Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “NaTl”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2

Au 3 -to-Ag 3 coordinate-covalent bonding and other supramolecular interactions with covalent bonding strength

An efficient strategy for designing charge-transfer complexes using coinage metal cyclic trinuclear complexes (CTCs) is described herein. Due to opposite quadrupolar electrostatic contributions from metal ions and ligand substituents, [Au(m-Pz-(i-C 3 H7) 2 )] 3 ∙[Ag(m-Tz-(n-C 3 F 7 ) 2 )] 3 (Pz = pyrazolate, Tz = triazolate) has been obtained and its structure verified by single crystal X-ray diffraction – representing the 1st crystallographically-verified M 3 @M' 3 stacked adduct of monovalent coinage metal CTCs. Abundant supramolecular interactions with aggregate covalent bonding strength arise from a combination of M–M' (Au / Ag), metal–π, π–π interactions and hydrogen bonding in this charge-transfer complex, according to density functional theory analyses, yielding a computed binding energy of 66 kcal mol -1 between the two trimer moieties – a large value for intermolecular interactions between adjacent d 10 centres (nearly doubling the value for a recently claimed Au(I) / Cu(I) polar-covalent bond: Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E5042) – which becomes 87 kcal mol -1 with benzene stacking. Surprisingly, DFT analysis suggests that: (a) some other literature precedents should have attained a stacked M 3 @M' 3 product akin to the one herein, with similar or even higher binding energy; and (b) a high overall intertrimer bonding energy by inferior electrostatic assistance, underscoring genuine orbital overlap between M and M' frontier molecular orbitals in such polar-covalent M–M' bonds in this family of molecules. The Au / Ag bonding is reminiscent of classical Werner-type coordinate-covalent bonds such as H 3 N: → Ag in [Ag(NH 3 ) 2 ] + , as demonstrated herein quantitatively. Solidstate and molecular modeling illustrate electron flow from the p-basic gold trimer to the p-acidic silver trimer with augmented contributions from ligand-to-ligand’ (LL'CT) and metal-to-ligand (MLCT) charge transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Binding of noble gas atoms by superhalogens

Because of their closed shells, noble gas (Ng) atoms (Ng = Ne, Ar, Kr, and Xe) seldom take part in chemical reactions, yet finding such mechanisms not only is of scientific interest but also has practical significance. Following a recent work by Mayer et al. [Proc. Natl. Acad. Sci. U. S. A. 116, 8167–8172 (2019)] on the room temperature binding of Ar to a superelectrophilic boron site embedded in a negative ion complex, B 12 (CN) 11 - , we have systematically studied the effect of cluster size and terminal ligands on the interaction of Ng by focusing on B 12 X 11 (Ng) (X = H, CN, and BO) and B 12 X 10 (Ng) 2 (X = CN and BO) whose stabilities are governed by the Wade–Mingos rule and on C 5 BX 5 (Ng) (X = H, F, and CN) and C 4 B 2 (CN) 4 (Ng) 2 whose stabilities are governed by the Huckel’s aromaticity rule. Our conclusion, based on density functional theory, is that both the cluster size and the terminal ligands matter—the interaction between the cluster and the Ng atoms becomes stronger with increasing cluster size and the electron affinity of the terminal ligands. Our studies also led to a counter-intuitive finding—removing multiple terminal ligands can enable electrophilic centers to bind multiple Ng atoms simultaneously without compromising their binding strength.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol.13, 1280–1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149–21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations—one short (~66 Å height) and the other long (~100 Å height)—reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

59 BASIC BIOLOGICAL SCIENCES↗

Stochastic and a posteriori optimization to mitigate coil manufacturing errors in stellarator design

Abstract It was recently shown in Wechsung et al (2022 Proc. Natl Acad. Sci. USA 119 e2202084119) that there exist electromagnetic coils that generate magnetic fields, which are excellent approximations to quasi-symmetric fields and have very good particle confinement properties. Using a Gaussian process-based model for coil perturbations, we investigate the impact of manufacturing errors on the performance of these coils. We show that even fairly small errors result in noticeable performance degradation. While stochastic optimization yields minor improvements, it is not possible to mitigate these errors significantly. As an alternative to stochastic optimization, we then formulate a new optimization problem for computing optimal adjustments of the coil positions and currents without changing the shapes of the coil. These a-posteriori adjustments are able to reduce the impact of coil errors by an order of magnitude, providing a new perspective for dealing with manufacturing tolerances in stellarator design.

Physics↗

Twisted bilayer graphene. I. Matrix elements, approximations, perturbation theory, and a k · p two-band model

We investigate the twisted bilayer graphene (TBG) model of Bistritzer and MacDonald (BM) [Bistritzer and MacDonald, Proc. Natl. Acad. Sci. 108, 12233 (2011)] to obtain an analytic understanding of its energetics and wave functions needed for many-body calculations. We provide an approximation scheme for the wave functions of the BM model, which first elucidates why the BM K M -point centered original calculation containing only four plane waves provides a good analytical value for the first magic angle (θ M ≈ 1°). The approximation scheme also elucidates why most of the many-body matrix elements in the Coulomb Hamiltonian projected to the active bands can be neglected. By applying our approximation scheme at the first magic angle to a Γ M -point centered model of six plane waves, we analytically understand the reason for the small Γ M -point gap between the active and passive bands in the isotropic limit w 0 = w 1 . Furthermore, we analytically calculate the group velocities of the passive bands in the isotropic limit, and show that they are almost doubly degenerate, even away from the Γ M point, where no symmetry forces them to be. Furthermore, moving away from the Γ M and K M points, we provide an explicit analytical perturbative understanding as to why the TBG bands are flat at the first magic angle, despite the first magic angle is defined by only requiring a vanishing K M -point Dirac velocity. We derive analytically a connected “magic manifold” w 1 = $2\sqrt{1 + w^{2}_{0}}$ $-\sqrt{2 + 3w^2_0}$, on which the bands remain extremely flat as w 0 is tuned between the isotropic (w 0 = w 1 ) and chiral (w 0 = 0) limits. We analytically show why going away from the isotropic limit by making w 0 less (but not larger) than w 1 increases the Γ M -point gap between the active and the passive bands. Finally, by perturbation theory, we provide an analytic Γ M point k ∙ p two-band model that reproduces the TBG band structure and eigenstates within a certain w 0 , w 1 parameter range. Further refinement of this model are discussed, which suggest a possible faithful representation of the TBG bands by a two-band Γ M point k ∙ p model in the full w 0 , w 1 parameter range.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Direct driving of electronic and phononic degrees of freedom in a honeycomb bilayer with infrared light

Here, we study theoretically AB-stacked honeycomb bilayers driven by light in resonance with an infrared phonon within a tight-binding description. We characterize the phonon properties of honeycomb bilayers with group theory and construct an electronic time-dependent tight-binding model for the system following photoexcitation in resonance with an infrared phonon. We adopt an atomically adiabatic approximation [V. Mohanty and E. J. Heller, Proc. Natl. Acad. Sci. 116, 18316 (2019)] to describe classically vibrating nuclei, but obtain the Floquet quasienergy spectrum associated with the time-dependent model exactly. We introduce a general scheme to disentangle the complex low-frequency Floquet spectrum to elucidate the relevant Floquet bands. As a prototypical example, we consider bilayer graphene. We find that light in the low-frequency regime can induce a band gap in the quasienergy spectrum in the vicinity of the $K$ points even if it is linearly polarized, in contrast with the expectations within the Born-Oppenheimer approximation and the high-frequency regime. Finally, we analyze the diabaticity of the driven electron and driven phonon processes and find contrasting effects on the autocorrelation functions at the same driving frequency: Driven phonons preserve the character of the initial state while driven electrons exhibit strong deviations within a few drive cycles. The procedure outlined here can be applied to other materials to describe the combined effects of low-frequency light on phonons and electrons.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Niobium substitution suppresses the superconducting critical temperature of pressurized MoB 2

A recent study has demonstrated that MoB 2 , transforming to the same structure as MgB 2 (P 6 /mmm), superconducts at temperatures above 30 K near 100 GPa [C. Pei et al., Natl. Sci. Rev. 10, nwad034 (2023)], and Nb substitution in MoB 2 stabilizes the P6/mmm structure down to ambient pressure [A. C. Hire et al., Phys. Rev. B 106, 174515 (2022)]. Here, the current work explores the high-pressure superconducting behavior of Nb-substituted MoB 2 (Nb 0.25 Mo 0.75 B 2 ). High-pressure x-ray diffraction measurements show that the sample remains in the ambient pressure P6/mmm structure to at least 160 GPa. Electrical resistivity measurements demonstrate that from an ambient pressure T c of 8K (confirmed by specific heat to be a bulk effect), the critical temperature is suppressed to 4 K at 50 GPa, before gradually rising to 5.5 K at 170 GPa. The critical temperature at high pressure is thus significantly lower than that found in MoB 2 under pressure (30 K), revealing that Nb substitution results in a strong suppression of the superconducting critical temperature. Our calculations indeed find a reduced electron-phonon coupling in Nb 0.25 Mo 0.75 B 2 , but do not account fully for the observed suppression, which may also arise from inhomogeneity and enhanced spin fluctuations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Gradient sensing via cell communication

Experimental evidence lends support to the conjecture that cell-to-cell communication plays a role in the gradient sensing of chemical species by certain chains of cells. Models have been formulated to explore this idea. For cells with no identifiable sensing structure, Mugler et al. [Proc. Natl. Acad. Sci. (U.S.A.) 113, E689 (2016)] have defined a particular local excitation, global inhibition (LEGI) model that pits nearest-neighbor communication against local reactions in a noisy environment to suggest how this sensing capability might arise in a physical system. In this study, we generalize the nearest-neighbor communication mechanism in the aforementioned LEGI model in order to explore the extent to which the gradient sensing characteristics depend on the parametrization of the communication itself, as well as on the cell size, the radius of influence of neighboring cells, and the influence of the background noise. Using our generalization and a collection of particular candidate communication models, we find that the precision of gradient sensing is indeed sensitive to the particular communication model, and we derive physical and analytic explanations for these results. The framework established and the associated results should prove useful in understanding the appropriateness of particular cell-to-cell communication models in gradient sensing studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics of genetic code evolution: The emergence of universality

We study the dynamics of genetic code evolution. The model of Vetsigian et al. [Proc. Natl. Acad. Sci. USA 103, 10696 (2006)] and Vetsigian [Collective evolution of biological and physical systems, Ph.D. thesis, 2005] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on convergence and optimality score. We show that by allowing specific parameters to vary with time, the solution exhibits attractor dynamics. Finally, we study automorphisms of the genetic code arising due to this model. We use this to examine the scaling of the solutions to re-examine universality and find that there is a direct link to mutation rate.

59 BASIC BIOLOGICAL SCIENCES↗

Destructive Error Interference in Product-Formula Lattice Simulation

Quantum computers can efficiently simulate the dynamics of quantum systems. Here, we study the cost of digitally simulating the dynamics of several physically relevant systems using the first-order product-formula algorithm. We show that the errors from different Trotterization steps in the algorithm can interfere destructively, yielding a much smaller error than previously estimated. In particular, we prove that the total error in simulating a nearest-neighbor interacting system of n sites for time t using the first-order product formula with r time slices is O ( n t / r + n t 3 / r 2 ) when n t 2 / r is less than a small constant. Given an error tolerance ϵ , the error bound yields an estimate of max { O ( n 2 t / ϵ ) , O ( n 2 t 3 / 2 / ϵ 1 / 2 ) } for the total gate count of the simulation. The estimate is tighter than previous bounds and matches the empirical performance observed in Childs et al. [ Proc. Natl. Acad. Sci. U.S.A. 115 , 9456 (2018) ]. We also provide numerical evidence for potential improvements and conjecture an even tighter estimate for the gate count.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Efficient machine learning interatomic potentials robust for liquid and multiple solid polymorphs of NaF and KF

Achieving atomic-level understanding of crystallization of molten salts is of importance to a wide range of technological applications. Recent work [Fan et al., Proc. Natl. Acad. Sci. USA 122, e2425702122 (2025)] revealed that crystal nucleation in molten LiF salt is a multistage process according to the molecular-dynamics (MD) simulations based on an atomic cluster expansion (ACE) machine-learning interatomic potential (MLIP). In order to understand the influence of increasing cation size on nucleation pathways and nucleation rates of molten fluoride salts, here we develop two new ACE MLIPs for NaF and KF. The two ACE MLIPs feature DFT-SCAN-level accuracy for liquid and multiple solid polymorphs over a wide temperature (0–2000 K) and pressure (0–100 GPa) range, and also reproduce well a number of experimental data for solid and liquid equilibrium properties. The efficiency of the two ACE MLIPs enable million-atom-scale or microsecond-scale MD simulations. The two general-purpose ACE MLIPs are expected to be useful for atomistic simulations for different purposes, in addition to studying crystallization of molten NaF and KF salts.

Crystal melting↗

Tutorial on Chemical Pressure Analysis: How Atomic Packing Drives Laves/Zintl Intergrowth in K3Au5Tl

The tight atomic packing generally exhibited by alloys and intermetallics can create the impression of their being composed of hard spheres arranged to maximize their density. As such, the atomic size factor has historically been central to explanations of the structural chemistry of these systems. However, the role atomic size plays structurally has traditionally been inferred from empirical considerations. The recently developed DFT-Chemical Pressure (CP) analysis has opened a path to investigating these effects with theory. In this article, we provide a step-by-step tutorial on the DFT-CP method for non-specialists, along with advances in the approach that broaden its applicability. A new version of the CP software package is introduced, which features an interactive system that guides the user in preparing the necessary electronic structure data and generating the CP scheme, with the results being readily visualized with a web browser (and easily incorporated into websites). For demonstration purposes, we investigate the origins of the crystal structure of K3Au5Tl, which represents an intergrowth of Laves and Zintl phase domains. Here, CP analysis reveals that the intergrowth is supported by complementary CP features of NaTl-type KTl and MgCu2-type KAu2 phases. In this way, K3Au5Tl exemplifies how CP effects can drive the merging for geometrical motifs derived from different families of intermetallics through a mechanism referred to as epitaxial stabilization.

36 MATERIALS SCIENCE↗

Effects of Silver and Other Metals on the Cytoskeleton

Directly or indirectly, trace concentrations of silver ion (Ag(+)) stabilize microtubules (Conrad, A.H., et al. Cell Motil. & Cytoskel. 27:117-132), as does taxol (Conrad, A.H., et al. J. Exp. Zool. 262:154-165), an effect with major consequences for cellular shape changes and development. Polymerization of microtubules is gravity-sensitive (Tabony and Job, Proc. Natl. Acad. Sci. USA 89:6948-6952), so trace amounts of Ag(+) may alter cellular ability to respond to gravity. If Ag electrolysis is used to purify water on NASA space vehicles, plants and animals/astronauts will be exposed continuously to Ag(+), a regimen with unknown cellular and developmental consequences. Fertilized eggs of the marine mudsnail, Ilyanassa obsoleta, are the cells in which the effects of A(+) on microtubules were discovered. They distribute visible cytoplasmic contents according to gravity and contain cytoplasmic morphogenetic determinants for heart development. The objectives are to determine if the effects of Ag(+), AU(3+), (of biosensor relevance), or Gd(3+) (inhibitor of some stretch-activated ion channels) on the cytoskeleton (in the presence and absence of mechanical loading) will affect cellular responses to gravity.

Conrad, Gary W.↗

Balanced Branching in Transcription Termination

The theory of stochastic transcription termination based on free-energy competition [von Hippel, P. H. & Yager, T. D. (1992) Science 255,809-812 and van Hippel, P. H. & Yager, T. D. (1991) Proc. Natl. Acad. Sci. USA 88, 2307-2311] requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this balancing should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle, but do find many troubling Inconsistencies, most notably, anomalous memory effects. These effects suggest that termination has a deterministic component and may conceivably not be stochastic at all. We find that a key experiment by Wilson and von Hippel [Wilson, K. S. & von Hippel, P. H. (1994) J. Mol. Biol. 244,36-51] thought to demonstrate stochastic termination was an incorrectly analyzed regulatory effect of Mg(2+) binding.

Harrington, K. J.↗

XMM-Newton X-ray Observatory Guest Observer program (AO-1) at CASA

In this research program, we obtained and analyzed X-ray observations of the Wolf-Rayet (WR) star WR 110 (HD 165688) using the XMM-Newton space-based observatory. Radio observations were also obtained using the Very Large Array (VLA) radio telescope located in New Mexico and operated by the Natl. Radio Astronomy Observatory (NRAO). This star was targeted for observations primarily because it is believed to be a single WR star without a companion. Single WR stars are thought to emit X-rays from cool plasma in shocks distributed throughout their powerful stellar winds. However, there has been little observational work done to test this idea since single WR stars are relatively weak X-ray sources and have been difficult to detect with previous generation telescopes. The launch of XMM-Newton provides a new telescope that is much more sensitive than its predecessors, allowing single WR stars to be studied in detail for the first time. X-ray emission was clearly detected from WR 110. Analysis of its spectrum yields a surprising result. Its X-ray emitting plasma is distributed over a range of temperatures and is dominated by relatively cool plasma with a characteristic temperature T is approximately 6 million K. Such plasma can be explained by existing theoretical wind shock models. However, the spectrum also shows hotter plasma whose temperature is uncertain but is thought to be in excess of T approximately 30 million K. The origin of this hotter plasma is yet unknown, but possible mechanisms are identified

Skinner, Stephen L.↗

Low-shear modeled microgravity: a global environmental regulatory signal affecting bacterial gene expression, physiology, and pathogenesis

Bacteria inhabit an impressive variety of ecological niches and must adapt constantly to changing environmental conditions. While numerous environmental signals have been examined for their effect on bacteria, the effects of mechanical forces such as shear stress and gravity have only been investigated to a limited extent. However, several important studies have demonstrated a key role for the environmental signals of low shear and/or microgravity in the regulation of bacterial gene expression, physiology, and pathogenesis [Chem. Rec. 1 (2001) 333; Appl. Microbiol. Biotechnol. 54 (2000) 33; Appl. Environ. Microbiol. 63 (1997) 4090; J. Ind. Microbiol. 18 (1997) 22; Curr. Microbiol. 34(4) (1997) 199; Appl. Microbiol. Biotechnol. 56(3-4) (2001) 384; Infect Immun. 68(6) (2000) 3147; Cell 109(7) (2002) 913; Appl. Environ. Microbiol. 68(11) (2002) 5408; Proc. Natl. Acad. Sci. U. S. A. 99(21) (2002) 13807]. The response of bacteria to these environmental signals, which are similar to those encountered during prokaryotic life cycles, may provide insight into bacterial adaptations to physiologically relevant conditions. This review focuses on the current and potential future research trends aimed at understanding the effect of the mechanical forces of low shear and microgravity analogues on different bacterial parameters. In addition, this review also discusses the use of microgravity technology to generate physiologically relevant human tissue models for research in bacterial pathogenesis.

NASA Discipline Cell Biology↗

Kinetic studies on the control of the bean rust fungus (Uromyces phaseoli L.) by an inhibitor of polyamine biosynthesis

alpha-Difluoromethylornithine (DFMO), a specific and irreversible inhibitor of the polyamine biosynthetic enzyme ornithine decarboxylase, effectively inhibits mycelial growth of several phytopathogenic fungi on defined media in vitro and provides systemic protection of bean plants against infection by Uromyces phaseoli L. race 0 (MV Rajam, AW Galston 1985 Plant Cell Physiol 26: 683-692; MV Rajam et al. 1985 Proc Natl Acad Sci USA 82: 6874-6878). We now find that application of 0.5 millimolar DFMO to unifoliolate leaves of Pinto beans up to 3 days after inoculation with uredospores of U. phaseoli completely inhibits the growth of the pathogen, while application 4 or 5 days after inoculation results in partial protection against the pathogen. Spores do not germinate on the surface of unifoliolate leaves treated with DFMO 1 day before infection, but addition of spermidine to the DFMO treatments partially reverses the inhibitory effect. The titer of polyamines in bean plants did not decline after DFMO treatment; rather, putrescine and spermidine contents actually rose, probably due to the known but paradoxical stimulation of arginine decarboxylase activity by DFMO.

Non-NASA Center↗

Characterization of auxin-binding proteins from zucchini plasma membrane

We have previously identified two auxin-binding polypeptides in plasma membrane (PM) preparations from zucchini (Cucurbita pepo L.) (Hicks et al. 1989, Proc. Natl. Acad. Sci. USA 86, 4948-4952). These polypeptides have molecular weights of 40 kDa and 42 kDa and label specifically with the photoaffinity auxin analog 5-N3-7-3H-IAA (azido-IAA). Azido-IAA permits both the covalent and radioactive tagging of auxin-binding proteins and has allowed us to characterize further the 40-kDa and 42-kDa polypeptides, including the nature of their attachment to the PM, their relationship to each other, and their potential function. The azido-IAA-labeled polypeptides remain in the pelleted membrane fraction following high-salt and detergent washes, which indicates a tight and possibly integral association with the PM. Two-dimensional electrophoresis of partially purified azido-IAA-labeled protein demonstrates that, in addition to the major isoforms of the 40-kDa and 42-kDa polypeptides, which possess isoelectric points (pIs) of 8.2 and 7.2, respectively, several less abundant isoforms that display unique pIs are apparent at both molecular masses. Tryptic and chymotryptic digestion of the auxin-binding proteins indicates that the 40-kDa and 42-kDa polypeptides are closely related or are modifications of the same polypeptide. Phase extraction with the nonionic detergent Triton X-114 results in partitioning of the azido-IAA-labeled polypeptides into the aqueous (hydrophilic) phase. This apparently paradoxical behavior is also exhibited by certain integral membrane proteins that aggregate to form channels. The results of gel filtration indicate that the auxin-binding proteins do indeed aggregate strongly and that the polypeptides associate to form a dimer or multimeric complex in vivo. These characteristics are consistent with the hypothesis that the 40-kDa and 42-kDa polypeptides are subunits of a multimeric integral membrane protein which has an auxin-binding site, and which may possess transporter or channel function.

NASA Program Space Biology↗