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At least 577 records · Page 32

On Master-Length Scale Formulations for Stable Conditions in Turbulence Closure Models

Three formulations of the turbulence-length scales used in numerical modelling of atmospheric flows are compared. The comparison is made using the Mellor–Yamada–Nakanishi–Niino turbulence closure model within the stable boundary layer local similarity framework. With an appropriate choice of model constants, the model predictions are barely discernible and compare well with the empirical data obtained from the SHEBA campaign.

54 ENVIRONMENTAL SCIENCES↗

Closure of Earth’s Global Seasonal Cycle of Energy Storage

Abstract The global seasonal cycle of energy in Earth’s climate system is quantified using observations and reanalyses. After removing long-term trends, net energy entering and exiting the climate system at the top of the atmosphere (TOA) should agree with the sum of energy entering and exiting the ocean, atmosphere, land, and ice over the course of an average year. Achieving such a balanced budget with observations has been challenging. Disagreements have been attributed previously to sparse observations in the high-latitude oceans. However, limiting the local vertical integration of new global ocean heat content estimates to the depth to which seasonal heat energy is stored, rather than integrating to 2000 m everywhere as done previously, allows closure of the global seasonal energy budget within statistical uncertainties. The seasonal cycle of energy storage is largest in the ocean, peaking in April because ocean area is largest in the Southern Hemisphere and the ocean’s thermal inertia causes a lag with respect to the austral summer solstice. Seasonal cycles in energy storage in the atmosphere and land are smaller, but peak in July and September, respectively, because there is more land in the Northern Hemisphere, and the land has more thermal inertia than the atmosphere. Global seasonal energy storage by ice is small, so the atmosphere and land partially offset ocean energy storage in the global integral, with their sum matching time-integrated net global TOA energy fluxes over the seasonal cycle within uncertainties, and both peaking in April.

54 ENVIRONMENTAL SCIENCES↗

OsPRX2 contributes to stomatal closure and improves potassium deficiency tolerance in rice

Highlights: • The function of 2-Cys Prxs in rice associated with potassium deficiency tolerance is presented. • OsPRX2 contributes to stomatal closure and improves potassium deficiency tolerance is proposed. • OsPRX2 may be a good candidate to improve K{sup +} efficient tolerance in rice. Peroxiredoxins (Prxs) which are thiol-based peroxidases have been implicated in the toxic reduction and intracellular concentration regulation of hydrogen peroxide. In Arabidopsis thaliana At2-CysPrxB (At5g06290) has been demonstrated to be essential in maintaining the water-water cycle for proper H{sub 2}O{sub 2} scavenging. Although the mechanisms of 2-Cys Prxs have been extensively studied in Arabidopsis thaliana, the function of 2-Cys Prxs in rice is unclear. In this study, a rice homologue gene of At2-CysPrxB, OsPRX2 was investigated aiming to characterize the effect of 2-Cys Prxs on the K{sup +}-deficiency tolerance in rice. We found that OsPRX2 was localized in the chloroplast. Overexpressed OsPRX2 causes the stomatal closing and K{sup +}-deficiency tolerance increasing, while knockout of OsPRX2 lead to serious defects in leaves phenotype and the stomatal opening under the K{sup +}-deficiency tolerance. Detection of K{sup +} accumulation, antioxidant activity of transgenic plants under the starvation of potassium, further confirmed that OsPRX2 is a potential target for engineering plants with improved potassium deficiency tolerance.

60 APPLIED LIFE SCIENCES↗

An arc-length method for controlled cohesive crack propagation using high-order XFEM and Irwin’s crack closure integral

Numerical modeling of cohesive crack growth in quasi-brittle materials is challenging, primarily due to the combination of (i) nonlinearity associated with the fracture process zone (FPZ), (ii) arbitrary directions to which a crack may propagate, and (iii) snap-back or snap-through instabilities encountered in the response of the structure. To address these challenges, here we propose a novel arc-length method that can follow the equilibrium path of cohesive crack propagation. The proposed approach is based on the extended finite element method (XFEM) with scalar high-order enrichment functions and Irwin’s crack closure integral, which allows for direct control of the applied loads necessary to propagate cohesive cracks. This is achieved by augmenting a constraint equation written in terms of stress intensity factors (SIFs), and expressed explicitly in terms of the enriched degrees of freedom, which is an attractive feature achieved with Irwin’s integral, since SIFs can be written in closed-form. Note that singular enrichments are active in an unstable crack propagation state and automatically vanish in stable crack configurations. Furthermore, to propagate cracks in arbitrary directions, we employ a maximum circumferential stress criterion implemented by (i) direct usage of the SIFs, and by (ii) a new stress-based nonlocal implementation of this principle. Various benchmark problems including pure mode I and mixed-mode fracture are solved to demonstrate the predictive capability of the present framework for cohesive crack modeling.

42 ENGINEERING↗

Exact PDF equations and closure approximations for advective-reactive transport

Mathematical models of advection–reaction phenomena rely on advective flow velocity and (bio) chemical reaction rates that are notoriously random. By using functional integral methods, we derive exact evolution equations for the probability density function (PDF) of the state variables of the advection–reaction system in the presence of random transport velocity and random reaction rates with rather arbitrary distributions. These PDF equations are solved analytically for transport with deterministic flow velocity and a linear reaction rate represented mathematically by a heterog eneous and strongly-correlated random field. Our analytical solution is then used to investigate the accuracy and robustness of the recently proposed large-eddy diffusivity (LED) closure approximation [1]. We find that the solution to the LED-based PDF equation, which is exact for uncorrelated reaction rates, is accurate even in the presence of strong correlations and it provides an upper bound of predictive uncertainty.

PDF methods, Uncertainty quantification, Heterogen↗

Analytical closure to the spatially-filtered Euler equations for shock-dominated flows

To ensure numerical stability in the vicinity of shocks, a variety of methods have been used, including shock-capturing schemes such as weighted essentially non-oscillatory schemes, as well as the addition of artificial diffusivities to the governing equations. Centered finite difference schemes are often avoided near discontinuities due to the tendency for significant oscillations. However, such schemes have desirable conservation properties compared to many shock-capturing schemes. The objective of this work is to derive all necessary viscous/diffusion terms from first principles and then demonstrate the performance of these analytical terms within a centered differencing framework. The physical Euler equations are spatially-filtered with a Gaussian-like filter. Sub-filter scale (SFS) terms arise in the momentum and energy equations. Analytical closure is provided for each of them by leveraging the jump conditions for a shock. No SFS terms are present in the continuity or species equations. Here, this approach is tested for several problems involving shocks in one and two dimensions. Implemented within a centered difference code, the SFS terms perform well for a range of flow conditions without introducing excessive diffusion.

97 MATHEMATICS AND COMPUTING↗

No evidence of a reduction in the dipole polarisability at shell closures

Photoabsorption reactions have a long and productive history as probes of the response of nuclei to electromagnetic fields. In recent years, there has been a suggestion that the dipole polarisability may be reduced at shell closures, potentially due to the reduced level density. In the current paper, more recent photoabsorption strengths are reanalysed including nuclei on closed proton shells to search for a similar reduction. The previously reported reduction is not reproduced. We conclude that the previously observed reduction may be due to incomplete evaluations of the photoabsorption due to missing cross section contributions and experimental artefacts. More experimental data are necessary to draw a firm conclusion about whether shell effects persist into high excitation energies, especially data which can obviate any systematic effects and look at relative photoabsorption strengths between nuclei.

Giant dipole response↗

Deep learning closure models for large-eddy simulation of flows around bluff bodies

Near-wall flow simulation remains a central challenge in aerodynamics modelling: Reynolds-averaged Navier–Stokes predictions of separated flows are often inaccurate, and large-eddy simulation (LES) can require prohibitively small near-wall mesh sizes. A deep learning (DL) closure model for LES is developed by introducing untrained neural networks into the governing equations and training in situ for incompressible flows around rectangular prisms at moderate Reynolds numbers. The DL-LES models are trained using adjoint partial differential equation (PDE) optimization methods to match, as closely as possible, direct numerical simulation (DNS) data. They are then evaluated out-of-sample – for aspect ratios, Reynolds numbers and bluff-body geometries not included in the training data – and compared with standard LES models. The DL-LES models outperform these models and are able to achieve accurate LES predictions on a relatively coarse mesh (downsampled from the DNS mesh by factors of four or eight in each Cartesian direction). We study the accuracy of the DL-LES model for predicting the drag coefficient, near-wall and far-field mean flow, and resolved Reynolds stress. A crucial challenge is that the LES quantities of interest are the steady-state flow statistics; for example, a time-averaged velocity component $\langle {u}_i\rangle (x) = \lim _{t \rightarrow \infty } ({1}/{t}) \int _0^t u_i(s,x)\, {\rm d}s$ . Calculating the steady-state flow statistics therefore requires simulating the DL-LES equations over a large number of flow times through the domain. It is a non-trivial question whether an unsteady PDE model with a functional form defined by a deep neural network can remain stable and accurate on $t \in [0, \infty )$ , especially when trained over comparatively short time intervals. Our results demonstrate that the DL-LES models are accurate and stable over long time horizons, which enables the estimation of the steady-state mean velocity, fluctuations and drag coefficient of turbulent flows around bluff bodies relevant to aerodynamics applications.

Mechanics↗

Methods for Carbon Mass Closure in Polyolefin Hydrocracking

Heterogeneous catalytic hydrocracking of polyolefins is a promising approach for the processing of postconsumer plastics, but product quantification methods remain inconsistent across the literature. In systems that generate a large fraction of vapor-phase products, typical product capture methods can result in large carbon balance deficits, exceeding 50%, compromising reported yields and selectivities. Here, we identify the major sources of product loss and develop enhanced capture methods to improve the quantification accuracy. Seven supplemental techniques were evaluated, targeting either increased vapor recovery (by increasing the volatility or system volume) or enhanced retention in the liquid phase (by decreasing volatility). Among these, a flow collection approach using a continuous helium sweep and downstream gas sampling bag capture yielded the highest recovery, achieving a 96 ± 9.2% carbon balance closure. We show that the efficacy of these methods is strongly dependent on product distribution. In general, solvent addition was most effective when condensable species dominate the product distribution, while flow collection was preferred when both condensable species and light gases are present in high concentrations. These results highlight the need for method-specific workup strategies and demonstrate that no single protocol is universally optimal. We provide general guidelines for selecting and implementing robust product capture techniques, enabling accurate yield and selectivity determinations in polyolefin hydrocracking systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Validation of anisotropic electron fluid closure through in situ spacecraft observations of magnetic reconnection

A valid fluid model for electrons in collisionless space plasmas is desirable for understanding the structure and evolution of magnetic reconnection geometries. Additionally, such a fluid model would be useful for the simulation of systems too large to be tractable in a fully-kinetic model. Using MMS spacecraft observations, we provide direct confirmation of the Le 2009 equations of state for the electron pressure tensor during guide field reconnection and demonstrate how the closure can be applied in efficient numerical simulation, yielding new physical insight to the electron heating problem. Furthermore, we use the Le 2009 equations of state to predict a scaling of electron heating in the exhaust comparable to the available observational data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Nonequilibrium Thermodynamic Approach for Surface Energy Balance Closure

Abstract The surface energy imbalance, viz. that the turbulent dissipation does not fully account for available energy, has for long been an outstanding challenge in geophysical studies. In this study, we developed a novel approach based on nonequilibrium thermodynamics by representing the atmospheric boundary layer as a heat engine. In addition, an analytically tractable approach was used to estimate the ground heat flux based on Green's function approach, which in turn determines the available energy that drives the atmospheric heat engine. The proposed model was evaluated using heat fluxes measured by eight AmeriFlux eddy covariance towers with atmospheric temperature profiles recorded at adjacent radiosonde sites. The surface energy balance closure can be improved by ~11% over various landscapes, by including the estimated power production from the atmospheric heat engine.

Li, Peiyuan↗

Improving Time Step Convergence in an Atmosphere Model With Simplified Physics: The Impacts of Closure Assumption and Process Coupling

Convergence testing is a common practice in the development of dynamical cores of atmospheric models but is not as often exercised for the parameterization of sub-grid physics. An earlier study revealed that the stratiform cloud parameterizations in several predecessors of the Energy Exascale Earth System Model (E3SM) showed strong time-step sensitivity and slower-than-expected convergence when the model's time step was systematically refined. In this work, a simplified atmosphere model is configured that consists of the spectral-element dynamical core of the E3SM atmosphere model coupled with a large-scale condensation parameterization based on commonly used assumptions. This simplified model also resembles E3SM and its predecessors in the numerical implementation of process coupling and shows poor time-step convergence in short ensemble tests. We present a formal error analysis to reveal the expected time-step convergence rate and the conditions for obtaining such convergence. Numerical experiments are conducted to investigate the root causes of convergence problems. We show that revisions in the process coupling and closure assumption help to improve convergence in short simulations using the simplified model; the same revisions applied to a full atmosphere model lead to significant changes in the simulated long-term climate. This work demonstrates that causes of convergence issues in atmospheric simulations can be understood by combining analyses from physical and mathematical perspectives. Addressing convergence issues can help to obtain a discrete model that is more consistent with the intended representation of the physical phenomena.

54 ENVIRONMENTAL SCIENCES↗

Band gap closure, incommensurability and molecular dissociation of dense chlorine

Diatomic elemental solids are highly compressible due to the weak interactions between molecules. However, as the density increases the intra- and intermolecular distances become comparable, leading to a range of phenomena, such as structural transformation, molecular dissociation, amorphization, and metallisation. Here we report, following the crystallization of chlorine at 1.15(30) GPa into an ordered orthorhombic structure (oC8), the existence of a mixed-molecular structure (mC8, 130(10)–241(10) GPa) and the concomitant observation of a continuous band gap closure, indicative of a transformation into a metallic molecular form around 200(10) GPa. The onset of dissociation of chlorine is identified by the observation of the incommensurate structure (i-oF4) above 200(10) GPa, before finally adopting a monatomic form (oI2) above 256(10) GPa.

74 ATOMIC AND MOLECULAR PHYSICS↗

Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism

The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.

59 BASIC BIOLOGICAL SCIENCES↗

Bowing to ferroelectric artificial flux closure

Here by inserting an epitaxial in-plane buffer layer of Bi 5 FeTi 3 O 15 , an artificial flux closure architecture enables ferroelectric polarization from a single unit cell of BaTiO 3 or BiFeO 3 .

36 MATERIALS SCIENCE↗

Increased water availability at various timescales has different effects on stomatal closure point in isohydric piñon pine and anisohydric juniper

Abstract Stomatal Closure Point (SCP) has commonly been used to describe drought response strategies in plants, with isohydric species maintaining relatively high, constant SCP compared to anisohydric species that can lower SCP with increasing drought severity. However, there is evidence that, within these groups, SCP may respond dynamically to environmental conditions. Here, we explored how increasing water availability affects SCP in classically isohydric piñon pine and anisohydric one-seed or Utah juniper at various spatial- (i.e., from branch, to tree, to ecosystem) and temporal- (i.e., hours to decades) scales. Our results show that short-term increases in water availability decreased SCP in isohydric piñon pine, making it more anisohydric, while short-term rehydration had no effect on SCP in anisohydric juniper. Increasing mean annual precipitation, on the other hand, increased SCP in both species. Our findings are consistent with documented differences in the use of ABA to control stomata in iso- and aniso-hydric species on short timescales, and with structural acclimation in both species at long timescales. These results illustrate that the local environment plays a large role in determining SCP.

Kraklow, Vachel↗