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At least 1,441 records · Page 80

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a “swinging gate” allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

2D-NMR↗

DNS/LES Study of Representative Wall-Bounded Turbulent Flows using SIERRA/Fuego

This report summarizes a series of SIERRA/Fuego validation efforts of turbulent flow models on canonical wall-bounded configurations. In particular, direct numerical simulations (DNS) and large eddy simulations (LES) turbulence models are tested on a periodic channel, a periodic pipe, and an open jet for which results are compared to the velocity profiles obtained theoretically or experimentally. Velocity inlet conditions for channel and pipe flows are developed for application to practical simulations. To show this capability, LES is performed over complex terrain in the form of two natural hills and the results are compared with other flow solvers. The practical purpose of the report is to document the creation of inflow boundary conditions of fully developed turbulent flows for other LES calculations where the role of inflow turbulence is critical.

42 ENGINEERING↗

Hydrated Metal and Metal-Nitrate Complexes in Water: Full Lanthanide(III) Series plus Miscellaneous Metal Ions

This is a dataset of hydrated metal complexes and metal–nitrate hydrated complexes intended for public use, reproducibility, and downstream structural analysis. A key feature is coverage across the full lanthanide(III) series (La–Lu), enabling systematic comparisons of coordination motifs and bonding trends across the entire lanthanide sequence. In addition to the lanthanides, the dataset also includes other metal ions such as UO2(VI), Fe(II), and Fe(III). The dataset provides optimized geometries for hydrated and nitrate-containing hydrated complexes, together with representative ab initio molecular dynamics (AIMD) trajectories saved in standard XYZ formats. The accompanying NWChem input decks enable reproduction of the reported calculations and provide a starting point for extending the simulations to related coordination environments. Computationally, DFT calculations employ the B3LYP functional with DFT-D3BJ dispersion corrections and a COSMO continuum solvent model (dielectric constant 78.4) to represent solvation beyond the explicitly treated first hydration shell. AIMD simulations are performed with the NWChem qmd module at 298 K, integrating nuclear motion with the velocity-Verlet algorithm and controlling temperature using a Nosé–Hoover thermostat. Trajectories are approximately 4.8 ps in length and are used primarily to assess short-time stability of candidate coordination motifs, including (for lanthanides) differences between 8- versus 9-water coordination and comparisons between nitrate-bound and nitrate-free hydrated complexes.

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗

Low NO subx heavy fuel combustor concept program. Phase 1A: Coal gas addendum

The performance and emissions from a rich-lean combustor fired on simulated coal gas fuels were investigated using a 12.7-cm diameter axially-staged burner originally designed for operation with high heating value liquid fuels. A simple, tubular fuel injector was substituted for the liquid fuel nozzle; no other combustor modifications were made. Four test fuels were studied including three chemically bound nitrogen-free gas mixtures with higher heating values of 88, 227, and 308 kj/mol (103, 258 and 349 Btu/scf), and a 227 kj/mol (258 Btu/scf) heating value doped with ammonia to produce a fuel nitrogen content of 0.5% (wt). Stable, ultra-low nitrogen oxide, smoke-free combustion was attained for the nitrogen-free fuels. Results with the doped fuel indicated that less than 5% conversion of NH3 to nitrogen oxide levels below Environmental Protection Agency limits could be achieved. In some instances, excessive CO levels were encountered. It is shown that use of a burner design employing a less fuel-rich primary zone than that found optimum for liquid fuels would yield more acceptable CO emissions.

Rosfjord, T.↗

An efficient computational method for characterizing the effects of random surface errors on the average power pattern of reflectors

Based on the works of Ruze (1966) and Vu (1969), a novel mathematical model has been developed to determine efficiently the average power pattern degradations caused by random surface errors. In this model, both nonuniform root mean square (rms) surface errors and nonuniform illumination functions are employed. In addition, the model incorporates the dependence on F/D in the construction of the solution. The mathematical foundation of the model rests on the assumption that in each prescribed annular region of the antenna, the geometrical rms surface value is known. It is shown that closed-form expressions can then be derived, which result in a very efficient computational method for the average power pattern. Detailed parametric studies are performed with these expressions to determine the effects of different random errors and illumination tapers on parameters such as gain loss and sidelobe levels. The results clearly demonstrate that as sidelobe levels decrease, their dependence on the surface rms/wavelength becomes much stronger and, for a specified tolerance level, a considerably smaller rms/wavelength is required to maintain the low sidelobes within the required bounds.

Rahmat-Samii, Y.↗

Coolant passage heat transfer with rotation. A progress report on the computational aspects

Turbine airfoils are subjected to increasingly higher heat loads which escalate the cooling requirements in order to satisfy life goals for the component materials. If turbine efficiency is to be maintained, however, cooling requirements should be as low as possible. To keep the quantity of cooling air bounded, a more efficient internal cooling scheme must be developed. One approach is to employ airfoils with multipass cooling passages that contain devices to augment internal heat transfer while limiting pressure drop. Design experience with multipass cooling passage airfoils has shown that a surplus of cooling air must be provided as a margin of safety. This increased cooling air leads to a performance penalty. Reliable methods for predicting the internal thermal and aerodynamic performance of multipass cooling passage airfoils would reduce or eliminate the need for the safety margin of surplus cooling air. The objective of the program is to develop and verify improved analytical methods that will form the basis for design technology which will result in efficient turbine components with improved durability without sacrificing performance. The objective will be met by: (1) establishing a comprehensive experimental data base that can form the basis of an empirical design system; (2) developing computational fluid dynamic techniques; and (3) analyzing the information in the data base with both phenomenological modeling and mathematical modeling to derive a suitable design and analysis procedure.

Aceto, L. D.↗

Resonances in low-energy positron-alkali scattering

Close-coupling calculations were performed with up to five target states at energies in the excitation threshold region for positron scattering from Li, Na and K. Resonances were discovered in the L = 0, 1 and 2 channels in the vicinity of the atomic excitation thresholds. The widths of these resonances vary between 0.2 and 130 MeV. Evidence was found for the existence of positron-alkali bound states in all cases.

Horbatsch, M.↗

Dynamics of Disorder-Order Transitions in Hard Sphere Colloidal Dispersions in micro-g

We performed a series of experiments on 0.518 millimeter PMMA spheres suspended in an index matching mixture of decalin and tetralin the microgravity environment provided by the Shuttle Columbia on mission STS-73. The samples ranged in concentration from 0.49 to 0.62. volume fraction (phi) of spheres, which covers the range in which liquid, coexistence, solid and glass phases are expected from Earth bound experiments. Light scattering was used to probe the static structure, and the particle dynamics. Digital and 35 mm photos provided information on the morphology of the crystals. In general, the crystallites grew considerably larger (roughly an order of magnitude larger) than the same samples with identical treatment in 1 g. The dynamic light scattering shows the typical short time diffusion and long time caging effects found in 1 g. The surprises that were encountered in microgravity include the preponderance of random hexagonal close packed (RHCP) structures and the complete absence of the expected face centered cubic (FCC) structure, existence of large dendritic crystals floating in the coexistence samples (where liquid and solid phases coexist) and the rapid crystallization of samples which exist only in glass phase under the influence of one g. These results suggest that colloidal crystal growth is profoundly effected by gravity in yet unrecognized ways. We suspect that the RCHP structure is related to the nonequilibrium growth that is evident from the presence of dendrites. An analysis of the dendritic growth instabilities is presented within the framework of the Ackerson-Schatzel equation.

Zhu, J. X.↗

Experimental Evaluation of Fatigue Crack Initiation from Corroded Hemispherical Notches in Aerospace Structural Materials

A test program was developed and executed to evaluate the influence of corroded hemispherical notches on the fatigue crack initiation and propagation in aluminum 7075-T7351, 4340 steel, and D6AC steel. Surface enhancements such as shot peening and laser shock peening were also incorporated as part of the test effort with the intent of improving fatigue performance. In addition to the testing, fracture mechanics and endurance limit based analysis methods were evaluated to characterize the results with the objective of challenging typical assumptions used in modeling fatigue cracks from corrosion pits. The results specifically demonstrate that the aluminum and steel alloys behave differently with respect to fatigue crack initiation from hemispherical corrosion pits. The aluminum test results were bounded by the fracture mechanics and endurance limit models while exhibiting a general insensitivity to the residual stress field generated by shot peening. The steel specimens were better characterized by the endurance limit fatigue properties and did exhibit sensitivities to residual stresses from the shot peening and laser shock peening

Garcia, Daniel B.↗

Orion GN&C Fault Management System Verification: Scope And Methodology

In order to ensure long-term ability to meet mission goals and to provide for the safety of the public, ground personnel, and any crew members, nearly all spacecraft include a fault management (FM) system. For a manned vehicle such as Orion, the safety of the crew is of paramount importance. The goal of the Orion Guidance, Navigation and Control (GN&C) fault management system is to detect, isolate, and respond to faults before they can result in harm to the human crew or loss of the spacecraft. Verification of fault management/fault protection capability is challenging due to the large number of possible faults in a complex spacecraft, the inherent unpredictability of faults, the complexity of interactions among the various spacecraft components, and the inability to easily quantify human reactions to failure scenarios. The Orion GN&C Fault Detection, Isolation, and Recovery (FDIR) team has developed a methodology for bounding the scope of FM system verification while ensuring sufficient coverage of the failure space and providing high confidence that the fault management system meets all safety requirements. The methodology utilizes a swarm search algorithm to identify failure cases that can result in catastrophic loss of the crew or the vehicle and rare event sequential Monte Carlo to verify safety and FDIR performance requirements.

Brown, Denise↗

GTOC9: Methods and Results from the Jet Propulsion Laboratory Team

The removal of 123 pieces of debris from the Sunsynchronous LEO environment is accomplished by a 10-spacecraft campaign wherein the spacecraft, flying in succession over an 8-yr period, rendezvous with a series of the debris objects, delivering a de-orbit package at each one before moving on to the next object by means of impulsive manoeuvres. This was the GTOC9 problem, as posed by the European Space Agency. The methods used by the Jet Propulsion Laboratory team are described, along with the winning solution found by the team. Methods include branch-and-bound searches that exploit the natural nodal drift to compute long chains of rendezvous with debris objects, beam searches for synthesising campaigns, ant colony optimisation, and a genetic algorithm. Databases of transfers between all bodies on a fine time grid are made, containing an easyto- compute yet accurate estimate of the transfer V . Lastly, a final non-linear programming optimisation is performed to ensure the trajectories meet all the constraints and are locally optimal in initial mass.

Sims, Jon↗

Evaluation of the MARVEL Reactor Inhalation Dose Consequences

A dose consequence analysis was performed to support the preliminary Microreactor Applications Research Validation and Evaluation Project (MARVEL) design effort. The purpose of the MARVEL project is to develop a nuclear microreactor applications test bed at Idaho National Laboratory (INL) to perform research and development on various operational features of microreactors to ultimately improve integration of microreactors to end-user applications. The MARVEL concept is a 100 kilowatt (kW) thermal (kWth) and approximately 20-kW electric (kWe) generating microreactor. The MARVEL system will be located in the INL TREAT facility in the north high-bay equipment pit. The analysis considers the bounding release fractions of the MARVEL reactor concept and documents the dose consequences to the public and collocated worker.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

ECAR-5127 Rev 1 Evaluation of the MARVEL Reactor Inhalation Dose Consequences

The following dose consequence analysis is performed to support the preliminary Microreactor Applications Research Validation and Evaluation Project (MARVEL) design effort. The purpose of the MARVEL project is to develop a nuclear microreactor applications test bed at Idaho National Laboratory (INL) to perform research and development on various operational features of microreactors to ultimately improve integration of microreactors to end-user applications. The MARVEL concept is a 100 kilowatt (kW) thermal (kWth) and approximately 20-kW electric (kWe) generating microreactor. The MARVEL system will be located in the INL TREAT facility in the north high-bay equipment pit. This ECAR considers the bounding release fractions of the MARVEL reactor concept and documents the dose consequences to the public and collocated worker.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

On the large eddy simulation of turbulent flows in complex geometry

Application of the method of Large Eddy Simulation (LES) to a turbulent flow consists of three separate steps. First, a filtering operation is performed on the Navier-Stokes equations to remove the small spatial scales. The resulting equations that describe the space time evolution of the 'large eddies' contain the subgrid-scale (sgs) stress tensor that describes the effect of the unresolved small scales on the resolved scales. The second step is the replacement of the sgs stress tensor by some expression involving the large scales - this is the problem of 'subgrid-scale modeling'. The final step is the numerical simulation of the resulting 'closed' equations for the large scale fields on a grid small enough to resolve the smallest of the large eddies, but still much larger than the fine scale structures at the Kolmogorov length. In dividing a turbulent flow field into 'large' and 'small' eddies, one presumes that a cut-off length delta can be sensibly chosen such that all fluctuations on a scale larger than delta are 'large eddies' and the remainder constitute the 'small scale' fluctuations. Typically, delta would be a length scale characterizing the smallest structures of interest in the flow. In an inhomogeneous flow, the 'sensible choice' for delta may vary significantly over the flow domain. For example, in a wall bounded turbulent flow, most statistical averages of interest vary much more rapidly with position near the wall than far away from it. Further, there are dynamically important organized structures near the wall on a scale much smaller than the boundary layer thickness. Therefore, the minimum size of eddies that need to be resolved is smaller near the wall. In general, for the LES of inhomogeneous flows, the width of the filtering kernel delta must be considered to be a function of position. If a filtering operation with a nonuniform filter width is performed on the Navier-Stokes equations, one does not in general get the standard large eddy equations. The complication is caused by the fact that a filtering operation with a nonuniform filter width in general does not commute with the operation of differentiation. This is one of the issues that we have looked at in detail as it is basic to any attempt at applying LES to complex geometry flows. Our principal findings are summarized.

Ghosal, Sandip↗

Bounds on galaxy stochasticity from halo occupation distribution modeling

The joint probability distribution of matter overdensity and galaxy counts in cells is a powerful probe of cosmology, and the extent to which variance in galaxy counts at fixed matter density deviates from Poisson shot noise is not fully understood. The lack of informed bounds on this stochasticity is currently the limiting factor in constraining cosmology with the galaxy–matter probability distribution function (PDF). We investigate stochasticity in the conditional distribution of galaxy counts along lines of sight with fixed matter density, and we present a halo occupation distribution (HOD)-based approach for obtaining plausible ranges for stochasticity parameters. To probe the high-dimensional space of possible galaxy–matter connections, we derive a set of HODs that conserve the galaxies’ linear bias and number density to produce RED M A G I C-like galaxy catalogs within the A BACUS S UMMIT suite of N -body simulations. We study the impact of individual HOD parameters and cosmology on stochasticity and perform a Monte Carlo search in HOD parameter space subject to the constraints on bias and density. In mock catalogs generated by the selected HODs, shot noise in galaxy counts spans both sub-Poisson and super-Poisson values, ranging from 80% to 133% of Poisson variance for cells with mean matter density. Nearly all of the derived HODs show a positive relationship between local matter density and stochasticity. For galaxy catalogs with higher stochasticity, modeling galaxy bias to second order is required for an accurate description of the conditional PDF of galaxy counts at fixed matter density. The presence of galaxy assembly bias also substantially extends the range of stochasticity in the super-Poisson direction. This HOD-based approach leverages degrees of freedom in the galaxy–halo connection to obtain informed bounds on nuisance model parameters and can be adapted to study other parametrizations of shot noise in galaxy counts, in particular to motivate prior ranges on stochasticity for cosmological analyses.

Britt, Dylan (ORCID:000000019905601X)↗

Dirichlet absorbing boundary conditions for classical and peridynamic diffusion-type models

Diffusion-type problems in (nearly) unbounded domains play important roles in various fields of fluid dynamics, biology, and materials science. The aim of this paper is to construct accurate absorbing boundary conditions (ABCs) suitable for classical (local) as well as nonlocal peridynamic (PD) diffusion models. The main focus of the present study is on the PD diffusion formulation. The majority of the PD diffusion models proposed so far are applied to bounded domains only. In this study, we propose an effective way to handle unbounded domains both with PD and classical diffusion models. For the former, we employ a meshfree discretization, whereas for the latter the finite element method (FEM) is employed. The proposed ABCs are time-dependent and Dirichlet-type, making the approach easy to implement in the available models. The performance of the approach, in terms of accuracy and stability, is illustrated by numerical examples in 1D, 2D, and 3D.

36 MATERIALS SCIENCE↗

Efficient proximal subproblem solvers for a nonsmooth trust-region method

In [R. J. Baraldi and D. P. Kouri, Mathematical Programming, (2022), pp. 1-40], we introduced an inexact trust-region algorithm for minimizing the sum of a smooth nonconvex and nonsmooth convex function. The principle expense of this method is in computing a trial iterate that satisfies the so-called fraction of Cauchy decrease condition—a bound that ensures the trial iterate produces sufficient decrease of the subproblem model. In this paper, we expound on various proximal trust-region subproblem solvers that generalize traditional trust-region methods for smooth unconstrained and convex-constrained problems. We introduce a simplified spectral proximal gradient solver, a truncated nonlinear conjugate gradient solver, and a dogleg method. Finally, we compare algorithm performance on examples from data science and PDE-constrained optimization.

97 MATHEMATICS AND COMPUTING↗

Jensen–Shannon divergence based novel loss functions for Bayesian neural networks

Bayesian neural networks (BNNs) are state-of-the-art machine learning methods that can naturally regularize and systematically quantify uncertainties using their stochastic parameters. Kullback–Leibler (KL) divergence-based variational inference used in BNNs suffer from unstable optimization and challenges in approximating light-tailed posteriors due to the unbounded nature of the KL divergence. To resolve these issues, we formulate a novel loss function for BNNs based on a new modification to the generalized Jensen–Shannon (JS) divergence, which is bounded. In addition, we propose a Geometric JS divergence-based loss, which is computationally efficient since it can be evaluated analytically. We found that the JS divergence-based variational inference is intractable, and hence employed a constrained optimization framework to formulate these losses. Our theoretical analysis and empirical experiments on multiple regression and classification data sets suggest that the proposed losses perform better than the KL divergence-based loss, especially when the data sets are noisy or biased. Specifically, there are approximately 5% and 8% improvements in accuracy for a noise-added CIFAR-10 dataset and a regression dataset, respectively. There is about 13% reduction in false negative predictions of a biased histopathology dataset. Additionally, we quantify and compare the uncertainty metrics for the regression and classification tasks.

97 MATHEMATICS AND COMPUTING↗