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At least 883 records · Page 49

Unconventional lignin monomers—Extension of the lignin paradigm

Lignin is largely produced by the oxidative radical coupling of the three monolignols, pcoumaryl, coniferyl, and sinapyl alcohols, which form the p-hydroxyphenyl, guaiacyl, and syringyl lignin units in the lignin polymer. However, it is increasingly appreciated that other “unconventional” phenolic compounds can also behave as lignin monomers participating in oxidative radical reactions during the lignification process and being also integrated into the lignin polymer in some plants. Various phenolic compounds have been found incorporated into the lignin, including phenolic compounds derived from the monolignol biosynthetic pathway (e.g., monolignol ester conjugates, caffeyl and 5-hydroxyconiferyl alcohols, hydroxycinnamaldehydes, among others). More fascinating still was the discovery in some plants of a series of phenolic compounds arising from other polyphenolic biosynthetic pathways, including flavonoids (tricin, dihydrotricin, naringenin, naringenin chalcone), hydroxystilbenes (resveratrol, piceatannol, and isorhapontigenin, and their O-glucosylated counterparts piceid, astringin, and isorhapontin), and ferulic acid amides (feruloyltyramine, and diferuloylputrescine), that are integrated into the lignin polymer. All of these discoveries indicate that the lignin structure is far more complex than previously thought, that the definition of lignin should not be restricted to a polymer derived solely from the three traditional monolignols, and that other unconventional lignin monomers must be considered, thus expanding the established definition of lignin. Here, the overriding factor remains, however, that lignification, the process of polymerization to the lignin polymer, allows this compositional flexibility because it is a simple chemical process.

59 BASIC BIOLOGICAL SCIENCES↗

Extensive nanoprecipitate morphology transformation in a nanostructured ferritic alloy due to extreme thermomechanical processing

Nano-oxide precipitates in a modern nanostructured ferritic alloy were investigated after extreme thermomechanical processing into a thin-walled tube geometry. It was found that the morphology of the precipitates changed from spherical to rod-shaped, with some increasing to aspect ratios of up to 9, despite the precipitate volume fraction (0.3%) and number density (> 10 23 m -3 ) of precipitates remaining unchanged. High-resolution electron microscopy showed that the precipitates likely remained coherent with the Fe-matrix, while atom probe tomography confirmed that the precipitate compositions remained unaffected by the transformation. The morphological change was attributed to the shearable nature of the (Y,Ti,O)-rich precipitates, indicating they should be considered as “soft” obstacles to dislocation motion. The elongation was most pronounced in larger (>5 nm) precipitates, which may be caused by preferential dissolution of the smallest (1–3 nm) precipitates followed by the competition between re-precipitation and solute diffusion to larger precipitates during recovery heat treatments.

36 MATERIALS SCIENCE↗

A Geometric Volume of Fluid-Based Multiphase Flow Solver Extension to the Reacting Flow Solver, PeleLM

A new algorithm is presented to simulate multiphase flows with surface tension in a pathway for spray combustion simulation. The algorithm combines capabilities from two open-source packages, including the interface reconstruction library (IRL), a library of computational geometry routines to enable the volume of fluid (VOF) method, and PeleLM, a solver for the reacting Navier-Stokes equations. Additionally, surface tension is implemented using the continuum surface force (CSF) model with an improved height function technique in the volume fraction field. Spurious errors in volume fraction arising from our combined strategy are corrected through a topology-based method that improves both numerical stability and accuracy. Multiple validation simulations are conducted, including (i) translations and rotations of Zalesak's disk, (ii) a stationary circular droplet with surface tension, (iii) an oscillating elliptical droplet, and (iv) three-dimensional deformation of a spherical droplet. Results indicate that the combined scheme retains the favorable properties of each of the component algorithms.

42 ENGINEERING↗

An extension of Darcy’s law incorporating dynamic length scales

We propose a physics-based, macroscale formulation of multiphase porous-media flows that both honors the validity of Darcy’s law in steady or near-steady flows and accommodates the effects of heterogeneities and nonlinearities in unsteady flows. The new formulation recognizes that parameters characterizing the system operate at different length-scales. In particular, the use of Darcy’s law, predicated on the assumption of near-steady flows, requires dynamic length scales, owing to the possibility of rapid fluctuations in rock properties and fluid saturations attributable to heterogeneity and nonlinearity. We accommodate these dynamic length-scales through dynamic spatial averaging. The length and position of the averaging window are characterized by the length of the mixing zone and the direction of propagation of information in the transport process. Here, we validate the proposed formulation by comparing highly accurate,two dimensional numerical solutions against core-scale displacement experiments. The proposed paradigm is consistent with the classical multiphase Darcy formulation, in the sense that the latter also represents the results of an averaging approach.

42 ENGINEERING↗

Extension of SCALE/Sampler’s sensitivity analysis

Nuclear data are a major source of uncertainties in reactor physics calculations. The propagation of nuclear data uncertainties to important system responses is instrumental when determining appropriate safety margins in reactor safety analyses. It is also important to understand the major contributors to the observed uncertainties to make recommendations for further measurements and evaluations and aid in the understanding of the studied system. The SCALE code system allows for nuclear data uncertainty analysis based on the random sampling approach as implemented in SCALE’s Sampler sequence. Sampler was recently extended by a sensitivity analysis in terms of the calculation of two correlation-based sensitivity indices. This analysis allows for the identification of the top contributing nuclear reactions to any analyzed output uncertainty. This paper presents the sensitivity indices, along with their interpretation and limitations. It demonstrates the application in an eigenvalue and decay heat analysis for a boiling water reactor fuel assembly.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Extension of the discrete generalized multigroup method using SPH factors

The discrete generalized multigroup (DGM) method provides a way to treat the energy dependence of neutron transport similarly to the standard multigroup approximation. However, DGM uses an orthogonal basis to retain the energy dependence in higher-order terms. Using correction factors similar to traditional Superhomogénéisation (SPH) factors, the DGM method may be extended to produce cross sections that are homogenized over both space and energy. Additionally, since some fine-group energy dependence is retained, the resulting homogenized cross sections are more problem-independent than cross sections homogenized by SPH factors alone. In particular, a 44-group set of cross sections is collapsed to approximately a 1% error in the pincell fission densities for a test problem using three DOF per coarse energy group.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Scattering amplitudes for multi-indexed extensions of solvable potentials

New solvable one-dimensional quantum mechanical scattering problems are presented. They are obtained from known solvable potentials by multiple Darboux transformations in terms of virtual and pseudo virtual wavefunctions. The same method applied to confining potentials, e.g. Pöschl–Teller and the radial oscillator potentials, has generated the multi-indexed Jacobi and Laguerre polynomials. Simple multi-indexed formulas are derived for the transmission and reflection amplitudes of several solvable potentials. -- Highlights: •Scattering amplitudes calculated for infinitely many new solvable potentials. •New scattering potentials obtained by deforming six known solvable potentials. •Multiple Darboux transformations in terms of (pseudo) virtual states employed. •Scattering amplitudes checked to obey the shape invariance relation. •Errors in scattering amplitudes of some undeformed potentials in the literature corrected.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Phenomenology of SUGRA extensions of the Starobinsky model

We analyze BI-extended model in a complete form and compare the predictions with that of Starobinsky model. Under the parameter constraints in Planck 2018, we find that the dynamics of the whole inflation process described by BI-extended and Starobinsky models are nearly the same, even though there are some differences in the regions out of inflation. We also find the scales of parameters in BI-extended model and inflaton values at the first horizon crossing required to implement inflation. The changes of (n{sub s},r) fingerprints of BI-extended model and that of evolutions of inflaton field due to the variations of relevant parameters are also investigated.

79 ASTRONOMY AND ASTROPHYSICS↗

Muscle spindles exhibit core lesions and extensive degeneration of intrafusal fibers in the Ryr1{sup I4895T/wt} mouse model of core myopathy

Muscle spindles from the hind limb muscles of adult Ryr1{sup I4895T/wt} (IT/+) mice exhibit severe structural abnormalities. Up to 85% of the spindles are separated from skeletal muscle fascicles by a thick layer of connective tissue. Many intrafusal fibers exhibit degeneration, with Z-line streaming, compaction and collapse of myofibrillar bundles, mitochondrial clumping, nuclear shrinkage and pyknosis. The lesions resemble cores observed in the extrafusal myofibers of this animal model and of core myopathy patients. Spindle abnormalities precede those in extrafusal fibers, indicating that they are a primary pathological feature in this murine Ryr1-related core myopathy. Muscle spindle involvement, if confirmed for human core myopathy patients, would provide an explanation for an array of devastating clinical features characteristic of these diseases and provide novel insights into the pathology of RYR1-related myopathies. - Highlights: • Muscle spindles exhibit structural abnormalities in a mouse model of core myopathy. • Myofibrillar collapse and mitochondrial clumping is observed in intrafusal fibers. • Myofibrillar degeneration follows a pattern similar to core formation in extrafusal myofibers. • Muscle spindle abnormalities are a part of the pathological phenotype in the mouse model of core myopathy. • Direct involvement of muscle spindles in the pathology of human RYR1-related myopathies is proposed.

60 APPLIED LIFE SCIENCES↗

Interpretable, extensible linear and symbolic regression models for charge density prediction using a hierarchy of many-body correlation descriptors

Here, density functional theory (DFT) is routinely used to make electronic structure predictions for high-throughput screening of materials and molecules for technologically relevant areas, like the identification of better catalysts, electronic materials, and drug discovery. However, the DFT formalism is limited by (a) its poor (quadratic-to-quartic) scaling, and (b) the need to perform repeated eigenvalue computations of the electronic Hamiltonian as part of its self-consistent field (SCF) iteration procedure to obtain the converged ground state electron density, ρ (r). Approaches that directly predict ρ (r) of a structure with high accuracy can accelerate conventional SCF calculations and can also be used in linearly scaling methods such as orbital-free DFT. To this end, we present a procedure to predict the ground state electron density of molecular and periodic three-dimensional systems directly from the atomic structure with a particular emphasis on physical interpretability. In our framework, ρ (r) is modeled using many-body correlation descriptors that accurately capture the effects of local atomic arrangements in the neighborhood of a grid point. Our use of a linear regression scheme to fit to charge density data enables transparent analysis of the relative contributions of various types of local atomic correlations. By systematically including increasingly complex correlations, our model is shown to accurately predict ρ (r) for a variety of chemically and electronically diverse systems — amorphous Ge, Al(001) slab, crystalline Ga 2 O 3 , molecular benzene, and polyethylene. We then demonstrate a symbolic regression-based protocol to construct easily computable, interpretable features from lower-order correlations that significantly improves our electron density predictions with effectively no increase in the computational cost.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An extensible simulation environment and movement metrics for testing walking behavior in agent-based models

Human movement is a significant ingredient of many social, environmental, and technical systems, yet the importance of movement is often discounted in considering systems complexity. Movement is commonly abstracted in agent-based modeling (which is perhaps the methodological vehicle for modeling complex systems), despite the influence of movement upon information exchange and adaptation in a system. In particular, agent-based models of urban pedestrians often treat movement in proxy form at the expense of faithfully treating movement behavior with realistic agency. There exists little consensus about which method is appropriate for representing movement in agent-based schemes. In this paper, we examine popularly-used methods to drive movement in agent-based models, first by introducing a methodology that can flexibly handle many representations of movement at many different scales and second, introducing a suite of tools to benchmark agent movement between models and against real-world trajectory data. We find that most popular movement schemes do a relatively poor job of representing movement, but that some schemes may well be 'good enough' for some applications. We also discuss potential avenues for improving the representation of movement in agent-based frameworks.

99 GENERAL AND MISCELLANEOUS↗

Extension of Landau-fluid closure to weakly collisional plasma regime

Both collisionless and collisional Landau fluid (LF) closure have been developed and implemented in two-fluid plasma simulation framework BOUT++, taking full advantage of the fast non-Fourier method (Dimits, 2014). The spectral range of good fit can be conveniently extended to larger domain by adding more Lorentzians. The scaling for upper limit of wavenumber resolved in collisionless LF operator and the fitting coefficients for the collisional LF operator, the later is extended to weakly collisional regime (ν$^{*}_{e}$ ~ 0.01), are presented in this paper. The flux limited expression q$^{FL}_{∥e}$ is reduced to free streaming expression q$^{FS}_{∥e}$ in collisionless limit and gives classical Spitzer–Härm result q$^{SH}_{∥e}$ in collisional limit as we expected. The collisional LF closure recovers the classical Spitzer–Härm result q$^{SH}_{∥e}$ in collisional limit and is same as the collisionless LF closure in collisionless limit. The test cases also obviously reflect the nonlocal effects from LF closures and responding to different boundary conditions in open surface region. Our report will make it more applicable and possible to include the Landau damping kinetic effect in the fluid simulation of tokamak plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Adaptive Hybridizable Discontinuous Galerkin discretization of the Grad–Shafranov equation by extension from polygonal subdomains

In this work, we propose a high-order adaptive numerical solver for the semilinear elliptic boundary value problem modeling magnetic plasma equilibrium in axisymmetric confinement devices. In the fixed boundary case, the equation is posed on curved domains with piecewise smooth curved boundaries that may present corners. The solution method we present is based on the hybridizable discontinuous Galerkin method and sidesteps the need for geometry-conforming triangulations thanks to a transfer technique that allows to approximate the solution using only a polygonal subset as computational domain. Moreover, the solver features automatic mesh refinement driven by a residual-based a posteriori error estimator. As the mesh is locally refined, the computational domain is automatically updated in order to always maintain the distance between the actual boundary and the computational boundary of the order of the local mesh diameter. Numerical evidence is presented of the suitability of the estimator as an approximate error measure for physically relevant equilibria with pressure pedestals, internal transport barriers, and current holes on realistic geometries.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗