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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Breaking Radial Dipole Symmetry in Planar Macrocycles Modulates Edge‐to‐Edge Packing and Disrupts Cofacial Stacking

Dipolar interactions are ever-present in supramolecular architectures, though their impact is typically revealed by making dipoles stronger. While it is also possible to assess the role of dipoles by altering their orientations by using synthetic design, doing so without altering the molecular shape is not straightforward. We have now done this by flipping one triazole unit in a rigid macrocycle, tricarb. The macrocycle is composed of three carbazoles (2 Debye) and three triazoles (5 Debye) defining an array of dipoles aligned radially but organized alternately in and out. These dipoles are believed to dictate edge-to-edge tiling and face-to-face stacking. We modified our synthesis to prepare isosteric macrocycles with the orientation of one triazole dipole rotated 40°. The new dipole orientation guides edge-to-edge contacts to reorder the stability of two surface-bound 2D polymorphs. The impact on dipole-enhanced π stacking, however, was unexpected. Our stacking model identified an unchanged set of short-range (3.4 Å) anti-parallel dipole contacts. Despite this situation, the reduction in self-association was attributed to long-range (~6.4 Å) dipolar repulsions between π-stacked macrocycles. This work highlights our ability to control the build-up and symmetry of macrocyclic skeletons by synthetic design, and the work needed to further our understanding of how dipoles control self-assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Ring patterns generated by an expanding colloidal meniscus

The drop-and-dry is a common technique allowing for creation of periodic nanoparticle (NP) structures for sensing, photonics, catalysis, etc. However, the reproducibility and scalability of this approach for fabrication of NP-based structures faces serious challenges due to the complexity of the simple, at first glance, evaporation process. In this work we study the effect of the spatial confinement on the NP self-assembly under slow solvent evaporation, when the air-liquid-substrate contact line (CL) expands from the center towards the walls of a cylindrical cell, forming a toroid. Using in situ video monitoring of the stick-slip CL motion, we find regular hydrodynamic perturbations in the meniscus, and reveal fine details of the formation of quasiperiodic rings of close packed NP layers. We report that drying of the toroidal NP droplet has a number of important differences from drying of the classical hemispherical colloidal drops. In toroidal drops we observe linear-in-time average meniscus motion, in contrast to the hemispherical drops where the meniscus moves as a square root of time. While both droplet geometries produce NP ring patterns, the ring width for the toroidal drop decreases with increasing ring radius, while it decreases with decreasing the radius of the hemispherical drop. We suggest that free ligands are the main cause of the Marangoni instabilities driving the periodic vorticity in the meniscus. Finally, we show that the usually ignored contact line tension may yield a considerable contribution to the CL pinning causing the CL slip-stick motion and the ring formation.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Perspective on solid-phase epitaxy as a method for searching novel topological phases in pyrochlore iridate thin films

Pyrochlore iridates exhibit various novel topological phenomena due to their topology and electron correlation. Notably, pyrochlore iridate was the first proposed material system shown to host the time-reversal symmetry broken Weyl semimetal phase. After this profound theoretical proposal, extensive experimental attempts have been made to synthesize high-quality samples in both bulk and film forms. In particular, adjusting thin film geometry represents a practical way to tune the U/ t ( U: Coulomb interaction and t: for hopping parameter) and identify the various topological phases in the regime U ~ λ ( λ: spin–orbit interaction). However, the instability of pyrochlore iridates at high temperature and low oxygen pressure has long been a barrier to growing pyrochlore iridate thin films by conventional film growth methods. To overcome this, pyrochlore iridate films have often been grown by the solid-phase epitaxy method, which uses a metastable amorphous layer grown at low temperature. During a high temperature post-annealing process, the layer in contact with a single crystalline substrate will crystallize epitaxially in the solid state by rearranging atoms at the interface. Here, we present a perspective on the solid-phase epitaxy as a method to synthesize epitaxial pyrochlore iridate thin films and a way to search for novel correlated phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Characterizing Surface Ice-Philicity Using Molecular Simulations and Enhanced Sampling

The formation of ice, which plays an important role in diverse contexts ranging from cryopreservation to atmospheric science, is often mediated by solid surfaces. Although surfaces that interact favorably with ice (relative to liquid water) can facilitate ice formation by lowering nucleation barriers, the molecular characteristics that confer ice-philicity to a surface are complex and incompletely understood. To address this challenge, here we introduce a robust and computationally efficient method for characterizing surface ice-philicity that combines molecular simulations and enhanced sampling techniques to quantify the free energetic cost of increasing surface–ice contact at the expense of surface–water contact. Using this method to characterize the ice-philicity of a family of model surfaces that are lattice matched with ice but vary in their polarity, we find that the nonpolar surfaces are moderately ice-phobic, whereas the polar surfaces are highly ice-philic. In contrast, for surfaces that display no complementarity to the ice lattice, we find that ice-philicity is independent of surface polarity and that both nonpolar and polar surfaces are moderately ice-phobic. Furthermore, our work thus provides a prescription for quantitatively characterizing surface ice-philicity and sheds light on how ice-philicity is influenced by lattice matching and polarity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Electronic interactions and stability issues at the copper-graphene interface in air and in alkaline solution under electrochemical control

A micro-electrochemical cell is sealed with a polymer-free single-layer graphene (SLG) membrane to monitor the stability of Cu nanoparticles (NPs) attached to SLG, as well as the interfacial electronic interactions between Cu NPs and SLG both in air and in a mildly alkaline aqueous solution under electrochemical control. A combination of techniques, including in-situ Kelvin probe force microscopy (KPFM) and ex-situ electron microscopy, are applied. When Cu NPs are metallic at cathodic potentials, there is a relatively bias-independent offset in the SLG work function due to charge transfer at the Cu-SLG contact. When Cu NPs are oxidized at anodic potentials, on the other hand, the work function of SLG also depends on the applied bias in a quasi-linear fashion due to electrochemical gating, in addition to charge transfer at the CuOx-SLG contact. Furthermore, Cu NPs were found to oxidize and detach from SLG when kept under anodic potentials for a few hours, whereas they remain adhered to SLG at cathodic potentials. This is attributed to water intercalation at the CuO-SLG interface associated with the enhanced hydrophilicity of positively polarized graphene, as supported by the absence of Cu detachment following oxidation by galvanic corrosion in air.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structure and Stability of Pristine and Carboxylate-Covered Anatase TiO 2 (001) in Aqueous Environment

The interactions of carboxylic acids and water with TiO 2 surfaces are important in applications ranging from solar cells to biomedical devices. Here we focus on the aqueous interface with the minority (001) surface of anatase TiO 2 (A-001) and the behavior of adsorbed formic and acetic acid monolayers at this interface. We investigated the structure and stability of the pristine reconstructed and formic/acetic acid covered A-001 surfaces in contact with water using density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations. The (1 × 4) reconstruction of the pristine surface is found to be stable in aqueous environment, within the time scale of our simulation. Here, carboxylic acids adsorb in deprotonated bidentate (BD) form on A-001, with the dissociated proton transferred to a surface oxygen to form a bridging hydroxyl. Of the two possible configurations, BD bridging and BD straddling, of the adsorbed species, the latter is found to rapidly transform to a monodentate structure during our simulations. Further investigation of mixed acetate–formate monolayers on A-001 in water indicates that also BD bridging species can become unstable at the boundaries between formate and acetate-covered regions, transforming to a monodentate form that does not prevent water adsorption on the TiO 2 surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structures of CTCF–DNA complexes including all 11 zinc fingers

The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12–15-bp CORE sequence, some of the CTCF binding sites contain 5' upstream and/or 3' downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1–ZF7 and ZF3–ZF11 in complex with DNA that incorporates the CORE sequence together with either 3' downstream or 5' upstream motifs. Like conventional tandem ZF array proteins, ZF1–ZF7 follow the right-handed twist of the DNA, with each finger occupying and recognizing one triplet of three base pairs in the DNA major groove. ZF8 plays a unique role, acting as a spacer across the DNA minor groove and positioning ZF9–ZF11 to make cross-strand contacts with DNA. We ascribe the difference between the two subgroups of ZF1–ZF7 and ZF8–ZF11 to residues at the two positions -6 and -5 within each finger, with small residues for ZF1–ZF7 and bulkier and polar/charged residues for ZF8–ZF11. ZF8 is also uniquely rich in basic amino acids, which allows salt bridges to DNA phosphates in the minor groove. Highly specific arginine–guanine and glutamine–adenine interactions, used to recognize G:C or A:T base pairs at conventional base-interacting positions of ZFs, also apply to the cross-strand interactions adopted by ZF9–ZF11. The differences between ZF1–ZF7 and ZF8–ZF11 can be rationalized structurally and may contribute to recognition of high-affinity CTCF binding sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Tetracene Functionalized Si(111) Achieves Enhanced Solar-to-Chemical Energy Conversion via Molecular Acceptor States

The properties of semiconductor|liquid interfaces play a critical role in determining the efficiency of solar-to-hydrogen (STH) conversion. Here, we investigate how molecular functionalization of Si(111) and Si(111)|TiO 2 surfaces impacts photoelectrochemical (PEC) hydrogen production efficiency. We find that functionalization of ∼3% of the atop sites of Si(111) with either 9-anthracene (Anth) or 5-tetracene (Tet), with the remaining sites passivated by methyl groups, provides substrates with high electronic quality and low surface oxide densities, as determined by X-ray photoelectron spectroscopy (XPS) measurements. Surface photovoltage (SPV) spectroscopy shows that surfaces modified with Anth or Tet exhibit an increased photovoltage, with Tet-functionalized surfaces yielding an additional 192 meV relative to methyl-terminated Si(111), indicating improved charge separation for Si-Tet. Further improvement in onset potential was achieved by replacing a nitrogen-containing TiO 2 atomic layer deposition (ALD) precursor (TDMAT) with a precursor lacking nitrogen (TTIP), which eliminates the parasitic defect band in the TiO 2 overlayer (p-Si(111)-Tet|TTIP-TiO 2 |Pt: V OC = +0.283 ± 0.041 V vs RHE). Density functional theory (DFT) analysis demonstrates that compared with Anth-modified Si(111), the Tet-modified surface exhibits more hybridized Si(111)-Tet states closer to the silicon band edges. Mercury contact current–voltage (I–V, dark) measurements quantified the relative interfacial density of states of Si-Tet, Si-Anth and Si-Me surfaces─revealing that the interfacial state density was highest for Si-Tet. This suggests that such hybridized interfaces serve to capture better photoexcited charge, which enables facile electron transfer to molecular acceptors in solution. Altogether, the data indicate that beneficial hybrid molecular LUMO surface states interacting with the Si conduction band edge results in improved hydrogen evolution (HER) performance for p-Si devices.

Group theory↗
DOE OSTI2020

Time-Resolved Spectroscopy of Insulator-Metal Transitions: Exploring Low-Energy Dynamics in Strongly Correlated Systems. Final Report

Transition metal oxides (TMOs) have attracted much attention in recent years. The strong coupling between charge, spin, and orbital degrees of freedom creates novel functional properties. The research at the interplay between ferromagnetism, ferroelectricity and conductivity provides a promising way to the development of future spintronic devices. The interface characterization of multifunctional oxide heterostructures is crucial to understand deeply the magnetic response, spin injection and spin transport. In year one, we characterized optically the magnetic property with the method of magnetization-induced second-harmonic generation (MSHG), which is a sensitive technique to selectively probe the interface where the spatial inversion symmetry is broken. The interface of n-type BaTiO 3 (BTO)/La 0.67 Sr 0.33 MnO 3 (LSMO) forms a Schottky barrier and displays a good diode effect. By applying an external electric field across the sample, we observe the magnetoelectric (ME) coupling effect to modulate the interface magnetization. The voltage dependent magnetic contrast sharply vanishes at positive voltage (applied to LSMO contact) and reveals a ferromagnetic (FM)-to- antiferromagnetic (AFM) transition occurring at the interface, while the magneto-optic Kerr effect (MOKE) indicates that the bulk property is not affected. The strain mediated mechanism and ferroelectric (FE) polarization induced charge medicated mechanism are both discussed, but they do not play an important role in the observed magnetization transition. A new mechanism is proposed - the injected minority spins through strong Hund's interaction with the local magnetic moments at positive voltage weaken the double-exchange interaction of nearby Mn e g electrons, thereby reducing the ferromagnetic (FM) ordering. The dominant superexchange interaction of localized t 2g electrons finally leads to the AFM configuration. By reducing the electron carrier concentration of BTO, a positive voltage shift of the transition is observed. The oxygen richer sample with lower carrier concentration requires a higher voltage to increase the hole doping level of LSMO to induce the interfacial AFM phase. By inserting a thin (1nm) La 0.5 Ca 0.5 MnO 3 layer between BTO and LSMO, the interface magnetic response from LSMO is enhanced. In year two, a non-multiferroic heterostructure SrTiO 3 (STO)/ La 0.5 Ca 0.5 MnO 3 (LCMO)/La 0.67 Sr 0.33 MnO 3 (LSMO) was studied. In this system, the interface FM-AFM transition is observed at negative voltage. The STO layer may act as a hole-donating layer, which induces the hole transfer to LSMO making it overdoped, while the LCMO interlayer at the 0.5 hole doping level displays complicated CE type AFM phase. Thus the AFM phase is dominant at the interface and electron accumulation is required to induce the FM phase by applying a negative voltage. For oxygen rich sample, the magnetic MSHG loop reappears at high positive voltage (around +2.5 V). At high doping level (x > 0.5), LSMO exhibits A-type AFM order, consisting of AFM superexchange coupling between adjacent layers and intralayer FM double-exchange coupling. The less tensile strain of STO and LSMO due to a smaller lattice mismatch as compared to BTO would result in a weaker interlayer coupling . Thus, interfacial A-type AFM order can occur in STO/LCMO/LSMO heterostructure at high hole doping concentration. The study of ME coupling of multifunctional oxide heterostructures is definitely important to the development and performance of future spintronic devices. The results presented here regarding the interfacial magnetic transition controlled by an external electric field offer some new perspective to study the spin transport of magnetic tunnel junctions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Software Quality Assurance Plan ANSYS LSDYNA Version 2023R1

ANSYS Inc. develops and markets engineering simulation software and services used in the aerospace, automotive, manufacturing, electronics, biomedical, energy, defense, and many other industries. ANSYS is dedicated to engineering simulation and is the world’s leading software provider. ANSYS was founded in 1970 and is headquartered in Canonsburg, Pennsylvania. ANSYS provides an engineering analysis tool combining structural, thermal, computational fluid dynamics, acoustic and electromagnetic simulation capabilities. ANSYS LS-DYNA is the most used explicit simulation program capable of simulating the response of materials to short periods of severe loading. Its many elements, contact formulations, material models, and other controls can be used to simulate complex models with control over all the details of the problem. ANSYS LS-DYNA has a vast array of capabilities to simulate extreme deformation problems using its explicit solver. Engineers can tackle simulations involving material failure and look at how the failure progresses through a part or through a system. Models with large amounts of parts or surfaces interacting with each other are also easily handled, and the interactions and load passing between complex behaviors are modeled accurately. Using computers with higher numbers of CPU cores can drastically reduce solution times. In addition, many consulting firms and hundreds of universities use ANSYS for analysis, research, and educational purposes. ANSYS is recognized worldwide as one of the most widely used and capable programs of its type. ANSYS has successfully passed over 100 customer quality system audits against American Society of Mechanical Engineers (ASME) NQA-1 and 10 CFR Part 50, Appendix B, since the company was founded, over 60 of which have been since 1997. ANSYS has successfully passed over 100 International Organization for Standardization (ISO) 9001 assessments. ANSYS design analysis software is the first created within a quality system with ISO 9001 certification, which is the internationally accepted quality standard. Product development, testing, maintenance, and support processes also meet the US Nuclear Regulatory Commission’s (NRC’s) quality requirements, as they have for nearly four decades. ANSYS staff perform more than 60,000 software verification tests before releasing each new product. ASME NQA-1-2012 (Subpart 2.7 is specific to software) is the industry- and NRC-accepted approach (consensus standard) for meeting 10 CFR Part 50, Appendix B, requirements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Mechanical Properties of Permanent Foaming Fixatives for Deactivation and Decommissioning Activities

DOE-EM have identified an operational requirement for a fixative that can immobilize and/or encapsulate residual contamination in 3D void volumes (pipes, gloveboxes, waste containers, etc.) during D and D activities. Failure to safely and effectively immobilize residual contamination can: Put workers at risk, Contaminate the public and environment, Drive up operational costs. Commercial-off-the-shelf (COTS) polyurethane (PU) foams is one possible solution and is currently being investigated in collaboration with Savannah River National Lab (SRNL). Mechanical property testing will dictate how well PU foams can withstand physical stressors outlined in safety documents while immobilizing residual contamination. Results can provide a performance criteria for Section 5 of ASTM E3191: Standard Specification for Permanent Foaming Fixatives Used to Mitigate Spread of Radioactive Contamination. Polyurethanes consists of repeating units of urethanes which are produced from an exothermic reaction between a polyol (an alcohol with two or more hydroxyl groups in a molecule) and an isocyanate [2]. PUs consists of 3D cells that are formed by a blowing agent which is normally water. Water interacting with the isocyanate creates carbon dioxide and urea which contributes to cells' growth and expansion. The cross-linking between the polyol and isocyanate solidify the cell faces and walls. Micro scale properties that can influence mechanical properties include: Relative density (ratio between density of cellular material and density of the solid of which the cell walls are made of). Cells connectivity between edges and faces, and number of cells contact neighbors [3]. Whether a foam is open-celled or closed-celled. Closed-celled foams have a thin membrane that encloses each cell which can contribute to the stiffness of the foam. Incorporating fillers in the PU matrix like carbon-based nanoparticles in the form of expandable graphite (EG) can increase the thermal and mechanical performance [4]. When exposed to heat, EG produces a char layer that prevents heat and oxygen transfer which is known as intumescing. Mechanical performance is dependent on amount of EG loading since the cell sizes are linearly dependent on it. Overall, the rigid foams (I-R2) proved superior. SEM Analysis: I-R2 had the most consistent spherical sizes (average cell diameter: 489 μm), which enhance the relative density the most [5]. Tensile Testing Results: I-R2 experienced the largest breaking load (103.65 lbf) and stress (289.42 psi). I-R2 also had a higher Young's Modulus compared to R1 (2.99 ksi to 2.09 ksi). Compression Testing Results: I-R2 had the highest stress at 80% deflection (360.67 psi), load (1387.48 lbf) and modulus (3.92 ksi)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Shocked Transport: Experiments to Study Dynamic Particle Behavior under Varying Volume Fraction Conditions

Shocks interacting with densely-packed porous media is common in volcanic eruptions or in engineering applications such as ordinance. Large-scale, exploratory experiments have been performed by Frost and collaborators examining the behavior of a bed of particles subjected to a detonation wave. The detonation replaces the central explosive with a high-density, high-temperature gas that propagates outward. A shock wave travels through the particle bed, followed by a contact discontinuity between the shocked air and the explosive products. In the early times, the detonation wave causes many of the particles to collide and compact with each other. As the particles disperse, the experiments demonstrate a series of large-scale jets or fingers that form in the advancing particle front.

42 ENGINEERING↗
DOE OSTI2024

Role of Dynamic Polarization Interactions in the Electrical Double Layer at Calcite (104) Interfaces with Aqueous Solutions

Reactions at mineral interfaces with aqueous solutions control many geochemical and biogeochemical processes in the Earth’s critical zone. At the molecular level, insights into important properties such as the structure of the electrical double layer (EDL) at specific mineral interfaces continue to improve due to the increasing fidelity of laboratory instrumentation and computational approaches. However, molecular simulation approaches suffer from limited reach into relevant scales of time, length, and system complexity. To span this gap, a novel hybrid approach that couples first principle plane-wave density functional theory (DFT) with classical DFT (cDFT) is demonstrated and applied to calcite (104) interfaces with various electrolytes. In this approach, a region of interest described using DFT interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. Benchmarking against experimental observations and entirely first principle DFT simulations demonstrates that this hybrid model efficiently encompasses the key short-range and collective interactions in the EDL. Simulations of calcite (104)/solution interfaces reveal the key static and dynamic polarization interactions that give rise to structuring of ions and water. Ion hydration interactions have the strongest effect on the depth of the first minimum in the density distribution of counterions at the surface, and the position and width of the first density peak is largely determined by the strength of ion-correlation forces. Finer details of ion distributions are controlled by mutual polarization of the calcite surface and interfacial electrolyte. Finally, this new ability to efficiently and rigorously predict EDL structure at mineral surfaces in contact with complex solutions paves the way to accurately modeling sorption, nucleation, dissolution, and growth in realistic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Confocal Raman Microscopy Investigation of Phospholipid Monolayers Deposited on Nitrile-Modified Surfaces in Porous Silica Particles

Phospholipid bilayers deposited on a variety of surfaces offer models for investigation of the lipid membrane structure and supports for biocompatible sensors. Hybrid-supported phospholipid bilayers (HSLBs) are stable membrane models for these investigations, typically prepared by self-assembly of a lipid monolayer over an n-alkane-modified surface. HSLBs have been prepared on n-alkyl chain-modified silica and used for lipophilicity-based chromatographic separations. The structure of these hybrid bilayers differs from vesicle membranes where the lipid head group spacing is greater due to interdigitation of the lipid acyl chains with the underlying n-alkyl chains bound to the silica surface. This interdigitated structure exhibits a broader melting transition at a higher temperature due to strong interactions between the lipid acyl chains and the immobile n-alkyl chains bound to silica. In the present work, we seek to reduce the interactions between a lipid monolayer and its supporting substrate by self-assembly of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) on porous silica functionalized with nitrile-terminated surface ligands. The frequency of Raman scattering of the surface -C≡N stretching mode at the lipid–nitrile interface is consistent with an n-alkane-like environment and insensitive to lipid head group charge, indicating that the lipid acyl chains are in contact with the surface nitrile groups. The head group area of this lipid monolayer was determined from the within-particle phospholipid concentration and silica specific surface area and found to be 54 ± 2 Å 2 , equivalent to the head group area of a DMPC vesicle bilayer. The structure of these nitrile-supported phospholipid monolayers was characterized below and above their melting transition by confocal Raman microscopy and found to be nearly identical to DMPC vesicle bilayers. Their narrow gel-to-fluid-phase melting transition is equivalent to dispersed DMPC vesicles, indicating that the acyl chain structure on the nitrile support mimics the outer leaflet structure of a vesicle membrane.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2

The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single–amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single– and multiple–amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Initial demonstration of automated fuel performance modeling with 1977 EBR-II metallic fuel pins using BISON code with FIPD and IMIS databases

Using the BISON fuel performance code, simulations were conducted using an automated process to read initial and operating conditions from the Fuels Irradiation and Physics Database (FIPD) and Integral Fast Reactor materials information system (IMIS) database, which contains metallic fuel data from the Experimental Breeder Reactor-II (EBR-II). This work demonstrates use of an integrated framework to access the vast majority of EBR-II experimental fuel pin data to support rapid development of fuel performance models for next-generation metallic fuel systems. With this capability, validation for fuel qualification can be performed rapidly. Between IMIS and FIPD, there is enough information to conduct 1977 unique EBR-II metallic fuel pin histories from 24 different experiments, at varying levels of detail between the two databases. Each of these histories includes a high-resolution power history, flux history, coolant channel flow rates, and coolant channel temperatures. Fission gas release (FGR), cumulative damage fraction (CDF), fuel axial swelling, cladding profilometry, and burnup were all simulated in BISON. The results were compared to post-irradiation examination (PIE) results for the initial demonstration of automated BISON modeling. BISON simulations conducted with IMIS and FIPD were in rough agreement with PIE measurements and calculations. Cladding profilometry, FGR, and fuel axial swelling were found to be in rough agreement with PIE measurements, depending on the physics used within the BISON input files. Here, the mechanical contact solver chosen was found to significantly impact axial fuel swelling and cladding strain predictions. CDF values were assessed to see whether pin failure may have been predicted (CDF ≥ 1). This work suggests that continued development of an automated tool for BISON should focus on inclusion of the Fast Flux Test Facility (FFTF) experimental data for a larger database for metallic fuel, improved physical models to better capture fuel performance, such as fuel-cladding interactions, and a more detailed comparison with available PIE data to further the BISON model development.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme–iron from human hemoglobin

Streptococcus pyogenes (group A Streptococcus ) is a clinically important microbial pathogen that requires iron in order to proliferate. During infections, S. pyogenes uses the surface displayed Shr receptor to capture human hemoglobin (Hb) and acquires its iron-laden heme molecules. Through a poorly understood mechanism, Shr engages Hb via two structurally unique N-terminal Hb-interacting domains (HID1 and HID2) which facilitate heme transfer to proximal NEAr Transporter (NEAT) domains. Based on the results of X-ray crystallography, small angle X-ray scattering, NMR spectroscopy, native mass spectrometry, and heme transfer experiments, we propose that Shr utilizes a “cap and release” mechanism to gather heme from Hb. In the mechanism, Shr uses the HID1 and HID2 modules to preferentially recognize only heme-loaded forms of Hb by contacting the edges of its protoporphyrin rings. Heme transfer is enabled by significant receptor dynamics within the Shr–Hb complex which function to transiently uncap HID1 from the heme bound to Hb’s β subunit, enabling the gated release of its relatively weakly bound heme molecule and subsequent capture by Shr’s NEAT domains. These dynamics may maximize the efficiency of heme scavenging by S. pyogenes , enabling it to preferentially recognize and remove heme from only heme-loaded forms of Hb that contain iron.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Neutrinoless double-β decay: Combining quantum Monte Carlo and the nuclear shell model with the generalized contact formalism

Neutrinoless double beta decay searches can determine the Majorana nature of neutrinos, the absolute neutrino mass, and provide invaluable insights on the matter dominance of the universe. However, the uncertainty in the nuclear matrix elements that govern the decay limits the physics reach of these experiments. Here, we devise a novel framework based on the generalized contact formalism that combines the nuclear shell model and quantum Monte Carlo methods and compute the neutrinoless double-beta decay of nuclei used in the most advanced experiments, including 76 Ge, 130 Te, and 136 Xe. Our results cover all relevant terms, including the leading-order short-range operator recognized recently. We validate our method in light nuclei by comparing against accurate variational Monte Carlo results. On heavy systems we obtain reduced nuclear matrix elements compared with previous calculations due to additional correlations captured by quantum Monte Carlo and introduced within the generalized contact formalism, suggesting longer decay half-lives than previously considered. On the other hand, we find an enhancement of the nuclear matrix elements due to the new short-range operator.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗