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At least 721 records · Page 40

Quantifying uncertainty in analysis of shockless dynamic compression experiments on platinum. I. Inverse Lagrangian analysis

Absolute measurements of solid-material compressibility by magnetically driven shockless dynamic compression experiments to multi-megabar pressures have the potential to greatly improve the accuracy and precision of pressure calibration standards for use in diamond anvil cell experiments. Here, to this end, we apply characteristics-based inverse Lagrangian analysis (ILA) to 11 sets of ramp-compression data on pure platinum (Pt) metal and then reduce the resulting weighted-mean stress–strain curve to the principal isentrope and room-temperature isotherm using simple models for yield stress and Grüneisen parameter. We introduce several improvements to methods for ILA and quasi-isentrope reduction, the latter including calculation of corrections in wave speed instead of stress and pressure to render results largely independent of initial yield stress while enforcing thermodynamic consistency near zero pressure. More importantly, we quantify in detail the propagation of experimental uncertainty through ILA and model uncertainty through quasi-isentrope reduction, considering all potential sources of error except the electrode and window material models used in ILA. Compared to previous approaches, we find larger uncertainty in longitudinal stress. Monte Carlo analysis demonstrates that uncertainty in the yield-stress model constitutes by far the largest contribution to uncertainty in quasi-isentrope reduction corrections. We present a new room-temperature isotherm for Pt up to 444 GPa, with 1-sigma uncertainty at that pressure of just under ±1.2%; the latter is about a factor of three smaller than uncertainty previously reported for multi-megabar ramp-compression experiments on Pt. The result is well represented by a Vinet-form compression curve with (isothermal) bulk modulus K 0 = 270.3 ± 3.8 GPa, pressure derivative K$^{'}_{0}$= 5.66 ± 0.10, and correlation coefficient $R_{K_{0},K^{'}_{0}}$= –0.843.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Numerical study of implosion instability mitigation in magnetically driven solid liner dynamic screw pinches

Magnetized liner inertial fusion experiments on the Z accelerator suffer from magneto-Rayleigh–Taylor instabilities (MRTI) that compromise integrity of the imploding cylindrical liner, limiting achievable fusion fuel conditions and ultimately reducing magneto-inertial fusion target performance. Dynamic screw pinches (DSP) provide a method to reduce MRTI in-flight via application of magnetic field line tension to the imploding liner outer surface. In contrast with z-pinches that drive implosions with an azimuthal magnetic field, dynamic screw pinches enforce an additional axial drive magnetic field component, making the overall drive magnetic field helical. As the liner implodes, cumulative MRTI development is reduced by dynamically shifting the orientation of the fastest growing instability modes. Three-dimensional magnetohydrodynamic simulations show that the DSP mechanism effectively stabilizes initially solid cylindrical liner implosions driven by Z-scale current pulses, indicating that MRTI mitigation increases with the ratio of axial to azimuthal drive magnetic field components (i.e., the drive field ratio). We also performed a spectral analysis of the simulated imploding density distributions, extracting wavelength and pitch angle of the simulated MRTI structures to study their dynamics during the implosion. Simulations of liners initially perturbed with drive-field-aligned sinusoidal structures indicate that MRTI mitigation in DSP implosions decreases with perturbation wavelength, once again suggestive of magnetic field line tension effects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Augmenting machine learning of Grad–Shafranov equilibrium reconstruction with Green's functions

This work presents a method for predicting plasma equilibria in tokamak fusion experiments and reactors. The approach involves representing the plasma current as a linear combination of basis functions using principal component analysis of plasma toroidal current densities (J t ) from the EFIT-AI equilibrium database. Then utilizing EFIT's Green's function tables, basis functions are created for the poloidal flux (ψ) and diagnostics generated from the toroidal current (J t ). Similar to the idea of a physics-informed neural network (NN), this physically enforces consistency between ψ, J t , and the synthetic diagnostics. First, the predictive capability of a least squares technique to minimize the error on the synthetic diagnostics is employed. The results show that the method achieves high accuracy in predicting ψ and moderate accuracy in predicting J t with median R 2 = 0.9993 and R 2 = 0.978, respectively. A comprehensive NN using a network architecture search is also employed to predict the coefficients of the basis functions. The NN demonstrates significantly better performance compared to the least squares method with median R 2 = 0.9997 and 0.9916 for J t and ψ, respectively. The robustness of the method is evaluated by handling missing or incorrect data through the least squares filling of missing data, which shows that the NN prediction remains strong even with a reduced number of diagnostics. Additionally, the method is tested on plasmas outside of the training range showing reasonable results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Drift kinetic electrostatic simulations of the edge localized mode heat pulse

In the present work, electrostatic drift kinetic simulations of parallel plasma transport within the tokamak scrape-off layer (SOL) are conducted using the COGENT code. The SOL configuration is represented in one-dimensional slab geometry, incorporating a heat source localized in the midplane. The heat source parameters correspond to those characterizing edge-localized modes observed in the Joint European Torus (JET) tokamak. The numerical model includes kinetic treatment of both ions and electrons, a simplified model for the gyrokinetic Poisson equation that allows one to step over short time scales associated with fast electrostatic shear Alfvèn waves, and the logical sheath boundary condition (LSBC) that enforces global system quasineutrality. A third-order accurate LSBC is derived to be consistent with the third-order accurate upwind advection scheme utilized in the code, and it was shown to noticeably impact the simulation results, especially parallel heat flux at the target plate. The findings of this study are in agreement with results from preceding fluid and kinetic simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Near-ideal relaxed MHD in slab geometry

We investigate the solutions of the relaxed magnetohydrodynamic (MHD) model (RxMHD) of R. Dewar and Z. Qu. This model generalizes Taylor relaxation by including the ideal Ohm's law constraint using an augmented Lagrangian method, providing a pathway to extend the multi-region relaxed MHD (MRxMHD) model. We present the first numerical solution of the RxMHD model by Dewar and Qu, demonstrating that it is mathematically well-defined and computationally feasible for constructing MHD equilibria in slab geometry. We also show that a cross-field flow can exist without enforcing an arbitrary constraint on the angular momentum, as is done in the case of MRxMHD with flow. Our results also demonstrate the self-organization of fully relaxed regions during the optimization, which was an important motivation behind developing this model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Monolithic optoelectronic circuit design for on-chip terahertz applications

We demonstrate a monolithic coplanar stripline platform for on-chip terahertz (THz) generation, transmission, and detection, addressing key challenges of mode purity, bandwidth, and referencing. Capacitive coupling of the photoconductive generator switch enforces pure odd-mode propagation, increases THz field strength, and extends the operational frequency range, achieving 0.05–1.4 THz. Our architecture enables fully monolithic fabrication with amorphous silicon switches, in situ field referencing, and galvanic isolation between generation and detection. Finite-element simulations and experiments confirm that suppressing parasitic modes improves signal integrity, providing a robust platform for high-fidelity THz spectroscopy, ultrafast electronics, and nanoscale quantum materials research.

Capacitive coupling↗

Crystal structure of an orthomyxovirus matrix protein reveals mechanisms for self-polymerization and membrane association

Many enveloped viruses encode a matrix protein. In the influenza A virus, the matrix protein M1 polymerizes into a rigid protein layer underneath the viral envelope to help enforce the shape and structural integrity of intact viruses. The influenza virus M1 is also known to mediate virus budding as well as the nuclear export of the viral nucleocapsids and their subsequent packaging into nascent viral particles. Despite extensive studies on the influenza A virus M1 (FLUA-M1), only crystal structures of its N-terminal domain are available. Here we report the crystal structure of the full-length M1 from another orthomyxovirus that infects fish, the infectious salmon anemia virus (ISAV). The structure of ISAV-M1 assumes the shape of an elbow, with its N domain closely resembling that of the FLUA-M1. The C domain, which is connected to the N domain through a flexible linker, is made of four α-helices packed as a tight bundle. In the crystal, ISAV-M1 monomers form infinite 2D arrays with a network of interactions involving both the N and C domains. Results from liposome flotation assays indicated that ISAV-M1 binds membrane via electrostatic interactions that are primarily mediated by a positively charged surface loop from the N domain. Furthemore, cryoelectron tomography reconstruction of intact ISA virions identified a matrix protein layer adjacent to the inner leaflet of the viral membrane. The physical dimensions of the virion-associated matrix layer are consistent with the 2D ISAV-M1 crystal lattice, suggesting that the crystal lattice is a valid model for studying M1–M1, M1–membrane, and M1–RNP interactions in the virion.

59 BASIC BIOLOGICAL SCIENCES↗

3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

Niemann–Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann–Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314–1,278), which—in contrast to previous lower resolution structures—features the entire CTD well resolved. Here, all eight cysteines of the CTD form four disulfide bonds, one of which (C909–C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD–NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.

59 BASIC BIOLOGICAL SCIENCES↗

Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane

Significance Understanding the structure of iron active sites that form in zeolites is critical to understanding the extreme reactivity of Fe-zeolite catalysts, which show promise in important industrial applications. This study defines the geometric structure of an Fe-zeolite active site that cleaves the inert C–H bond of methane at room temperature to form methanol. The high reactivity of this site derives from a constrained coordination geometry enforced by the rigid matrix of the catalyst. This insight into the relationship between catalyst structure and function is an important step toward cost-effective methanol fuels and chemical feedstocks derived from natural gas.

36 MATERIALS SCIENCE↗

Probabilistic control of HIV latency and transactivation by the Tat gene circuit

Significance The reservoir of HIV latently infected cells is the major obstacle for complete eradication of HIV infection. Latency and its transactivation in HIV-infected cells are controlled by the intracellular HIV Tat gene circuit. By reconstructing the probability landscape of the circuit through exact solution of the underlying chemical master equation we examined the detailed mechanism of probabilistic intracellular control of latency and transactivation. We show that while the Tat circuit lacks deterministic bistability its probability landscape exhibits bimodality. Moreover, by exploring changes in the probability landscapes under different perturbations, our study suggests effective therapeutic targets for strategies of “shock and kill” to eliminate latently infected cells and “block and lock” to enforce deep latency.

Cao, Youfang↗

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

The elongation factor G (EF-G)–catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Furthermore, although the mRNA also undergoes movement, codon–anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.

59 BASIC BIOLOGICAL SCIENCES↗

A structural framework for unidirectional transport by a bacterial ABC exporter

The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans (NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the NaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As NaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4 eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by NaAtm1. One of the disulfide crosslinked NaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.

59 BASIC BIOLOGICAL SCIENCES↗

Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12

Cobalamin is a complex organometallic cofactor that is processed and targeted via a network of chaperones to its dependent enzymes. AdoCbl (5'-deoxyadenosylcobalamin) is synthesized from cob(II)alamin in a reductive adenosylation reaction catalyzed by adenosyltransferase (ATR), which also serves as an escort, delivering AdoCbl to methylmalonyl-CoA mutase (MCM). The mechanism by which ATR signals that its cofactor cargo is ready (AdoCbl) or not [cob(II)alamin] for transfer to MCM, is not known. In this study, we have obtained crystallographic snapshots that reveal ligand-induced ordering of the N terminus of Mycobacterium tuberculosis ATR, which organizes a dynamic cobalamin binding site and exerts exquisite control over coordination geometry, reactivity, and solvent accessibility. Cob(II)alamin binds with its dimethylbenzimidazole tail splayed into a side pocket and its corrin ring buried. The cosubstrate, ATP, enforces a four-coordinate cob(II)alamin geometry, facilitating the unfavorable reduction to cob(I)alamin. The binding mode for AdoCbl is notably different from that of cob(II)alamin, with the dimethylbenzimidazole tail tucked under the corrin ring, displacing the N terminus of ATR, which is disordered. In this solvent-exposed conformation, AdoCbl undergoes facile transfer to MCM. The importance of the tail in cofactor handover from ATR to MCM is revealed by the failure of 5'-deoxyadenosylcobinamide, lacking the tail, to transfer. In the absence of MCM, ATR induces a sacrificial cobalt–carbon bond homolysis reaction in an unusual reversal of the heterolytic chemistry that was deployed to make the same bond. Finally, the data support an important role for the dimethylbenzimidazole tail in moving the cobalamin cofactor between active sites.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis

Abietadiene synthase from Abies grandis (AgAS) is a model system for diterpene synthase activity, catalyzing class I (ionization-initiated) and class II (protonation-initiated) cyclization reactions. Reported here is the crystal structure of AgAS at 2.3 {angstrom} resolution and molecular dynamics simulations of that structure with and without active site ligands. AgAS has three domains ({alpha}, {beta}, and {gamma}). The class I active site is within the C-terminal {alpha} domain, and the class II active site is between the N-terminal {gamma} and {beta} domains. The domain organization resembles that of monofunctional diterpene synthases and is consistent with proposed evolutionary origins of terpene synthases. Molecular dynamics simulations were carried out to determine the effect of substrate binding on enzymatic structure. Although such studies of the class I active site do lead to an enclosed substrate-Mg{sup 2+} complex similar to that observed in crystal structures of related plant enzymes, it does not enforce a single substrate conformation consistent with the known product stereochemistry. Simulations of the class II active site were more informative, with observation of a well ordered external loop migration. This 'loop-in' conformation not only limits solvent access but also greatly increases the number of conformational states accessible to the substrate while destabilizing the nonproductive substrate conformation present in the 'loop-out' conformation. Moreover, these conformational changes at the class II active site drive the substrate toward the proposed transition state. Docked substrate complexes were further assessed with regard to the effects of site-directed mutations on class I and II activities.

59 BASIC BIOLOGICAL SCIENCES↗

Active site and laminarin binding in glycoside hydrolase family 55

The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium . Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ~30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Furthermore, application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Weighted Least-Squares Transport Equation Compatible with Source Iteration and Voids

We present that second-order forms of the transport equation allow the use of continuous finite elements (CFEMs). This can be desired in multiphysics calculations where other physics require CFEM discretizations. Second-order transport operators are generally self-adjoint, yielding symmetric positive-definite (SPD) matrices, which allow the use of efficient linear algebra solvers with an enormous advantage in memory usage. Least-squares (LS) forms of the transport equation can circumvent the void problems of other second-order forms but are almost always nonconservative. Additionally, the standard LS form is not compatible with discrete ordinates method (SN) iterative solution techniques such as source iteration. A new form of the LS transport equation has recently been developed that is compatible with voids and standard SN iterative solution techniques. Performing nonlinear diffusion acceleration (NDA) using an independently differenced low-order equation enforces conservation for the whole system and makes this equation suitable for reactor physics calculations. In this context, “independent” means that both the transport and low-order solutions converge to the same scalar flux and current as the spatial mesh is refined, but for a given mesh, the solutions are not necessarily equal. In this paper we show that introducing a weight function into this LS equation improves issues with causality and can render our equation equal to the self-adjoint angular flux (SAAF) equation. Causality is a principle of the transport equation that states that information travels only downstream along characteristics. This principle can be violated numerically. We show how to limit the weight function in voids and demonstrate the effect of this limit on accuracy. Using the C5G7 benchmark, we compare our method to the SAAF formulation with a void treatment (SAAFτ) that is not self-adjoint and has a nonsymmetric coefficient matrix. Finallyl, we show that the weighted LS equation with NDA gives acceptable accuracy relative to the SAAFτ equation while maintaining a SPD system matrix.

97 MATHEMATICS AND COMPUTING↗

Mechanistic Investigation of Co(II) Extraction by TODGA to Aid Nuclear Forensic Separations

Nuclear forensic (NF) analysis supports law enforcement inquiries by analyzing evidence tainted with radioactive substances. Separation techniques can be used to identify and quantify actinides and fission 15 products in post-detonation (PD) debris. Environmental transition metals, also present in PD residues, have been observed to impact critical isotope extractions. For example, radio stable cobalt (Co), ubiquitous in urban environments, particularly in corrosion-resistant alloys, paint-drying agents, dyes, and pigments, can impact the separation of important actinides and fission products. The presented work aims to elucidate the chemistry Q2 governing Co extraction in samples pertinent to PDNF. Chemistry between Co and N,N,N,‘N’-tetraoctyl diglyco- 20 lamide (TODGA), the ligand present in the commercial chromatographic resin diglycolamide (DGA), were studied via solvent and chromatographic extraction and spectroscopic analyses. These results indicate that a tetrahedral Co(II) species is extracted by TODGA from highly acidic (>5M HCl) solutions via a spontaneous entropy-driven reaction. Furthermore, extraction trends in varied acid concentrations are consistent between solvent extraction and chromatographic extraction methods.

activation product↗

Enabling cooperative adaptive cruise control on strings of vehicles with heterogeneous dynamics and powertrains

Recent studies have shown that positive impact of Cooperative Adaptive Cruise Control (CACC) can only be guaranteed as market penetration rate increases. Removing the string homogeneity constraint is essential to encourage widespread adoption. In this work, a hierarchical architecture is proposed to enable CACC on vehicles with not only mixed dynamics but also different powertrain types. A low-level layer deals with the vehicle and powertrain dynamics to provide accurate and consistent reference speed tracking response. The high-level layer uses: (1) a Linear Parameter Varying feedback system to provide loop stability, robustness and enforce a variable time gap policy and (2) a feedforward system that processes Vehicle-to-Vehicle information to enhance string stability and response bandwidth, by dealing with the string heterogeneity. A gap management strategy is built on top of the CACC architecture to handle gap setting changes or cut-in/out situations, via a dynamics constrained time gap trajectory planning algorithm. We report the proposed work has been designed, developed and validated on three different real passenger vehicles on public highways and test tracks, showing the potential of the proposed algorithm to enable robust string stable CACC, despite the different dynamics and powertrains considered.

33 ADVANCED PROPULSION SYSTEMS↗