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At least 379 records · Page 21

Loamy sand soil approaches organic carbon saturation after 37 years of conservation tillage

Conservation tillage is reported to increase soil organic carbon (SOC) and total nitrogen (TN) contents, but long-term (>30 yr) field results quantifying the responses in Coastal Plain Ultisols are sparse. The distribution, accumulation, and topsoil storage of SOC and TN after 37 yr of crop production using conventional (CvT) or conservation tillage (CnT) on a Norfolk loamy sand (fine-loamy, kaolinitic, thermic, Typic Kandiudults) were quantified. Soil samples were collected annually from the 0-5-, 5-10-, and 10-15-cm depth increments beneath corn (Zea mays L.), soybean [Glycine max (L.) Merr.], and cotton (Gossypium hirsutum L.) crops. Overall, SOC and TN accumulation in the 0-5-cm depth were highest for Norfolk soil under CnT. Focusing on total long-term changes for the 0-15-cm sampling depth beneath various corn crops shows that CnT and CvT sequestered 24.7 and 21.4 Mg C ha -1 , respectively. Between 1978 and 2016, there was a highly significant (P < .0001) exponential increase in SOC within the top 5-cm soil depth. However, the exponential curves began to plateau suggesting the Norfolk topsoil was approaching its organic carbon (OC) storage capacity. These field measurements strongly indicate that additional topsoil SOC increases with current tillage and crop management practices are limited.

54 ENVIRONMENTAL SCIENCES↗

Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii , Arabidopsis thaliana , and Setaria viridis

Abstract The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome‐wide protein‐coding gene annotation. A substantial fraction of protein‐coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): Arabidopsis thaliana (eudicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high‐value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.

59 BASIC BIOLOGICAL SCIENCES↗

Exact solution for the non-equilibrium attractor in number-conserving relaxation time approximation

We extend previous studies of the conformal 0+1d kinetic non-equilibrium attractor in relaxation time approximation by enforcing number conservation through the introduction of a dynamical fugacity (chemical potential). We derive two coupled integral equations for the effective temperature and fugacity which are then solved numerically to obtain the exact solution. The resulting solutions exhibit convergence to a unique nonequilibrium attractor when the scaled moments of the distribution function are plotted as a function of the rescaled time w = τ /τeq. This occurs even though the system is out of chemical equilibrium at late times. In addition, compared to the case where number conservation was not imposed, we find that the moments converge to their respective attractors more quickly, particularly for moments with m = 0. Finally, we compare the resulting attractor moments with predictions from different hydrodynamic frameworks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Archeological wood conservation with selected organosilicon compounds studied by XFM and nanoindentation

Waterlogged wood conservation is a complex and challenging task. Detailed knowledge about the interactions between the applied chemicals and wood is necessary to ensure the effective and safe conservation of wooden artifacts. The present research aims to determine the mechanism of dimensional stabilization of archeological wood by organosilicon compounds using the combination of synchrotron-based X-ray fluorescence microscopy (XFM) and nanoindentation. Archeological oak wood was treated with methyltrimethoxysilane, (3-mercaptopropyl)trimethoxysilane, or 1,3-bis-[(diethylamino)-3-(propoxy)propan-2-ol]-1,1,3,3-tetramethyldisiloxane, which in previous studies were found to be more effective than other organosilicons in stabilizing wood dimensions. The XFM and nanoindentation results showed that all three organosilicons infiltrated wood cell walls and enhanced their mechanical properties. The XFM also showed that part of the chemicals filled some void spaces like cell lumina. Based on the results obtained here and in our previous research, it is determined that the mechanism of archeological wood dimensional stabilization by organosilicon treatment is complex and likely involves both filling cell lumina and infiltration into cell walls where organosilicons interact with wood polymers.

59 BASIC BIOLOGICAL SCIENCES↗

Density Large Deviations for Multidimensional Stochastic Hyperbolic Conservation Laws

We investigate the density large deviation function for a multidimensional conservation law in the vanishing viscosity limit, when the probability concentrates on weak solutions of a hyperbolic conservation law. When the mobility and diffusivity matrices are proportional, i.e. an Einstein-like relation is satisfied, the problem has been solved in Bellettini and Mariani (Bull Greek Math Soc 57:31–45, 2010). When this proportionality does not hold, we compute explicitly the large deviation function for a step-like density profile, and we show that the associated optimal current has a non trivial structure. We also derive a lower bound for the large deviation function, valid for a more general weak solution, and leave the general large deviation function upper bound as a conjecture.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cone-grid scheme for solving hyperbolic systems of conservation laws and one application

In this work, we introduce a new numerical method, the so-called cone-grid scheme for solving hyperbolic systems of conservation laws. The formulation and the theoretical analysis for this scheme are slightly simpler than other algorithms. Simultaneously, our technique leads to a more efficacious numerical scheme. The Riemann solution is the basic ingredient for this scheme. We also give the main application of this technique, namely the global weak solutions for the one-dimensional model prescribes heat conduction in solids at low temperature, which called phonon–Bose model. This system consists of a conservation equation for the energy density and the heat flux. The scheme also satisfies positivity. The cone-grid scheme was compared with exact solution by three numerical examples, where explicit solutions are known. These numerical results verify the accuracy of the proposed scheme qualitatively and quantitatively.

97 MATHEMATICS AND COMPUTING↗

Current-conserving relativistic linear response for collisional plasmas

Here we investigate the response of a relativistic plasma to electromagnetic fields in the framework of the Boltzmann equation incorporating a collision term in the relaxation rate approximation selected in a form assuring current conservation. We obtain an explicit solution for the linearized perturbation of the Fermi–Dirac equilibrium distribution in terms of the average relaxation rate k. We study the resulting covariant, gauge invariant, and current conserving form of the polarization tensor in the ultrarelativistic and non-relativistic limits. We evaluate the susceptibility in the ultrarelativistic limit and explore their dependence on k. Finally, we study the dispersion relations for the longitudinal and transverse poles of the propagator. We show that for k >2ω p , where ω p is the plasma frequency, the plasma wave modes are overdamped. In the opposite case, k$\ll$ ω p , the propagating plasma modes are weakly damped.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Renewable energy and biological conservation in a changing world

Without a shift to renewable energy sources, climate change will have adverse effects on many terrestrial and aquatic species. On the other hand, replacing fossil fuels with renewable energy will have different effects on wildlife, some negative. To protect biota, while navigating the complexities surrounding the transition to renewable energy, will require sharing knowledge between energy experts and wildlife experts, as well as policy makers and resource managers. This special issue is intended to advance the conversation. Interactions between renewable energy facilities and fauna are complex. Each source of renewable energy has its own conservation concerns, and each presents its own set of opportunities for mitigation; Other concerns and mitigations are shared. In this overview, we review climate risks to biota, clarify the complementarities among renewables for the conservation community, and summarize research on energy effects on biota for the energy community. The papers invited for this special issue address fossil (coal, oil, natural gas) and renewable energy (terrestrial biomass energy, hydropower, marine-hydrokinetic energy, wind energy, solar energy) and affected fauna. Finally, we hope that the results of these studies, and others like them, set us on a path toward low-carbon energy systems that provide society with energy while protecting future biodiversity.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

ECsim-CYL: Energy Conserving Semi-Implicit particle in cell simulation in axially symmetric cylindrical coordinates

Based on the previously developed Energy Conserving Semi Implicit Method (ECsim) code, we present its cylindrical implementation, called ECsim-CYL, to be used for axially symmetric problems. The main motivation for the development of the cylindrical version is to greatly improve the computational speed by utilizing cylindrical symmetry. The ECsim-CYL discretizes the field equations in two-dimensional cylindrical coordinates using the finite volume method. For the particle mover, it uses a modification of ECsim’s mover for cylindrical coordinates by keeping track of all three components of velocity vectors, while only keeping radial and axial coordinates of particle positions. In this paper, we describe the details of the algorithm used in the ECsim-CYL and present a series of tests to validate the accuracy of the code including a wave spectrum in a homogeneous plasma inside a cylindrical waveguide and free expansion of a spherical plasma ball in vacuum. Finally, the ECsim-CYL retains the stability properties of ECsim and conserves the energy within machine precision, while accurately describing the plasma behavior in the test cases.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

EZ: An efficient, charge conserving current deposition algorithm for electromagnetic particle-in-cell simulations

Here, we present EZ, a novel current deposition algorithm for particle-in-cell (PIC) simulations. EZ calculates the current density on the electromagnetic grid due to macro-particle motion within a time step by solving the continuity equation of electrodynamics. Being a charge conserving hybridization of Esirkepov's method and ZigZag, we refer to it as “EZ” as shorthand for “Esirkepov meets ZigZag”. Simulations of a warm, relativistic plasma with PIConGPU show that EZ achieves the same level of charge conservation as the commonly used method by Esirkepov, yet reaches higher performance for macro-particle assignment-functions up to third-order. In addition to a detailed description of the functioning of EZ, reasons for the expected and observed performance increase are given, and guidelines for its implementation aiming at highest performance on GPUs are provided.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

An arbitrary-order Runge–Kutta discontinuous Galerkin approach to reinitialization for banded conservative level sets

Here, we present a Runge-Kutta discontinuous Galerkin method for solving conservative reinitialization in the context of the conservative level set method. This represents an extension of the method recently proposed by Owkes and Desjardins [21], by solving the level set equations on the refined level set grid and projecting all spatially-dependent variables into the full basis used by the discontinuous Galerkin discretization. By doing so, we achieve the full k+1 order convergence rate in the L1 norm of the level set field predicted for RKDG methods given kth degree basis functions when the level set profile thickness is held constant with grid refinement. Shape and volume errors for the 0.5-contour of the level set, on the other hand, are found to converge between first and second order. We show a variety of test results, including the method of manufactured solutions, reinitialization of a circle and sphere, Zalesak's disk, and deforming columns and spheres, all showing substantial improvements over the high-order finite difference traditional level set method studied for example by Herrmann. We also demonstrate the need for kth order accurate normal vectors, as lower order normals are found to degrade the convergence rate of the method.

97 MATHEMATICS AND COMPUTING↗

Conservative fourth-order finite-volume Vlasov–Poisson solver for axisymmetric plasmas in cylindrical (r,v r ,v θ ) phase space coordinates

In this paper, a fourth-order finite-volume Vlasov–Poisson algorithm is developed for simulating axisymmetric plasma configurations in ( r , v r , v θ ) phase space coordinates. The Vlasov equation for cylindrical phase space coordinates is cast into conservation-law form and is discretized on a structured grid. The conservative finite-volume discretization is based on fifth-order upwind reconstructions of the distribution function and a fourth-order quadrature rule that accounts for transverse variations of fluxes along control volume surfaces. High-order specular reflection boundary conditions enable high-fidelity treatment of plasma distribution functions at the axis and at wall boundaries. The numerical method is applied to simulate a confined uniform neutral gas to assess convergence properties for an equilibrium system in which effects of finite-temperature and acceleration due to centrifugal and Coriolis forces are present. The discretization is also applied to a Z-pinch configuration to study electrostatic ion confinement and the dynamics of the associated breathing mode. Simulations show that the ion distribution function exhibits non-Maxwellian features and that a temperature anisotropy develops and is sustained. Finally, the finite-volume implementation is demonstrated to converge at fourth-order for both applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Conservative explicit local time-stepping schemes for the shallow water equations

Here we develop explicit local time-stepping (LTS) schemes with second and third order accuracy for the shallow water equations. The system is discretized in space by a C-grid staggering method, namely the TRiSK scheme adopted in MPAS-Ocean, a global ocean model with the capability of resolving multiple resolutions within a single simulation. The time integration is designed based on the strong stability preserving Runge–Kutta (SSP-RK) methods, but different time step sizes can be used in different regions of the domain through the coupling of coarse-fine time discretizations on the interface, and are only restricted by respective local CFL conditions. The proposed LTS schemes are of predictor–corrector type in which the predictors are constructed based on Taylor series expansions and SSP-RK stepping algorithms. The schemes preserve some important physical quantities in the discrete sense, such as exact conservation of the mass and potential vorticity and conservation of the total energy within time truncation errors. Moreover, they inherit the natural parallelism of the original explicit global time-stepping schemes. Extensive numerical tests are presented to illustrate the performance of the proposed algorithms.

58 GEOSCIENCES↗

An energy-conserving and asymptotic-preserving charged-particle orbit implicit time integrator for arbitrary electromagnetic fields

Here we present a new implicit asymptotic preserving time integration scheme for charged-particle orbit computation in arbitrary electromagnetic fields. The scheme is built on the Crank-Nicolson integrator and continues to recover full-orbit motion in the small time-step limit, but also recovers all the first-order guiding center drifts as well as the correct gyroradius when stepping over the gyration time-scale. In contrast to previous efforts in this direction, the new scheme also features exact energy conservation. In the derivation of the scheme, we find that a new numerical time-scale is introduced. This scale is analyzed and the resulting restrictions on time-step are derived. Based on this analysis, we develop an adaptive time-stepping strategy the respects these constraints while stepping over the gyration scale when physically justified. It is shown through numerical tests on single-particle motion that the scheme's energy conservation property results in tremendous improvements in accuracy, and that the scheme is able to transition smoothly between magnetized and unmagnetized regimes as a result of the adaptive time-stepping.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A mass conservative, well balanced, tangency preserving and energy decaying method for the shallow water equations on a sphere

Here a fully discrete surface finite element method is proposed for solving the viscous shallow water equations in a bounded Lipschitz domain on the sphere based on a general triangular mesh. The method consists of a modified Crank–Nicolson method in time and a Galerkin surface finite element method in space for the fluid thickness H and the fluid velocity u. A finite element space tangential to the sphere at all finite element nodes is proposed to approximate the fluid velocity u. The proposed method has second-order accuracy in time and first-order accuracy in space, and preserves mass conservation, well balancedness, tangency of velocity to the sphere, and energy decay. Numerical experiments are presented to illustrate the accuracy of the proposed method and the preservation of the physical properties, including mass conservation, well balancedness, and energy decay. A numerical simulation of ocean mesoscale activity on a circular basin with a continental shelf is provided.

97 MATHEMATICS AND COMPUTING↗

Conservative remapping of material-dependent fields between possibly misaligned material regions

In this work, we propose an interpolation or remapping algorithm of material-dependent fields on polyhedral meshes where any source or target cell contains only one material. It is conservative and it preserves sharp material boundaries on the target mesh, even if the source and target regions delineating the same material are slightly misaligned. If those material regions are aligned, then the algorithm is also linearity-preserving and bounds-preserving. For a given material, it consists of a conservative field reconstruction on a target mesh part from a source mesh part associated with that material, followed by a repair step in case of misaligned boundaries. No assumption is made regarding the topology of the input meshes

36 MATERIALS SCIENCE↗

Conservative high-order data transfer method on generalized polygonal meshes

A conservative data transfer (remap) between two meshes is an important step of arbitrary Lagrangian-Eulerian (ALE) hydrodynamics simulations. High-order numerical methods for ALE simulations require both high-order (curvilinear) meshes and high-order remap algorithms. Here we develop a conservative and bounds-preserving method for accurate remapping of discrete fields on generalized polygonal meshes with curvilinear edges. The properties of the proposed method are studied theoretically and numerically for various (smooth and non-smooth) mesh deformations and discrete fields that represent smooth and discontinuous functions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A lattice Maxwell system with discrete space–time symmetry and local energy–momentum conservation

A lattice Maxwell system is developed here with gauge-symmetry, symplectic structure and discrete space–time symmetry. Noether's theorem for Lie group symmetries is generalized to discrete group symmetries for the lattice Maxwell system. As a result, the lattice Maxwell system is shown to admit a discrete local energy–momentum conservation law corresponding to the discrete space–time symmetry. A lattice model that respects all local conservation laws and geometric structures is as good as and probably more preferable than standard models on continuous space–time. It can also be viewed as an effective algorithm for the governing differential equations on continuous space–time.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗