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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 289 records · Page 16

Spectrum of end of the world branes in holographic BCFTs

We study overlaps between two regularized boundary states in conformal field theories. Regularized boundary states are dual to end of the world branes in an AdS black hole via the AdS/BCFT. Thus they can be regarded as microstates of a single sided black hole. Owing to the open-closed duality, such an overlap between two different regularized boundary states is exponentially suppressed as $\langle$ψ a |ψ b $\rangle$~e -O (h$^{(min)}_{ab}$) , where h$^{(min)}_{ab}$ is the lowest energy of open strings which connect two different boundaries a and b. Our gravity dual analysis leads to h$^{(min)}_{ab}$ = c/24 for a pure AdS 3 gravity. This shows that a holographic boundary state is a random vector among all left-right symmetric states, whose number is given by a square root of the number of all black hole microstates. We also perform a similar computation in higher dimensions, and find that h$^{(min)}_{ab}$ depends on the tensions of the branes. In our analysis of holographic boundary states, the off diagonal elements of the inner products can be computed directly from on-shell gravity actions, as opposed to earlier calculations of inner products of microstates in two dimensional gravity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Comparative Analysis of Capacitive Sensors with Different Geometrical layouts for Cable Insulation Degradation Detection

This paper presents a comparative analysis between an Interdigital Capacitor (IDC) sensor and a Serpentine Capacitive (SRC) sensor. The effects of electrode layouts on sensor performance are studied by means of finite element simulation where the geometrical dimensions (except electrode length) and material characteristics of both sensors are identical. Conformal IDC and SRC sensors with equal sensor area are modeled on a cable surface. The simulation results show a tradeoff between IDC and SRC sensors in terms of sensitivity and penetration depth. The SRC sensor shows 13.3% increase in sensitivity and 16.8% increase in capacitance compared to the IDC sensor, though the electric field penetration depth of the SRC sensor is 18.8% lower than the IDC sensor. In addition, the effects of change in electrode width, inter-electrode gap, and number of electrodes on SRC and IDC sensor comparative performance are evaluated.

Interdigital Capacitance, Serpentive Capacitive Se↗

NMR Studies of Block Copolymer-Based Supramolecules in Solution

Hierarchical assemblies from block copolymer (BCP)-based supramolecules have shown immense potential as programmable materials owing to their versatility for incorporating functional molecules and provide access to arrays of hierarchical structures. However, there remains a knowledge gap on the formation of the supramolecule in solution. Here, we applied NMR techniques to investigate the solution-phase behavior of the most studied supramolecular systems, polystyrene-block-poly(4-vinylpyridine)(3-pentadecylphenol) (PS-b-P4VP(PDP) r ). The results show that the supramolecule likely adopts a coil-comb conformation, despite the small molecule's (PDP) rapid exchange between the bonded and free states. The exchange rate (>10 4 s -1 ) exceeds the NMR time scale at the frequency of interest. The supramolecules form under dilute conditions (~2 vol %) and are attributed to the enthalpic gain of the hydrogen bonding between the PDP and 4VP. As the solute concentration increases (>10 vol %), the supramolecule forms micelle-like aggregates with PDP accumulated within the comb-block's pervaded volume based on analysis of the apparent molecular weight, viscosity, and chain dynamics. Overall, this work sheds light on the long-standing question regarding the evolution of the constituents in the BCP-based supramolecule in solution and provides valuable guidance toward their solution-based processing and morphological control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dissecting neurofilament tail sequence-phosphorylation-structure relationships with multicomponent reconstituted protein brushes

Neurofilaments (NFs) are multisubunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton. Each NF subunit contains a long intrinsically disordered tail domain, which protrudes from the NF core to form a “brush” surrounding each NF. Precisely how the tails’ variable charge patterns and repetitive phosphorylation sites mediate their conformation within the brush remains an open question in axonal biology. We address this problem by grafting recombinant NF tail protein constructs NF-Light, -Medium, and -Heavy (NFL, NFM, and NFH) to surfaces, yielding protein brushes of defined stoichiometry that can be phosphorylated in vitro. Atomic force microscopy measurements reveal that brush height depends on composition monotonically but not always linearly for binary NFL:NFM or NFL:NFH systems, and that NFM-based brushes are highly extended, while brushes incorporating the much larger NFH are surprisingly compact even after multisite phosphorylation. Complementary self-consistent field theory (SCFT) predicts multilayer brush morphologies for NFM and phosphorylated NFH brushes. Further experiments and SCFT analysis with designed mutants reveal that N-terminal negative charges in the NFH tail repel phosphorylated residues to generate the multilayer morphology, while the C-terminal charge-neutral region contributes to multilayer brush morphology but not total brush height. Charge-shuffled NFM variants show that charge segregation promotes brush collapse near physiological ionic strengths. Collectively, this study supports a role for NFM in establishing a dynamic range for NF brush conformation, lending insight into previous in vitro and in vivo findings. More broadly, this work establishes a platform for dissecting contributions of disordered protein sequence to conformation at interfaces.

Science & Technology - Other Topics↗

The Acetylene Bridge in Intramolecular Singlet Fission: A Boon or A Nuisance?

Various analogues of the alkylsilylacetylene group are frequently used as auxiliary groups to enhance the solubility and stability of the acene dimer core, widely used as platforms to investigate intramolecular singlet fission (iSF) mechanisms. However, while in the 2,2’-linked dimers they are primarily auxiliary groups, these are essential fragments of the bridging units in 6,6’/5,5’-linked dimers, the two preferred choices for dimerization. The starkly different iSF dynamics observed in the two variants raise the question of what role the acetylene bridges play. Here, we systematically designed a set of (oligo-)para-phenylene bridged 2,2’-linked pentacene dimers with an additional acetylene fragment in the bridging unit to mimic the structure of 6,6’-linked dimers. Contrasting the results with previously reported analogous 2,2’-linked and 6,6’-linked pentacene dimers reveals that the acetylene bridges contribute to significant conformational freedom. This effect provides a mechanism to promote spin evolution within the triplet pair to achieve free triplets but also offers new parasitic pathways for triplet-pair recombination, revealing that this structural motif can be both a boon and a nuisance. Additionally, our analysis reveals that these bridges directly modify the electronic states, highlighting significant pitfalls of the standard chromophore-bridge-chromophore framework used to design and interpret photophysics of iSF materials.

14 SOLAR ENERGY↗

INTERFACES. A Program for Determining the 3D Structures of Surfaces Sites Using NMR Data

Dynamic nuclear polarization surface enhanced NMR spectroscopy has enabled the determination of high-resolution structures from surface-supported molecules, including singlesite heterogeneous catalysts. Structure determinations have largely mimicked the approaches used in biomolecular NMR spectroscopy, namely, using distance measurements to constrain a conformational search. These early demonstrations made use of purpose-built software, which has limited the adoption of the technique. Herein, we describe the open-source program INTERFACES (Interpret NMR to Elucidate or Reconstruct the Full Atomistic Configurations of External Surfaces) which automates the analysis of RE(SP)DOR data as well as the structure determination for surface sites. Distances, angles, dihedral angles, complex orientation, and distance from the support can all be sampled to find all structures that agree with the experimental data. A χ 2 metric is used to define the error ranges of the REDOR fits and produce structures with an arbitrary level of confidence. Structural solutions are then provided as both overlays and ORTEP-like probability ellipsoids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structure and mechanism of Staphylococcus aureus oleate hydratase (OhyA)

Flavin adenine dinucleotide (FAD)-dependent bacterial oleate hydratases (OhyAs) catalyze the addition of water to isolated fatty acid carbon–carbon double bonds. Staphylococcus aureus uses OhyA to counteract the host innate immune response by inactivating antimicrobial unsaturated fatty acids. Mechanistic information explaining how OhyAs catalyze regiospecific and stereospecific hydration is required to understand their biological functions and the potential for engineering new products. In this study, we deduced the catalytic mechanism of OhyA from multiple structures of S. aureus OhyA in binary and ternary complexes with combinations of ligands along with biochemical analyses of relevant mutants. The substrate-free state shows Arg81 is the gatekeeper that controls fatty acid entrance to the active site. FAD binding engages the catalytic loop to simultaneously rotate Glu82 into its active conformation and Arg81 out of the hydrophobic substrate tunnel, allowing the fatty acid to rotate into the active site. FAD binding also dehydrates the active site, leaving a single water molecule connected to Glu82. This active site water is a hydronium ion based on the analysis of its hydrogen bond network in the OhyA•PEG400•FAD complex. We conclude that OhyA accelerates acid-catalyzed alkene hydration by positioning the fatty acid double bond to attack the active site hydronium ion, followed by the addition of water to the transient carbocation intermediate. Structural transitions within S. aureus OhyA channel oleate to the active site, curl oleate around the substrate water, and stabilize the hydroxylated product to inactivate antimicrobial fatty acids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6

Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. As a critical inflammation mediator, hIL-6 is associated with a diverse range of diseases and monoclonal antibodies in clinical use that either target IL-6Rα or hIL-6 to inhibit signaling. Here, we perform high-throughput structure-based computational screening using ensemble docking for small-molecule antagonists for which the target conformations were taken from 600 ns long molecular dynamics simulations of the apo protein. Prior knowledge of the contact sites from binary complex studies and experimental work was incorporated into the docking studies. The top 20 scoring ligands from the in silico studies after post analysis were subjected to in vitro functional assays. Among these compounds, the ligand with the second-highest calculated binding affinity experimentally showed an ~84% inhibitory effect on IL6-induced STAT3 reporter activity at 10 μM concentration. This finding may pave the way for designing small-molecule inhibitors of hIL-6 of therapeutic significance.

Human Interleukin-6↗

Code and Solution Verification Assessment of the CTF Thermal Hydraulic Subchannel Code

CTF is a thermal-hydraulics subchannel code jointly developed by Oak Ridge National Laboratory and North Carolina State University. Over the past seven years, the Consortium for Advanced Simulation of Light Water Reactors (CASL) has made a significant investment in developing CTF so it can be used to model light water reactors, including nominal operating conditions, departure from nucleate boiling analysis, and transients ranging from loss of flow to reactivity insertion accidents. In addition to implementing new modeling capabilities and developing the user input and output interface, extensive work has been performed to improve the code’s quality assurance program, resulting in a development process that conforms with NQA-1 requirements. The CASL program follows the Predictive Capability Maturity Model (PCMM) approach for assessing code quality, which emphasizes performing code verification(ensuring the code converges to the correct answer) and solution verification (ensuring the code converges for the intended application). Code and solution verification are used to identify uncertainty errors introduced by numerical approximations in the code and are important for demonstrating that the model is coded without error, which is an important aspect of the Best Estimate plus Uncertainty method. This paper presents a comprehensive overview of the code and solution verification testing that has been performed on CTF. A top-down approach is taken in which the intended CTF applications are presented, followed by the code features required for their modeling. These features are then linked to the applicable code and solution verification tests that demonstrate proper functioning. Past testing efforts are summarized, and new tests are added to help close gaps in the presented test matrix. Rather than performing “one-off” exercises, these tests are added to the automated CTF regression test suite to ensure continual code quality.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗

Technical and Economic Evaluation of the First Ever Polymer Flood Field Pilot to Enhance the Recovery of Heavy Oils on Alaska's North Slope via Machine Assisted History Matching

Polymer flooding has become globally established as a potential enhanced oil recovery method for heavy oils. To determine whether this technology may be useful in developing the substantial heavy oil resources on the Alaska North Slope, a polymer flood field pilot commenced at the Milne Point Unit in August 2018. This study seeks to evaluate the results of the field pilot on a technical and economic basis. A reservoir simulation model is constructed and calibrated to predict the oil recovery performance of the pilot through machine-assisted reservoir simulation techniques. To replicate the early water breakthrough observed during waterflooding, transmissibility contrasts are introduced into the simulation model, forcing viscous fingering effects. In the ensuing polymer flood, these transmissibility contrasts are reduced to replicate the restoration of injection conformance during polymer flooding. Transmissibility contrasts are later reinstated to replicate fracture overextension interpreted in one of the producing wells. The calibrated simulation models produced at each stage of the history matching process are used to forecast oil recovery. These forecasts are used as input for economic analysis, incremental to waterflooding expectations. The simulation forecasts indicate that polymer flooding significantly increases the heavy oil production for this field pilot compared to waterflooding alone, yielding attractive project economics. However, meaningful variations between simulation scenarios demonstrate that a simulation model is only valid for prediction if flow behavior in the reservoir remains consistent with that observed during the history matched period. Critically, this means that a simulation model calibrated for waterflooding may not fully capture the technical and economic benefits of an enhanced oil recovery process such as polymer flooding. Subsequently, the simulation model and economic model are used in conjunction to conduct a sensitivity analysis for polymer flood design parameters, from which recommendations are provided for both the continued operation of the current field pilot and future polymer flood designs. The results demonstrate that a higher polymer concentration can be injected due to the development of fractures in the reservoir. The throughput rate should remain high without exceeding operating constraints. A calculated point-forward polymer utilization parameter demonstrates the decreasing efficiency of the polymer flood at later times in the pattern life. Future projects will benefit from starting polymer injection earlier in the pattern life. A pattern with tighter horizontal well spacing will observe a greater incremental benefit from polymer flooding.

Keith, Cody↗

Human-System Interface Design Review Guidelines

The U.S. Nuclear Regulatory Commission (NRC) staff reviews the human factors engineering (HFE) aspects of nuclear power plants in accordance with the Standard Review Plan (NUREG-0800, Standard Review Plan for the Review of Safety Analysis Reports for Nuclear Power Plants: LWR Edition). The Human Factors Engineering Program Review Model (NUREG-0711, Revision 3, issued November 2012) contains detailed design review procedures. As part of the review process, the interfaces between plant personnel and the plant's systems and components are evaluated for conformance with HFE guidelines. This document, Human-System Interface Design Review Guidelines (NUREG-0700, Revision 3), provides the guidelines necessary to perform this evaluation. The review guidelines address the physical and functional characteristics of human-system interfaces (HSIs). Because these guidelines only address the HFE aspects of design and not other related considerations, such as instrumentation and control and structural design, they are referred to as HFE guidelines. In addition to the review of actual HSIs, the NRC staff can use the NUREG-0700 guidelines to evaluate a design-specific HFE guidelines document or style guide. The HFE guidelines are organized into four basic parts, which are divided into sections. Part I contains guidelines for the basic HSI elements: information displays, user-interface interaction and management, and analog displays and controls. These elements are used as building blocks to develop HSI systems to serve specific functions. Part II contains the guidelines for reviewing the following HSI systems: alarm system, safety parameter display system, group-view display system, soft control system, computer-based procedure system, automation system, and communication system. Part III provides guidelines for the review of workstations and workplaces. Part IV provides guidelines for the review of HSI support (i.e., maintainability of digital systems and degraded HSI and instrumentation and control conditions).

42 ENGINEERING↗

Interacting CFTs for all couplings: thermal versus entanglement entropy at large N

In this paper, I calculate the large N limit of marginal O(N) models with non-polynomial potentials in arbitrary odd dimensions d. This results in a new class of interacting pure conformal field theories (CFTs) in d = 3 + 4n for any n ϵ $\mathbb{Z}$ + . Similarly, in d = 3 + 4n I calculate the thermal entropy for all couplings on R 2+4n × S 1 for n = 0, 1, 2, 3. In 2+1 dimensions I find the strong-to-weak coupling ratio of the thermal entropy to be 4/5, matching recent results, and further extend this analysis to higher odd dimensions. Next, I calculated the vacuum entanglement entropy ${s}_{\textrm{EE}}^d$ on S d–2 for all couplings in arbitrary odd d in the large N limit. I find the vacuum entanglement entropy on S d–2 to be not only solvable but also constant for all couplings λ. Thus, in the large N limit, the vacuum entanglement entropy on S d–2 for odd d is constant for all λ, in contrast to the thermal entropy which is shown to also be monotonically decreasing with λ in d = 3 + 4n.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Pro5 is not essential for the formation of ‘Ni-hook’ in nickel superoxide dismutase

The N-terminus of nickel-dependent superoxide dismutase (NiSOD) forms a structural motif known as the "Ni-hook," where the peptide wraps around the metal to bring cysteine-2 and cysteine-6 into spatial proximity, allowing these residues to coordinate in a cis-geometry. A highly conserved proline-5 residue in the Ni-hook adopts a cis-conformation that is widely considered important for its formation. Herein, we investigate this role by point mutation of Pro5 to alanine. The results obtained show that the variant exhibits wild-type-like redox catalysis and features a Ni(III) center very similar to that found in enzyme. Structural analysis using x-ray absorption spectroscopy of the nickel sites in as-isolated P5A-NiSOD reveals changes in the variant and are consistent with a six-coordinate Ni site with (N/O) 4 S 2 coordination. These changes are attributed to changes in the Ni(II) site structure. Nickel-binding studies using isothermal titration calorimetry reveal two binding events with K d = 25(20) nM, and 250(60) nM. These events are attributed to i) Ni(II) binding to a preformed Ni-hook containing cis-Pro5 and ii) the combination of trans- to cis- isomerization upon Ni(II) binding, respectively. Finally, the higher-affinity binding event is absent in P5A-NiSOD, an observation attributed to the low abundance of the cis-Ala5 isomer in the apo-protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗

Structure–Function Insights into Thermoresponsive Copolymers as Lanthanide Precipitants

The synthetic toolbox for stimuli-responsive polymers has broadened to include many tunable variables, making these materials applicable in diverse technologies. However, unraveling the key composition–structure–function relationships to facilitate ground-up design remains a challenge due to the inherent dispersity in sequence and conformations for synthetic polymers. We here present a systematic study of these relationships using a model system of copolymers with a thermoresponsive (N-isopropylacrylamide) backbone in addition to metal-chelating (acrylic acid) and hydrophobic structural comonomers and evaluate their efficiency at isolating technologically critical lanthanide ions. The efficiency of lanthanide ion extraction by precipitation was quantitated with a metallochromic dye to reveal trends relating copolymer hydrophobicity to improved separations. Further, we examined the role of different hydrophobic comonomers in dictating the solution-phase conformation of the polymer in the presence and absence of lanthanide ions, and we correlated key features of the hydrophobic comonomer to extraction efficiency. Lastly, we identified how the local proximity of thermoresponsive, chelating, and hydrophobic subunits facilitates metal extraction by manipulating the copolymer sequence with multiblock polymerization. Through mechanistic analysis, we propose a binding-then-assembly process through which metal ions are coprecipitated with macromolecular chelators.

Copolymers↗