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DOE OSTI2020

Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics

The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is an essential lipid A biosynthetic enzyme that is conserved in the majority of gram-negative bacteria. It has emerged as an attractive novel antibiotic target due to the recent discovery of an LpxH-targeting sulfonyl piperazine compound (referred to as AZ1) by AstraZeneca. However, the molecular details of AZ1 inhibition have remained unresolved, stymieing further development of this class of antibiotics. In this paper we report the crystal structure of Klebsiella pneumoniae LpxH in complex with AZ1. We show that AZ1 fits snugly into the L -shaped acyl chain-binding chamber of LpxH with its indoline ring situating adjacent to the active site, its sulfonyl group adopting a sharp kink, and its N -CF 3 –phenyl substituted piperazine group reaching out to the far side of the LpxH acyl chain-binding chamber. Intriguingly, despite the observation of a single AZ1 conformation in the crystal structure, our solution NMR investigation has revealed the presence of a second ligand conformation invisible in the crystalline state. Together, these distinct ligand conformations delineate a cryptic inhibitor envelope that expands the observed footprint of AZ1 in the LpxH-bound crystal structure and enables the design of AZ1 analogs with enhanced potency in enzymatic assays. These designed compounds display striking improvement in antibiotic activity over AZ1 against wild-type K. pneumoniae , and coadministration with outer membrane permeability enhancers profoundly sensitizes Escherichia coli to designed LpxH inhibitors. Remarkably, none of the sulfonyl piperazine compounds occupies the active site of LpxH, foretelling a straightforward path for rapid optimization of this class of antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

The microstructure of a selective laser melting (SLM)-fabricated NiTi shape memory alloy with superior tensile property and shape memory recoverability

A selective laser melting (SLM)-fabricated NiTi with superior tensile property and shape memory recoverability was obtained by using a unique stripe rotation scanning strategy. Here, the alloy characteristics, formation mechanisms and evolution in terms of twins, dislocations and precipitations of the alloy were systematically studied. Compared to the conventional smelting-followed-by-machining, the SLM fabrication process involves rapid solidification and repeated heating, which confer distinctive characteristics to the microstructures of SLM-fabricated NiTi alloys. Rapid solidification promotes the formation of a supersaturation solid solution matrix containing a high concentration vacancies, which in turn aggregate to generate a high density of dislocations. During subsequent repeated heating stages, these dislocations occur thermal motion along three directions of <001 > , <111> and <110 >, leading to the formation of thermal kinks, helical dislocations and wave morphology. Simultaneously, precipitated particles Ti 3 Ni 4 repeatedly nucleate and heterogeneous grow with the movement of dislocation. Such precipitation behavior, termed repeated precipitation, has not been previously reported in the conventional NiTi alloys, suggesting that it could be a unique characteristic of such alloy. After martensitic transformation, only two twins, {1 1¯ 1} type I twin and compound twin, are detected. The twinning lamellae of these two twins, where precipitation and dislocation pile-ups exist, often have uneven thickness and chaotic arrangement. Besides, the unique self-accommodated microstructures, such as secondary {1 1¯ 1} type I twin and compound twin with “herring-bone’’ lamellae, which often appear in the deformed or nanocrystalline NiTi, can also be observed. These unique microstructures may confer the distinctive properties to the SLM-fabricated NiTi.

36 MATERIALS SCIENCE↗

NASA NTRS2000

Protein Crystal Growth Dynamics and Impurity Incorporation

The general concepts and theories of crystal growth are proven to work for biomolecular crystallization. This allowed us to extract basic parameters controlling growth kinetics - free surface energy, alpha, and kinetic coefficient, beta, for steps. Surface energy per molecular site in thermal units, alpha(omega)(sup 2/3)/kT approx. = 1, is close to the one for inorganic crystals in solution (omega is the specific molecular volume, T is the temperature). Entropic restrictions on incorporation of biomolecules into the lattice reduce the incorporation rate, beta, by a factor of 10(exp 2) - 10(exp 3) relative to inorganic crystals. A dehydration barrier of approx. 18kcal/mol may explain approx. 10(exp -6) times difference between frequencies of adding a molecule to the lattice and Brownian attempts to do so. The latter was obtained from AFM measurements of step and kink growth rates on orthorhombic lysozyme. Protein and many inorganic crystals typically do not belong to the Kossel type, thus requiring a theory to account for inequivalent molecular positions within its unit cell. Orthorhombic lysozyme will serve as an example of how to develop such a theory. Factors deteriorating crystal quality - stress and strain, mosaicity, molecular disorder - will be reviewed with emphasis on impurities. Dimers in ferritin and lysozyme and acetylated lysozyme, are microheterogeneous i.e. nearly isomorphic impurities that are shown to be preferentially trapped by tetragonal lysozyme and ferritin crystals, respectively. The distribution coefficient, K defined as a ratio of the (impurity/protein) ratios in crystal and in solution is a measure of trapping. For acetylated lysoyzme, K = 2.15 or, 3.42 for differently acetylated forms, is independent of both the impurity and the crystallizing protein concentration. The reason is that impurity flux to the surface is constant while the growth rate rises with supersaturation. About 3 times lower dimer concentration in space grown ferritin and lysozyme crystals might be examples explaining higher quality of the space grown protein crystal. Depletion of solution with respect to isomorphic impurities around a growing crystal may be K times deeper than with respect to the crystallizing protein.

Chernov, Alex A.↗

DOE OSTI2020

Stability of a tokamak plasma with diffuse toroidal rotation

The present work considers the stability of a high- $\beta$ , large aspect ratio, circular plasma with diffuse profiles for the safety factor and the angular toroidal frequency (López & Guazzotto, Phys. Plasmas , vol. 24, 032501). An application of the Frieman–Rotenberg formalism results in a system of scalar eigenmode equations whose coupling is retained at the plasma–vacuum transition but is disregarded across the plasma column, which is a standard practice. The solution technique consists of a multidimensional shooting method for the poloidal harmonics; robust initial guesses are constructed by solving the dispersion relation in the static scenario with vanishing magnetic shear. Flow shear appears as a high- $\beta$ toroidal contribution, and we illustrate its destabilizing influence on $n=1$ external kink modes in the presence of ideal and resistive walls. Internal resonances are avoided by means of the selection of appropriate equilibrium parameters. The stabilizing influence of a finite positive average magnetic shear is also exemplified.

Physics↗

NASA NTRS1989

Mechanics of the crack path formation

A detailed analysis of experimentally obtained curvilinear crack path trajectories formed in a heterogeneous stress field is presented. Experimental crack path trajectories were used as data for numerical simulations, recreating the actual stress field governing the development of the crack path. Thus, the current theories of crack curving and kinking could be examined by comparing them with the actual stress field parameters as they develop along the experimentally observed crack path. The experimental curvilinear crack path trajectories were formed in the tensile specimens with a hole positioned in the vicinity of a potential crack path. The numerical simulation, based on the solution of equivalent boundary value problems with the possible perturbations of the crack path, is presented here.

Rubinstein, Asher A.↗

NASA NTRS1991

Mechanics of the crack path formation

A detailed analysis of experimentally obtained curvilinear crack path trajectories formed in a heterogeneous stress field is presented. Experimental crack path trajectories were used as data for the numerical simulations, recreating the actual stress field governing the development of the crack path. Thus, the current theories of crack curving and kinking could be examined by comparing them with the actual stress field parameters as they develop along the experimentally observed crack path. The experimental curvilinear crack path trajectories were formed in the tensile specimens with a hole positioned in the vicinity of a potential crack path. The numerical simulation, based on the solution of equivalent boundary value problems with the possible perturbations of the crack path, is presented.

Rubinstein, Asher A.↗

NASA NTRS1975

A three-dimensional solution of flows over wings with leading-edge vortex separation

The application of a new, general, potential flow computational technique to the solution of the subsonic, three-dimensional flow over wings with leading-edge vortex separation is presented. The present method is capable of predicting forces, moments, and detailed surface pressures on thin, sharp-edged wings of rather arbitrary planform. The wing geometry is arbitrary in the sense that leading and trailing edges may be curved or kinked and the wing may have arbitrary camber and twist. The method employs an inviscid flow model in which the wing, the rolled-up vortex sheets, and the wake are represented by piecewise continuous quadratic doublet sheet distributions. The Kutta condition is imposed along all wing edges. Strengths of the doublet distributions as well as shape and position of the free fortex sheet spirals are computed in iterative fashion starting with an assumed initial sheet geometry. The method is verified by numerous computed results.

Weber, J. A.↗

NASA NTRS1993

Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

Pohorille, Andrew↗

DOE OSTI2024

Creating kinks with quantum mediation

We consider the creation of kink-antikink pairs of a scalar field ϕ by the scattering of classical wave packets of a second scalar field ψ when there are no direct interactions between ϕ and ψ . The creation becomes possible only due to a quantum field that interacts with both ϕ and ψ . We scan parameter space and find it favorable for kink production when the initial wave packets have large total energy and wide spatial extent but scatter at low velocities. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1990

Comment on high resolution simulations of cosmic strings. 1: Network evoloution

Comments are made on recent claims (Albrecht and Turok, 1989) regarding simulations of cosmic string evolution. Specially, it was claimed that results were dominated by a numerical artifact which rounds out kinks on a scale of the order of the correlation length on the network. This claim was based on an approximate analysis of an interpolation equation which is solved herein. The typical rounding scale is actually less than one fifth of the correlation length, and comparable with other numerical cutoffs. Results confirm previous estimates of numerical uncertainties, and show that the approximations poorly represent the real solutions to the interpolation equation.

Turok, Neil↗

NASA NTRS2002

Surface Processes of Faceted Growth

Atomic force microscopy and high precision optical interferometry allow to analyze the processes that are in the core of our present understanding of faceted crystal growth. Some of these processes will be reviewed. Recent experiments suggest that the Gibbs-Thomson Law (GTL) may not be applicable to the weakly fluctuating strongly polygonized steps, with low kink density. Propagation rate of a straight short step segment changes with the segment length much steeper than predicted by GTL. If the step fluctuations are still well developed, the typical transition length may be determined just by the radius of rounded comers of the polygonized step. If fluctuations do not have enough time to develop, the kinetic effects may be essential. Indeed, 'communications' between comers of a short straight step segment may occur and, thus, the GTL may be implemented only via kink exchange. E.g., dissolutions of this short segment at macroscopic equilibrium occurs as follows: The kinks are split from one comer as a result of fluctuations, and annihilate with kinks of the opposite sign generated by another comer. Similarly, an exchange via chain of kinks on a rough step is the mechanism to implement the GT Law. If there is a supersaturation with respect to a large crystal, the kinks not only diffuse along the step, but move back the generating comers. This 'wind' prevents communication between the comers and places upper limit supersaturation only below which GTL is applicable. Steps replace kinks in the 3D case, though, of course, another dimensionality brings about another physics. Another specific problem to think about is if fluctuations are always fast enough to provide enough kinks for linear dependence of step rate on supersaturation. Increasing azimuthal polygonization of growth hillocks is a sign of insufficient fluctuation rate. Morphological stability of vicinal faces is usually considered on the basis of mutually parallel steps. Azimuthal anisotropy and interlacing of step bunches inducing the well known bunch splitting is another challenge. Among other challenging problems are: existence of surface diffusion on the crystal/so1ution interface, step interaction in solutions, achievement of step flow modes from liquids, impurity effects. New phenomena essential in biomacromolecular crystallization is another interesting area.

Chernov, A.↗

DOE OSTI2022

New insights into Mn 2+ and Mg 2+ inhibition of calcite growth

Impurity ion and isotope partitioning into carbonate minerals provide a window into the molecular processes occurring at the fluid-mineral interface during crystal growth. Here, we employ calcium isotope fractionation together with process-based modeling to elucidate the mechanisms by which two divalent cations with starkly contrasting compatibility, magnesium and manganese, inhibit calcite growth and incorporate into the mineral lattice. Calcite growth inhibition by Mg 2+ is log-linear and K Mg is on the order of 0.02–0.03 throughout the range of {Mg 2+ }/{Ca 2+ } studied here (0.01–2.6). Mn 2+ exhibits much stronger log-linear growth rate inhibition at low Mn 2+ concentrations (fluid {Mn 2+ }/{Ca 2+ } = 0.001–0.02). Mn 2+ is readily incorporated into the calcite lattice to form a calcite-rhodochrosite solid solution, with large partition coefficients (K Mn 4.6–15.6) inversely correlated to growth rate. For both Mn 2+ and Mg 2+ , calcium isotope fractionation is found to be invariant with {Me 2+ }/{Ca 2+ } despite more than an order of magnitude decline in growth rate. This invariant Δ 44/40 Ca suggests that the presence of Mn 2 + or Mg 2+ does not significantly change the relative rates of Ca 2+ attachment and detachment at kink sites during growth, indicative of a dominantly kink blocking inhibition mechanism. Because the partitioning behavior dictates that Mn 2+ must attach to the surface significantly faster than Ca 2+ , attachment of Mn 2+ is likely to be as a non-monomer species such as an ion pair or possibly a larger polynuclear cluster. We propose that calcite growth rate inhibition by Mn is determined by the kinetics of carbonate attachment at Mn-occupied kink sites, potentially due to slow re-orientation kinetics of carbonate ions that have formed an inner-sphere complex with Mn 2+ at the surface but must reorient to incorporate into the lattice. We demonstrate that patterns in Mg 2+ partitioning and inhibition behavior are broadly consistent with growth inhibition driven by slow Mg 2+ -aquo complex dehydration relative to Ca 2+ but argue that this mechanism likely represents one endmember scenario, seen in Mg-calcite growth at low supersaturations and net precipitation rates. During growth at faster net precipitation rates, some portion of Mg 2+ is likely incorporated as a partially hydrated or otherwise complexed species, but calcite growth remains significantly inhibited by the kinetics of CO 3 2- attachment at Mg 2+ kink sites. These findings suggest a hybrid classical/nonclassical growth mechanism whereby Ca 2+ incorporates largely as a free ion at kink sites while Mn 2+ and some portion of Mg 2+ are incorporated via non-monomer attachment. This pattern may be generalizable; trace constituent cations with aquo-complex desolvation rates significantly slower than the mineral growth rate preferentially incorporate as a non-monomer species during otherwise classical crystal growth.

58 GEOSCIENCES↗

DOE OSTI2021

Isogeometric Bézier dual mortaring: The Kirchhoff–Love shell problem

Here in this paper we develop an isogeometric Bézier dual mortar method for coupling multi-patch Kirchhoff–Love shell structures. The proposed approach weakly enforces the continuity of the solution at patch interfaces through a dual mortar method and can be applied to both conforming and non-conforming discretizations. As the employed dual basis functions have local supports and satisfy the biorthogonality property, the resulting stiffness matrix is sparse. In addition, the coupling accuracy is optimal because the dual basis possesses the polynomial reproduction property. We also formulate the continuity constraints through the Rodrigues’ rotation operator which gives a unified framework for coupling patches that are intersected with G 1 continuity as well as patches that meet at a kink. Several linear and nonlinear examples demonstrated the performance and robustness of the proposed coupling techniques.

42 ENGINEERING↗

DOE OSTI2021

Active control of resistive wall mode via modification of external tearing index

Modification of the external tearing index, Δ ext ′ , by magnetic feedback is analytically investigated for the purpose of controlling the resistive plasma resistive wall mode (RP-RWM). The matching method is pursued by deriving expressions for the close-loop Δ ext ′ and by linking it to the counterpart from the inner layer. Various feedback coil configurations are found to generally reduce Δ ext ′ and stabilize the RWM, with either proportional or derivative control. Feedback modification of Δ ext ′ is found to be generally independent of the inner layer resistive interchange index D R , confirming that feedback action primarily modifies the solution in the outer ideal region for the RP-RWM. Exception occurs when either the inner layer favorable curvature effect becomes sufficiently large or the feedback action is sufficiently strong to introduce a rotating RP-RWM in the static plasma, leading to complex-valued close-loop Δ ext ′ . The perturbed magnetic energy dissipation in the outer region, associated with the eddy current in the resistive wall, is identified as the key physics reason for feedback induced complex Δ ext ′ . Similar results are also obtained for active control of the external kink instability, whose open-loop growth rate is significantly reduced by inclusion of the plasma resistivity. Within the single poloidal harmonic approximation, which is most suitable for the matching approach, external active coils combined with poloidal sensors are often found to be more efficient for feedback stabilization of the mode at large proportional gain values. This counter-intuitive result is explained as the lack of (non-resonant) poloidal harmonics for proper description of the feedback coil geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

The hierarchical energy landscape of screw dislocation motion in refractory high-entropy alloys

High-entropy alloys (HEAs) with concentrated solid solutions are conceived to possess a rugged atomic and energy landscape in which dislocation motion necessarily proceeds to accommodate mechanical deformation. Fundamental questions remain as to how rough the energy landscape is and to what extent it can be influenced by the local ordering of their constituent elements. Here, we construct and report the potential energy landscape (PEL) governing screw dislocation motion in refractory HEAs that reveals a hierarchical and multilevel structure with a collection of small basins nested in large metabasin. This striking feature pertaining to HEAs exerts a trapping force and back stress on saddle point activations, retarding dislocation movement. Further, by introducing chemical short-range order, the energy landscape is smoothed but skewed to different degrees that shifts the rate-liming process from kink-glide to kink-pair nucleation. The chemical disorder-roughened PEL in HEAs, analogous to structural disorder induced in metallic glasses, signifies the role of various barrier-hopping processes underlying the extraordinary mechanical behaviors of the two distinct groups of materials.

36 MATERIALS SCIENCE↗

DOE OSTI2026

ARC physics basis–magnetohydrodynamics

ARC is designed to produce 400 ⁢MW of net electricity and prove the commercial feasibility of a fusion power plant. In order to achieve this goal ARC has to operate with optimal core performance in a stationary scenario that minimises wear on the first wall and divertor. This requires avoiding or mitigating magnetohydrodynamic (MHD) instabilities which have the potential to not only degrade the plasma core but also lead to deleterious transient heat loads on plasma facing components. Therefore, this work aims at characterising the MHD stability of the high performance ARC scenario and inform the design of error field correction coils. Firstly, simulations of vertical displacement events show that an in-vessel coil is not needed and instead the poloidal shaping coils can be used to control vertical stability. These simulations also inform the demands on the corresponding coil power supplies. Stability analysis of the ideal kink mode with or without a conducting wall and kinetic effects suggests that the ARC baseline scenario operates deeply in the stable region. Using RDCON, tearing modes at the 𝑚/𝑛 =2/1 and 3/2 surfaces (with poloidal mode number 𝑚, and toroidal mode number 𝑛) are shown to be linearly stable, and including thermal transport effects in the rational surfaces lead to further stabilisation. However, other transient plasma instabilities can seed neoclassical tearing modes (NTMs). The marginally stable width of NTMs in ARC strongly depends on the internal inductance and can fall below 0.1% of the normalised poloidal flux. Furthermore, an empirical cross-machine model of the 𝑛 =1 error field leading to a disruption predicts a critical error field larger than SPARC but smaller than ITER. Three-dimensional coils can be designed with the Generalised Purturbed Equilbium Code based on a simple model that calculates the maximum correctable error field that is limited by the neoclassical toroidal viscosity torque. Broad scans of different coil geometries identify a set of 2 rows of off-midplane coils to be a suitable solution. It is also determined that such a set of three-dimensional coils is capable of correcting 𝑛 =2 error fields to some degree and creating strong enough 𝑛 =2 or 𝑛 =3 edge resonant perturbation fields for the suppression of edge-localised modes at reasonable coil currents. The final design of the first ARC will be further informed by results from SPARC.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗