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At least 901 records · Page 50

Photogalvanic Effects in Surface States of Topological Insulators under Perpendicular Magnetic Fields

We present a theoretical study of the nonlinear magneto-optical shift conductivity in the surface states of the prototypical topological insulator Bi$_2$Se$_3$ under a perpendicular quantizing magnetic field. By describing the electronic states as Landau levels and using a perturbative approach, we derive the microscopic expression for the shift conductivity $\sigma^{(2);\alpha\beta\gamma}(-\omega,\omega)$, where $\alpha,\beta,\gamma=\pm$ stand for the circular polarization of light and $\omega$ is the light frequency; the spectra are further decomposed into contributions from the interband and intraband optical transitions, for which the selection rules are identified. Considering that the system possesses $C_3$ point group of symmetry, the nonzero components of the conductivity tensor are $\sigma^{(2);-++}=[\sigma^{(2);+--}]^\ast$. Therefore, a pure circularly polarized light generates zero shift current. In the clean limit, the conductivities are nonzero only for discrete photon energies because of the discrete Landau levels and energy conservation, and they become Lorentzian lineshapes with the inclusion of damping, which relaxes the condition of energy conservation. The dependence of the spectra on the damping parameters, the magnetic fields, and the chemical potentials is investigated in detail. Our results reveal that the shift current is highly tunable by the chemical potential and the magnetic field. Furthermore, these results underscore the potential of topological insulators for tunable, strong nonlinear magneto-optical applications.

Landau level↗

Stable compression of a spherical tokamak plasma

In this study, an analysis of toroidal plasma compression by a collapsing flux conserver reveals linearly stable scenarios of operation to high compression ratios. The resistive and ideal MHD stability is calculated in full toroidal geometry using the asymptotic matching method in realistic conditions. A time dependent MHD simulation of the compression is conducted to confirm the conservation principles used to calculate the equilibrium states for the analysis. The near edge current profile, controlled by toroidal field ramping during compression, is shown to be critical to stability due to coupling between poloidal components of the least stable mode. Two cases with slight differences in edge current are examined, one with a stable corridor to high compression and one without.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A stable corridor for toroidal plasma compression

In this study, a toroidal plasma compressed by a collapsing flux conserver is analyzed to reveal stable scenarios of operation to high compression ratios. The resistive and ideal MHD stability is calculated in full toroidal geometry, using the asymptotic matching method in realistic conditions, and comparing with nonlinear simulations. The near edge current profile, controlled by toroidal field ramping during compression, is shown to be critical to stability due to coupling between poloidal components of the least stable mode. The extension of a length of shaft on axis is also found to be critical at high compression, as the resulting good curvature region in magnetic field stabilizes pressure driven modes that would otherwise be unstable. This work extends from previous studies, which initially showed the existence of a stable scenario, to include findings of more extensive stable zones, detailed effects of geometry, and nonlinear simulations of the instabilities. The nonlinear simulations of the compression are consistent with the linear analyses, confirming both the conservation and stability properties.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Runaway electron deconfinement in SPARC and DIII-D by a passive 3D coil

The operation of a 3D coil—passively driven by the current quench (CQ) loop voltage—for the deconfinement of runaway electrons (REs) is modeled for disruption scenarios in the SPARC and DIII-D tokamaks. Nonlinear magnetohydrodynamic (MHD) modeling is carried out with the NIMROD code including time-dependent magnetic field boundary conditions to simulate the effect of the coil. Further modeling in some cases uses the ASCOT5 code to calculate advection and diffusion coefficients for REs based on the NIMROD-calculated fields, and the DREAM code to compute the runaway evolution in the presence of these transport coefficients. Compared with similar modeling in Tinguely et al (2021 Nucl. Fusion 61 124003), considerably more conservative assumptions are made with the ASCOT5 results, zeroing low levels of transport, particularly in regions in which closed flux surfaces have reformed. Of three coil geometries considered in SPARC, only the n = 1 coil is found to have sufficient resonant components to suppress the runaway current growth. Without the new conservative transport assumptions, full suppression of the RE current is maintained when the thermal quench MHD is included in the simulation or when the RE current is limited to 250kA, but when transport in closed flux regions is fully suppressed, these scenarios allow RE beams on the order of 1–2 MA to appear. Additional modeling is performed to consider the effects of the close ideal wall. In DIII-D, the CQ is modeled for both limited and diverted equilibrium shapes. In the limited shape, the onset of stochasticity is found to be insensitive to the coil current amplitude and governed largely by the evolution of the safety-factor profile. In both devices, prediction of the q-profile evolution is seen to be critical to predicting the later time effects of the coil.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dynamical chemistry: non-equilibrium effective actions for reactive fluids

Abstract We present two approaches for describing chemical reactions taking place in fluid phase. The first method mirrors the usual derivation of the hydrodynamic equations of motion by relating conserved—or to account for chemical reactions, non-conserved—currents to local-equilibrium parameters. The second method involves a higher-brow approach in which we attack the same problem from the perspective of non-equilibrium effective field theory (EFT). Non-equilibrium effective actions are defined using the in–in formalism on the Schwinger–Keldysh contour and are therefore capable of describing thermal fluctuations and dissipation as well as quantum effects. The non-equilibrium EFT approach is especially powerful as all terms in the action are fully specified by the symmetries of the system; in particular the second law of thermodynamics does not need to be included by hand, but is instead derived from the action itself. We find that the equations of motion generated by both methods agree, but the EFT approach yields certain advantages. To demonstrate some of these advantages we construct a quadratic action that is valid to very small distance scales—much smaller than the scales at which ordinary hydrodynamic theories break down. Such an action captures the full thermodynamic and quantum behavior of reactions and diffusion at quadratic order. Finally, taking the low-frequency and low-wavenumber limit, we reproduce the linearized version of the well-known reaction–diffusion equations as a final coherence check.

Mechanics↗

Shifting agricultural practices to produce sustainable, low carbon intensity feedstocks for biofuel production

The carbon intensity (CI) of biofuel's well-to-pump life cycle is calculated by life cycle analysis (LCA) to account for the energy/material inputs of the feedstock production and fuel conversion stages and the associated greenhouse gas (GHG) emissions during these stages. The LCA is used by the California Air Resources Board's Low Carbon Fuel Standard (LCFS) program to calculate CI and monetary credits are issued based on the difference between a given fuel's CI and a reference fuel's CI. Through the Tier 2 certification program under which individual fuel production facilities can submit their own CIs with their facility input data, the LCFS has driven innovative technologies to biofuel conversion facilities, resulting in substantial reductions in GHG emissions as compared to the baseline gasoline or diesel. A similar approach can be taken to allow feedstock petition in the LCFS so that lower-CI feedstock can be rewarded. Here we examined the potential for various agronomic practices to improve the GHG profiles of corn ethanol by performing feedstock-level CI analysis for the Midwestern United States. Our system boundary covers GHG emissions from the cradle-to-farm-gate activities (i.e. farm input manufacturing and feedstock production), along with the potential impacts of soil organic carbon change during feedstock production. We conducted scenario-based CI analysis of ethanol, coupled with regionalized inventory data, for various farming practices to manage corn fields, and identified key parameters affecting cradle-to-farm-gate GHG emissions. The results demonstrate large spatial variations in CI of ethanol due to farm input use and land management practices. In particular, adopting conservation tillage, reducing nitrogen fertilizer use, and implementing cover crops has the potential to reduce GHG emissions per unit corn produced when compared to a baseline scenario of corn–soybean rotation. This work shows a large potential emission offset opportunity by allowing feedstock producers a path to Tier 2 petitions that reward low-CI feedstocks and further reduce biofuels' CI. The prevalence of significant acreage that has not been optimized for CI suggests that policy changes that incentivize optimization of this parameter could provide significant additionality over current trends in farm efficiency and adoption of conservation practice.

09 BIOMASS FUELS↗

A typological framework of non-floodplain wetlands for global collaborative research and sustainable use

Non-floodplain wetlands (NFWs) are important but vulnerable inland freshwater systems that are receiving increased attention and protection worldwide. However, a lack of consistent terminology, incohesive research objectives, and inherent heterogeneity in existing knowledge hinder cross-regional information sharing and global collaboration. To address this challenge and facilitate future management decisions, we synthesized recent work to understand the state of NFW science and explore new opportunities for research and sustainable NFW use globally. Results from our synthesis show that although NFWs have been widely studied across all continents, regional biases exist in the literature. We hypothesize these biases in the literature stem from terminology rather than real geographical bias around existence and functionality. To confirm this observation, we explored a set of geographically representative NFW regions around the world and characteristics of research focal areas. We conclude that there is more that unites NFW research and management efforts than we might otherwise appreciate. Furthermore, opportunities for cross-regional information sharing and global collaboration exist, but a unified terminology will be needed, as will a focus on wetland functionality. Based on these findings, we discuss four pathways that aid in better collaboration, including improved cohesion in classification and terminology, and unified approaches to modeling and simulation. In turn, legislative objectives must be informed by science to drive conservation and management priorities. Finally, an educational pathway serves to integrate the measures and to promote new technologies that aid in our collective understanding of NFWs. Our resulting framework from NFW synthesis serves to encourage interdisciplinary collaboration and sustainable use and conservation of wetland systems globally.

54 ENVIRONMENTAL SCIENCES↗

Soil management practices can contribute to net carbon neutrality in California

Stabilizing climate requires reducing greenhouse gas (GHG) emissions and storing atmospheric carbon dioxide (CO 2 ) in land or ocean systems. Soil management practices can reduce GHG emissions or sequester atmospheric CO 2 into inorganic and organic forms. However, whether soil carbon strategies represent a viable and impactful climate mitigation pathway is uncertain. A specific question concerns the role that land-management practices and soil amendments can play in realizing California's ambition for carbon neutrality by 2045. Here we examine the carbon flux impacts of soil conservation (i.e., compost, reduced tillage, cover crop) and enhanced silicate rock weathering (EW) practices at different areal extents of implementation in cropland, grassland, and savanna in California under two climate change cases. We show that with implementation areas of 15% or 50% of private cultivated land, grassland, and savanna in California, soil conservation practices alone can contribute $1.4^{2.1}_{0.7}$% ($-1.8^{-2.7}_{ -0.9}$ Mt CO 2 eq y -1 ) and $4.6^{6.9}_{2.3}$% ($-6.0^{-8.9}_{-3.0}$ Mt CO 2 eq y -1 ) of the additional emissions reduction needed (beyond previous targets) to meet the 2045 net neutrality goal (-129.3 Mt CO 2 eq y -1 ), respectively, on an average annual basis, including climate uncertainty. Including EW in these scenarios increases the total contributions of management practices to $4.1^{5.6}_{2.5}$% ($-5.2^{-7.3}_{-3.2}$ Mt CO 2 eq y -1 ) and $13.5^{18.6}_{8.2}$% ($-17.5^{-24.2}_{-10.7}$ Mt CO 2 eq y -1 ), respectively, of this reduction. This highlights that the extent of implementation area is a major factor in determining benefits and that EW has the potential to make a real contribution to net reduction targets. Results are similar across climate cases, indicating that contemporary field data can be used to make future projections. With EW there remains mechanistic uncertainties, however, such as rock dissolution rate and environmental controls on weathering products, which require additional field research to improve understanding of the technological efficacy of this approach for California's 2045 carbon neutrality goal.

54 ENVIRONMENTAL SCIENCES↗

Cycle equivalence classes, orthogonal Weingarten calculus, and the mean field theory of memristive systems

Abstract It has been recently noted that for a class of dynamical systems with explicit conservation laws represented via projector operators, the dynamics can be understood in terms of lower dimensional equations. This is the case, for instance, of memristive circuits. Memristive systems are important classes of devices with wide-ranging applications in electronic circuits, artificial neural networks, and memory storage. We show that such mean-field theories can emerge from averages over the group of orthogonal matrices, interpreted as cycle-preserving transformations applied to the projector operator describing Kirchhoff’s laws. Our results provide insights into the fundamental principles underlying the behavior of resistive and memristive circuits and highlight the importance of conservation laws for their mean-field theories. In addition, we argue that our results shed light on the nature of the critical avalanches observed in quasi-two-dimensional nanowires as boundary phenomena.

97 MATHEMATICS AND COMPUTING↗

Müllerian mimicry and the coloration patterns of sympatric coral snakes

Abstract Coral snakes in the genus Micrurus are venomous, aposematic organisms that signal danger to predators through vivid coloration. Previous studies found that they serve as models to several harmless species of Batesian mimics. However, the extent to which Micrurus species engage in Müllerian mimicry remains poorly understood. We integrate detailed morphological and geographical distribution data to investigate if coral snakes are Müllerian mimics. We found that coloration is spatially structured and that Micrurus species tend to be more similar where they co-occur. Though long supposed, we demonstrate for the first time that coral snakes might indeed be Müllerian mimics as they show some convergence in coloration patterns. Additionally, we found that the length of red-coloured rings in Micrurus is conserved, even at large geographic scales. This finding suggests that bright red rings may be under more substantial stabilizing selection than other aspects of coloration and probably function as a generalized signal for deterring predators.

Evolutionary Biology↗

Dynamic zinc fluxes regulate meiotic progression in Caenorhabditis elegans

Abstract Zinc influx and efflux events are essential for meiotic progression in oocytes of several mammalian and amphibian species, but it is less clear whether this evolutionary conservation of zinc signals is also important in late-stage germline development in invertebrates. Using quantitative, single cell elemental mapping methods, we find that Caenorhabditis elegans oocytes undergo significant stage-dependent fluctuations in total zinc content, rising by over sevenfold from Prophase I through the beginning of mitotic divisions in the embryo. Live imaging of the rapid cell cycle progression in C. elegans enables us to follow changes in labile zinc pools across meiosis and mitosis in single embryo. We find a dynamic increase in labile zinc prior to fertilization that then decreases from Anaphase II through pronuclear fusion and relocalizes to the eggshell. Disruption of these zinc fluxes blocks extrusion of the second polar body, leading to a range of mitotic defects. We conclude that spatial temporal zinc fluxes are necessary for meiotic progression in C. elegans and are a conserved feature of germ cell development in a broad cross section of metazoa.

59 BASIC BIOLOGICAL SCIENCES↗

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Abstract Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

Gomes-dos-Santos, André (ORCID:0000000199734861)↗

Mob4 is essential for spermatogenesis in Drosophila melanogaster

Abstract Gamete formation is essential for sexual reproduction in metazoans. Meiosis in males gives rise to spermatids that must differentiate and individualize into mature sperm. In Drosophila melanogaster, individualization of interconnected spermatids requires the formation of individualization complexes that synchronously move along the sperm bundles. Here, we show that Mob4, a member of the Mps-one binder family, is essential for male fertility but has no detectable role in female fertility. We show that Mob4 is required for proper axonemal structure and its loss leads to male sterility associated with defective spermatid individualization and absence of mature sperm in the seminal vesicles. Transmission electron micrographs of developing spermatids following mob4RNAi revealed expansion of the outer axonemal microtubules such that the 9 doublets no longer remained linked to each other and defective mitochondrial organization. Mob4 is a STRIPAK component, and male fertility is similarly impaired upon depletion of the STRIPAK components, Strip and Cka. Expression of the human Mob4 gene rescues all phenotypes of Drosophila mob4 downregulation, indicating that the gene is evolutionarily and functionally conserved. Together, this suggests that Mob4 contributes to the regulation of the microtubule- and actin-cytoskeleton during spermatogenesis through the conserved STRIPAK complex. Our study advances the understanding of male infertility by uncovering the requirement for Mob4 in sperm individualization.

Santos, Inês B.↗

A mathematical model of asynchronous data flow in parallel computers *

Abstract We present a simplified model of data flow on processors in a high-performance computing framework involving computations necessitating inter-processor communications. From this ordinary differential model, we take its asymptotic limit, resulting in a model which treats the computer as a continuum of processors and data flow as an Eulerian fluid governed by a conservation law. We derive a Hamilton–Jacobi equation associated with this conservation law for which the existence and uniqueness of solutions can be proven. We then present the results of numerical experiments for both discrete and continuum models; these show a qualitative agreement between the two and the effect of variations in the computing environment’s processing capabilities on the progress of the modelled computation.

Barnard, Richard C.↗

Long-term variability of root production in bioenergy crops from ingrowth core measurements

Long-term determination of root biomass production upon land-use conversion to biofuel crops is rare. To assess land-use legacy influences on belowground biomass accumulation, we converted 22-year-old Conservation Reserve Program (CRP) grasslands and 50+-year-old agricultural (AGR) lands to corn (C), switchgrass (Sw) and restored prairie (Pr) biofuel crops. We maintained one CRP grassland as a reference (Ref). We hypothesized that land-use history and crop type have significant effects on root density, with perennial crops on CRP grasslands having a higher root biomass productivity, while corn grown on former agricultural lands produce the lowest root biomass. Methods The ingrowth core method was used to determine in situ ingrowth root biomass, alongside measurements of aboveground net primary productivity (ANPP). Ancillary measurements, including air temperature, growing season length and precipitation were used to examine their influences on root biomass production. Important Findings Root biomass productivity was the highest in unconverted CRP grassland (1716 g m-2 yr-1) and lowest in corn fields (526 g m-2 yr-1). All perennial sites converted from CRP and AGR lands had lower root biomass and ANPP in the first year of planting but peaked in 2011 for switchgrass and a year later for restored prairies. Ecosystem stability was higher in restored prairies (AGR-Pr: 4.3 ± 0.11; CRP-Pr: 4.1 ± 0.10), with all monocultures exhibiting a lower stability. Root biomass production was positively related to ANPP (R2 = 0.40). Overall, attention should be given to root biomass accumulation in large-scale biofuel production as it is a major source of carbon sequestration.

Environmental Sciences & Ecology↗

Cell wall biology of the moss Physcomitrium patens

Abstract The moss Physcomitrium (previously Physcomitrella) patens is a non-vascular plant belonging to the bryophytes that has been used as a model species to study the evolution of plant cell wall structure and biosynthesis. Here, we present an updated review of the cell wall biology of P. patens. Immunocytochemical and structural studies have shown that the cell walls of P. patens mainly contain cellulose, hemicelluloses (xyloglucan, xylan, glucomannan, and arabinoglucan), pectin, and glycoproteins, and their abundance varies among different cell types and at different plant developmental stages. Genetic and biochemical analyses have revealed that a number of genes involved in cell wall biosynthesis are functionally conserved between P. patens and vascular plants, indicating that the common ancestor of mosses and vascular plants had already acquired most of the biosynthetic machinery to make various cell wall polymers. Although P. patens does not synthesize lignin, homologs of the phenylpropanoid biosynthetic pathway genes exist in P. patens and they play an essential role in the production of caffeate derivatives for cuticle formation. Further genetic and biochemical dissection of cell wall biosynthetic genes in P. patens promises to provide additional insights into the evolutionary history of plant cell wall structure and biosynthesis.

Plant Sciences↗

Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca

Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, as its emergence may depend on simple regulatory changes to deeply conserved metabolic pathways. Modern CAM research relies heavily on interpretation of transcriptomic data, though regulation occurs at multiple levels following transcription. Additionally, while most research to date has focused on a handful of genes and metabolites in the core CAM pathway, the co-option of conserved regulatory and functional genes is bound to have wide-ranging effects on other aspects of primary metabolism. In this study, we integrate transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C 3 species, Y. filamentosa. We observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. We also find evidence of shifts in gene expression and metabolite accumulation outside of the central CAM pathway, suggesting that the shift to CAM has cascading effects across primary metabolism, especially nitrogen metabolism. Our findings provide insights into the metabolic shifts associated with CAM evolution, and highlight the complexity of its regulation at multiple biological levels.

59 BASIC BIOLOGICAL SCIENCES↗

Accuracy of power spectra in dissipationless cosmological simulations

Abstract We exploit a suite of large N-body simulations (up to N = 40963) performed with abacus, of scale-free models with a range of spectral indices n, to better understand and quantify convergence of the matter power spectrum. Using self-similarity to identify converged regions, we show that the maximal wavenumber resolved at a given level of accuracy increases monotonically as a function of time. At 1 per cent level it starts at early times from a fraction of $k_\Lambda$, the Nyquist wavenumber of the initial grid, and reaches at most, if the force softening is sufficiently small, ${\sim}2{-}3 k_\Lambda$ at the very latest times we evolve to. At the $5{{\ \rm per\ cent}}$ level, accuracy extends up to wavenumbers of order $5k_\Lambda$ at late times. Expressed as a suitable function of the scale-factor, accuracy shows a very simple n-dependence, allowing a extrapolation to place conservative bounds on the accuracy of N-body simulations of non-scale-free models like LCDM. We note that deviations due to discretization in the converged range are not well modelled by shot noise, and subtracting it in fact degrades accuracy. Quantitatively our findings are broadly in line with the conservative assumptions about resolution adopted by recent studies using large cosmological simulations (e.g. Euclid Flagship) aiming to constrain the mildly non-linear regime. On the other hand, we remark that conclusions about small-scale clustering (e.g. concerning the validity of stable clustering) obtained using PS data at wavenumbers larger than a few $k_\Lambda$ may need revision in light of our convergence analysis.

79 ASTRONOMY AND ASTROPHYSICS↗