of the Phase I 3-D HFM, resulting in the Phase II HFM (NSTec, 2014). Further drilling (Well ER-20-12), data collection, and interpretive work (e.g., Thirsty Canyon Lineament [Wurtz and Day, 2018]) were incorporated into the Pahute Mesa-Oasis Valley (PM-OV) HFM. The PM-OV HFM incorporates the area of interest from the Phase II HFM and adds additional areas, primarily to the north and west with minor additions to the south and east. The new, expanded area matches the PM-OV groundwater basin as defined in Fenelon et al. (2016) and includes Pahute Mesa, a former nuclear testing area at the Nevada National Security Site; and Oasis Valley, a groundwater discharge area downgradient from contaminant source areas on Pahute Mesa. The data and information necessary to build the PM-OV HFM are provided in Navarro (2019). The PM-OV HFM will be used by hydrologic modelers who are tasked with developing a model to determine how contaminants are transported by groundwater flow in an area of complex geology. The model area is large (more than 6,250 square kilometers) and geologically complex, including Paleozoic- to Mesozoic-age structures (e.g., thrust faults, Thirsty Canyon Lineament), at least seven Tertiary-age calderas, several intrusive bodies, and many relatively recent basin-and-range normal faults. Investigators from the U.S. Geological Survey; National Security Technologies, LLC; National Laboratories; and U.S. Department of Energy contractors have organized the more than 300 volcanic units and other rocks in the model area into 77 hydrostratigraphic units (HSUs). The volcanic rocks are subdivided into 42 aquifers, 11 confining units, and 9 composite units (containing both aquifer and confining unit rocks). The underlying pre-Tertiary rocks were divided into 5 HSUs, comprising 2 aquifers and 3 confining units. The model also includes 1 alluvial aquifer unit, 8 intrusive confining units, and 1 granite confining unit. The model depicts the thickness, extent, and geometric relationships of these HSUs (“layers” in the model) along with all the major structural features that control them, including calderas and faults. The most substantive differences between the Phase II HFM and the PM-OVHFM include (1) addition of the new data and resulting revised interpretations from the additional area encompassed by the PM-OV groundwater basin; (2) incorporation of 16 new faults; (3) 12 boreholes from the northern extension; (4) 2 additional caldera-collapse collars; and (5) correlation of the simulated faulting and hydrostratigraphy in the eastern part of the model domain with the delineations represented in the neighboring Rainier Mesa-Shoshone Mountain HFM-Prime and Yucca Flat-Climax Mine HFM. All PM-OV HFM delineations were based on published and unpublished data from geophysical investigations, surface geologic maps, and drill-hole records. Phase II approached model uncertainty using the model-building software to test model configurations and hydrologic consequences using a range of values for parameters such as fault offset amounts and HSU elevations. The PM-OV HFM expands on this approach to encompass the entire PM-OV groundwater basin.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1982

The origin of Uranus - Compositional considerations

Implications of two broad classes of theories for the origin of the solar system for the composition of Uranus are examined as an approach to the testing of alternative hypotheses. Consideration is given to accretional theories of planetary formation, which predict interior structures consisting of a rock core surrounded by an envelope of H2, He, H2O, NH3 and CH4 with different ratios of H2 to ice, and to theories postulating the formation of giant gaseous protoplanets as a result of an encounter with an extended protostar, the condensation of eddies (flocules) in a cloud, with supersonic turbulence and the breakup of a ring formed in a collapsing massive solar nebula. It is shown that whereas accretional theories can easily account for the high density of Uranus relative to Jupiter and Saturn, the apparent absence of NH3, and the observed D/H ratio being about three times the solar ratio, the giant protoplanet theories do not clearly demonstrate how the compositions were achieved.

Podolak, M.↗

NASA NTRS1983

Materials investigation of STS-3 parachute failure

Main parachute, No. 2 of SRB A-12 on STS-3, sustained damage during deployment or initial inflation that resulted in its collapse and failure to sustain load. During an investigation of the materials from this parachute, optical and scanning electron microscope analyses were conducted. This examination identified stains and abrasions on vent lines that appear to have been a result of friction contact with its flotation bag lanyard. Mechanical testing of the vent band indicated a reduction in strength of 37 percent obviously due to structural overload, heat, and ocean water exposure. It is concluded from this and other available data that entanglement of parachutes No. 1 and No. 2 during deployment caused adequate structural damage to main parachute No. 2 to render it unable to carry load.

Nichols, R. L.↗

NASA NTRS2016

Fatigue Life of Postbuckled Structures with Indentation Damage

The fatigue life of composite stiffened panels with indentation damage was investigated experimentally using single stringer compression specimens. Indentation damage was induced on one of the two flanges of the stringer. The experiments were conducted using advanced instrumentation, including digital image correlation, passive thermography, and in-situ ultrasonic scanning. Specimens with initial indentation damage lengths of 37 millimeters to 56 millimeters were tested in fatigue and the effects of cyclic load amplitude and damage size were studied. A means of comparison of the damage propagation rates and collapse loads based on a stress intensity measure and the Paris law is proposed.

Davila, Carlos G.↗

DOE OSTI2022

Phase transitions in ε-FeOOH at high pressure and ambient temperature

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99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2022

Chemical Cartography with APOGEE: Mapping Disk Populations with a 2-process Model and Residual Abundances

We apply a novel statistical analysis to measurements of 16 elemental abundances in 34,410 Milky Way disk stars from the final data release (DR17) of APOGEE-2. Building on recent work, we fit median abundance ratio trends [X/Mg] versus [Mg/H] with a 2-process model, which decomposes abundance patterns into a "prompt" component tracing core-collapse supernovae and a "delayed" component tracing Type Ia supernovae. For each sample star, we fit the amplitudes of these two components, then compute the residuals Δ[X/H] from this two-parameter fit. The rms residuals range from ~0.01–0.03 dex for the most precisely measured APOGEE abundances to ~0.1 dex for Na, V, and Ce. The correlations of residuals reveal a complex underlying structure, including a correlated element group comprised of Ca, Na, Al, K, Cr, and Ce and a separate group comprised of Ni, V, Mn, and Co. Selecting stars poorly fit by the 2-process model reveals a rich variety of physical outliers and sometimes subtle measurement errors. Residual abundances allow for the comparison of populations controlled for differences in metallicity and [α/Fe]. Relative to the main disk (R = 3–13 kpc), we find nearly identical abundance patterns in the outer disk (R = 15–17 kpc), 0.05–0.2 dex depressions of multiple elements in LMC and Gaia Sausage/Enceladus stars, and wild deviations (0.4–1 dex) of multiple elements in ω Cen. The residual abundance analysis opens new opportunities for discovering chemically distinctive stars and stellar populations, for empirically constraining nucleosynthetic yields, and for testing chemical evolution models that include stochasticity in the production and redistribution of elements.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2011

Using Dark Matter Haloes to Learn about Cosmic Acceleration: A New Proposal for a Universal Mass Function

Structure formation provides a strong test of any cosmic acceleration model because a successful dark energy model must not inhibit or overpredict the development of observed large-scale structures. Traditional approaches to studies of structure formation in the presence of dark energy or a modified gravity implement a modified Press-Schechter formalism, which relates the linear overdensities to the abundance of dark matter haloes at the same time. We critically examine the universality of the Press-Schechter formalism for different cosmologies, and show that the halo abundance is best correlated with spherical linear overdensity at 94% of collapse (or observation) time. We then extend this argument to ellipsoidal collapse (which decreases the fractional time of best correlation for small haloes), and show that our results agree with deviations from modified Press-Schechter formalism seen in simulated mass functions. This provides a novel universal prescription to measure linear density evolution, based on current and future observations of cluster (or dark matter) halo mass function. In particular, even observations of cluster abundance in a single epoch will constrain the entire history of linear growth of cosmological of perturbations.

Prescod-Weinstein, Chanda↗

NASA NTRS2016

Soft-Robotic Rover with Electrodynamic Power Scavenging: NIAC Final Report - Phase 1

The purpose of studying the capabilities of Electrodynamic Tethers (EDT) and Soft Robotics is to ascertain the feasibility of using cross-cutting EDT and soft robotics technologies to achieve future NASA mission objectives with mass and power budgets orders of magnitude lower than conventional spacecraft. In this context, the Phase I study focuses on three technological elements: the design of a soft-robotic rover that can operate in extraterrestrial oceans, demonstrating feasibility of electrodynamic tethers for power scavenging in the Europa environment, and utilizing electrolysis to power biomimetic propulsion.The Phase I results show that a soft robotic, underwater rover has many advantages over a traditional view of autonomous underwater vehicles. Many of these advantages stem from its ability to collapse or expand the body, which carries two key benefits: (i) cost savings in transport and (ii) buoyancy control. Furthermore, this rover's material offers properties that enable it to survive most oceanic conditions, withstand a likely radiation environment, and retard ice formation. The use of these soft robots under water is very attractive because buoyancy enables very large robots without the need for skeletal structures that limit their shape-changing ability. The prime limitation of soft robots for underwater exploration is their nascent state of development, an issue that this study has begun to address and that we hope to continue in Phase II. The theoretical calculations and experimental investigation on electrodynamic tethers discussed in this report show that their use in saltwater environments is feasible. However, magneto hydrodynamic effects require attention, which will be a priority in Phase II. A possible approach involves magnetic shielding of a portion of the EDT array to generate significant current from imposed alternating magnetic fields. The Phase I experiments show that this approach may enable enough power to be generated for a soft robotic rover of the scale contemplated here. This power is in the range of 1mW to 1W and determines the time required to collect and transmit science data.

Soft Robotics↗