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At least 253 records · Page 14

Plastome evolution in annual Brachypodium species reveals widespread heteroplasmy and chloroplast capture, lineage-specific codon usage bias, and low positive selection

Comparative genomics and plastome phylogenomics have advanced significantly in recent years, highlighting the diversity, possible admixture, and non-neutral evolution of the predominantly considered non-recombinant chloroplast genomes in angiosperms. The grass genus Brachypodium serves as a powerful model for studying evolutionary processes in monocots. We analyzed 287 plastomes across the native circum-Mediterranean range of the three annual Brachypodium species ( B. distachyon, B. stacei, B. hybridum ), focusing on their structural variation, selection patterns and phylogenomic relationships. Our analyses confirmed the differentiation of the S and D plastomes, inherited respectively from the diploid progenitor species B. stacei and B. distachyon . We identified novel structural rearrangements and indels, and unique repeat motifs, along with widespread heteroplasmy, particularly in ancestral B. hybridum -D plastotypes. SNP diversity varied among plastotypes, reflecting population dynamics and evolutionary histories, with B. hybridum -D plastotypes showing the highest normalized diversity and B. hybridum -S the lowest. Positive selection was detected in 29 plastid genes by Tajima’s neutrality test, and in nine genes by site and branch-site evolutionary models, including matK, ndhF, rbcL, and rpoC2. Phylogenomic analyses revealed well-supported clades corresponding to the S and D plastome lineages, with frequent chloroplast capture events and long-distance dispersals shaping their evolutionary trajectories.

allopolyploidy↗

Towards Energy-Positive Buildings through a Quality-Matched Energy Flow Strategy

Current strategies for net-zero buildings favor envelopes with minimized aperture ratios and limiting of solar gains through reduced glazing transmittance and emissivity. This load-reduction approach precludes strategies that maximize on-site collection of solar energy, which could increase opportunities for net-zero electricity projects. To better leverage solar resources, a whole-building strategy is proposed, referred to as “Quality-Matched Energy Flows” (or Q-MEF): capturing, transforming, buffering, and transferring irradiance on a building’s envelope—and energy derived from it—into distributed end-uses. A mid-scale commercial building was modeled in three climates with a novel Building-Integrated, Transparent, Concentrating Photovoltaic and Thermal fenestration technology (BITCoPT), thermal storage and circulation at three temperature ranges, adsorption chillers, and auxiliary heat pumps. BITCoPT generated electricity and collected thermal energy at high efficiencies while transmitting diffuse light and mitigating excess gains and illuminance. The balance of systems satisfied cooling and heating demands. Relative to baselines with similar glazing ratios, net electricity use decreased 71% in a continental climate and 100% or more in hot-arid and subtropical-moderate climates. Total EUI decreased 35%, 83%, and 52%, and peak purchased electrical demands decreased up to 6%, 32%, and 20%, respectively (with no provisions for on-site electrical storage). Decreases in utility services costs were also noted. These results suggest that with further development of electrification the Q-MEF strategy could contribute to energy-positive behavior for projects with similar typology and climate profiles.

54 ENVIRONMENTAL SCIENCES↗

Transitional Structures with Continuous Variations in Atomic Positions from Anatase to Rutile Improve Photocatalytic Activity

Abstract TiO 2 polymorphs have distinct properties that are widely employed in various applications. However, mechanisms of transformations between these polymorphs are not fully understood, especially at atomic scale, inhibiting advancing the design and application of the transitional phases. Here, based on results from semi‐in situ transmission electron microscopy, density functional theory, and X‐ray photoemission experiments, a physical picture of transitional structures is discovered, in which continuous variations in atomic positions form along a previously unreported anatase‐to‐rutile phase transformation path of [010] A –to–[] R and (004) A –to– (011) R . These gradient structures give rise to continuous band bending, which promotes electron‐hole separation and inhibits their recombination across the bulk of the particles, leading to a large functionally active volume fraction and resulting in high photoactivity. These findings suggest that interphase matter based on extended gradient structures can be designed to advance new functions not achievable using abrupt interfaces.

36 MATERIALS SCIENCE↗

The Influence of Mesoscale Particle Structure on the Electrode Degradation and Resultant Electrochemistry of Lithium Ion Cells With Nickel Rich Lithium Nickel Manganese Cobalt Oxide Positive Electrodes

Nickel-rich lithium nickel manganese cobalt oxide, NMC (LiNi x Mn y Co z O 2 ), materials are desirable positive electrodes in lithium ion batteries, providing high capacity and energy density. The mesoscale structure of NMC materials is commonly a polycrystalline aggregate, providing opportunity for short lithium ion transport distance of the small primary particles, yet facile material handling due to the larger secondary particles. On (de)lithiation the NMC unit cell changes volume, where the anisotropic strain can result in secondary particle fracture. This secondary particle fracture process during cycling has been associated with several degradation modes of NMC materials in LIBs. In this work, a milling process was determined whereby the secondary particles could be pre-fractured with retention of the parent primary particle crystallographic structure, crystallite size, and morphology, providing the ability to unambiguously determine the influence of NMC secondary particle size and mesostructure on resultant functional behavior. The bulk and interfacial properties and electrochemistry of as-received commercially obtained polycrystal NMC811 (LiNi 0.8 Mn 0.1 Co 0.1 O 2 , PC NMC) and its milled MPC NMC counterpart were compared. The smaller secondary particle size, higher surface area MPC NMC was found to result in 1) greater cathode tortuosity, 2) reduced surface Ni on the cycled MPC cathodes consistent with surface reconstruction, and 3) increased Ni deposition on the anodes from cathode-anode crosstalk. These factors manifested in unfavorable electrochemical behavior of MPC with lower functional capacity at both 1C and C/10 rates and higher impedance over extended moderate voltage (dis)charge cycling.

36 MATERIALS SCIENCE↗

Energetic Tug-of-War between Pt and Leaky TiO 2 : Positive and Negative Effects on the Function of Molecularly-Modified p -Si(111)|TiO 2 |Pt Photocathodes

Photoelectrochemical solar energy conversion to chemical products is a promising avenue towards renewable fuels, and TiO 2 deposition on semiconductor photocathodes is a widespread surface protection strategy. However, the electronic, thermodynamic, and kinetic effects of protection layers on interfacial energetics remains poorly understood. Here, electrochemical data (photocurrent onset and flatband potentials) of p-Si(111)|TiO 2 |Pt is collected in contact with an outer-sphere redox couple. We find that onset potentials shift negatively as a function of increasing oxide thickness, but this effect is not reflected in the flatband potentials. This reveals the mechanism of these shifts is kinetic rather than thermodynamic,and suggests that hole leakage through the TiO 2 is responsible. When Pt nanoparticles are deposited onto the TiO 2 , positive shifts in both the onset and flatband potentials are observed, revealing Pt catalysts are beneficial for more than just increased catalytic rates. These results highlight the importance of understanding the effects of surface modifications on the energetics at the interface in both catalytic and simple electron transfer systems.

14 SOLAR ENERGY↗

From subsidies to stressors: Positively skewed ecological gradients alter biological responses to nutrients in streams

Abstract Subsidy–stress gradients offer a useful framework for understanding ecological responses to perturbation and may help inform ecological metrics in highly modified systems. Historic, region‐wide shifts from bottomland hardwood forest to row crop agriculture can cause positively skewed impact gradients in alluvial plain ecoregions, resulting in tolerant organisms that typically exhibit a subsidy response (increased abundance in response to environmental stressors) shifting to a stress response (declining abundance at higher concentrations). As a result, observed biological tolerance in modified ecosystems may differ from less modified regions, creating significant challenges for detecting biological responses to restoration efforts. Using the agriculturally dominated Mississippi Alluvial Plain (MAP) ecoregion in Mississippi, USA, as a case study, we tested the hypothesis that macroinvertebrate taxa that typically display a subsidy response to nutrient enrichment in less modified ecoregions (i.e., nutrient‐tolerance) shift to a stress response to increasing nutrients in highly modified watersheds with elevated baseline nutrient conditions (i.e., nutrient intolerance). The abundance and diversity of MAP‐specific intolerant taxa identified with threshold indicator taxa analysis were either unresponsive or exhibited a subsidy response to increasing nutrients in less modified ecoregions in Mississippi with less land alteration and lower nutrient concentrations, but declined at higher concentrations, providing evidence for a stress response to elevated nutrients in the MAP. Additionally, MAP‐specific tolerant and intolerant taxa richness responded to increased nutrients predictably and consistently across space and time within the MAP. However, in MAP streams, elevated specific conductance was predicted to dampen the response of tolerant and intolerant taxa richness to increasing nutrient concentrations, highlighting the importance of considering multistressor interactions when interpreting biological data. Lastly, we demonstrate the efficacy of this approach with sediment bacterial communities characterized with amplicon sequencing, which lack sufficient life history characteristics necessary for the development of multimetric indices. Both macroinvertebrate and bacterial communities responded similarly to increasing nutrient concentrations, suggesting DNA‐based approaches may provide an efficient biological assessment tool for monitoring water quality improvements in highly modified watersheds.

DeVilbiss, Stephen E. [U.S. Geological Survey Lowe↗

Lithium-Ion Mobility in Layered Oxide Li 2 (La 0.75 Li 0.25 )(Ta 1.5 Ti 0.5 )O 7 Containing Lithium on both Intra and Inter‐Stack Positions

With the aid of neutron diffraction and electrochemical impedance spectroscopy, we have demonstrated the effect of the increase in lithium concentration and distribution on Li-ion conductivity. This has been done through the synthesis of a layered oxide Li 2 (La 0.75 Li 0.25 )(Ta 1.5 Ti 0.5 )O 7 , with the so-called Ruddlesden-Popper type structure, where bilayer stacks of (Ta/Ti)O 6 octahedra are separated by lithium ions, located in inter-stack spaces. There are also intra-stack spaces that are occupied by a mixture of La and Li, as confirmed by neutron diffraction. The distribution of lithium over both inter- and intra-stack positions leads to the enhancement of Li-ion conductivity in Li 2 (La 0.75 Li 0.25 )(Ta 1.5 Ti 0.5 )O 7 compared to Li 2 La(TaTi)O 7 , which has a lower concentration of lithium ions, located only in inter-stack spaces. Furthermore, the analyses of real and imaginary components of electrochemical impedance data confirm the enhanced mobility of ions in Li 2 (La 0.75 Li 0.25 )(Ta 1.5 Ti 0.5 )O 7 . While the Li-ion conductivity needs further improvement for practical applications, the success of the strategy implemented in this work offers a useful methodology for the design of layered ionic conductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

S -matrix positivity without Lorentz invariance: a case study

We investigate the analytic structure of scattering amplitudes in theories in which Lorentz invariance is spontaneously broken. We do so by computing and studying the S-matrix for a simple example: a superfluid described by a complex scalar with quartic interactions. The computation is confined to tree-level, for there are no absolutely stable single-particle states, though the lifetime can be made long by lowering the chemical potential. For the 2 → 2 amplitude in center-of-mass configurations, not only is crossing symmetry violated, there appears a tree level branch cut for unphysical kinematics. Its appearance is a consequence of non-analyticity in the dispersion relation. The branch point defines a new scale in the problem, which scales inversely with the chemical potential. In this example, even derivatives of the forward amplitude are positive while odd derivatives are negative. This pattern can be understood in a general way in the limit of a small chemical potential, or weak Lorentz breaking.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

On positive geometry and scattering forms for matter particles

We initiate the study of positive geometry and scattering forms for tree-level amplitudes with matter particles in the (anti-)fundamental representation of the color/flavor group. As a toy example, we study the bi-color scalar theory, which supplements the bi-adjoint theory with scalars in the (anti-)fundamental representations of both groups. Using a recursive construction we obtain a class of unbounded polytopes called open associahedra (or associahedra with certain facets at infinity) whose canonical form computes amplitudes in bi-color theory, for arbitrary number of legs and flavor assignments. In addition, we discuss the duality between color factors and wedge products, or "color is kinematics", for amplitudes with matter particles as well.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Perturbation theory for the logarithm of a positive operator

In various contexts in mathematical physics, such as out-of-equilibrium physics and the asymptotic information theory of many-body quantum systems, one needs to compute the logarithm of a positive unbounded operator. Examples include the von Neumann entropy of a density matrix and the flow of operators with the modular Hamiltonian in the Tomita-Takesaki theory. Often, one encounters the situation where the operator under consideration, which we denote by ∆, can be related by a perturbative series to another operator ∆ 0 , whose logarithm is known. We set up a perturbation theory for the logarithm log ∆. It turns out that the terms in the series possess a remarkable algebraic structure, which enables us to write them in the form of nested commutators plus some “contact terms”.

97 MATHEMATICS AND COMPUTING↗

Quantitative Measurement of Positive and Negative Ion Species Ejected from a Li–O–H Surface by Hydrogen and Noble Gas Ion Irradiation

We report sputtering yields of Li + , H - , O - , and OH x - ion species from an Li–O–H surface for H, D, He, Ne, and Ar ion irradiation at 45° incidence in the energy range of 30–2000 eV. A Li film was deposited on a stainless steel target using Li evaporators in the LTX-β vessel, using the LTX-β Sample Exposure Probe (SEP), which includes an ultrahigh vacuum suitcase for transferring targets without significant contamination from air exposure. The SEP was used to transfer the Li-coated target from LTX-β to a separate Sample Exposure Station (SES) to perform ion exposure measurements. The SEP was also used for characterization of the Li-coated target utilizing X-ray photoelectron spectroscopy in a different chamber, showing that the lithium film surface was oxidized. Ion exposures were performed using an electron cyclotron resonance plasma source in the SES. Sputtered/ejected species were sampled by a quadrupole mass spectrometer with capabilities for detecting positive and negative ions, and an energy filter for determining the mean kinetic energy of the ejected ion species. All ion irradiations caused Li + ions to be ejected, while causing impurity ions such as H + , H - , O - and OH - to be ejected. Measured ion energies of Li + ions from a Li–O–H surface suggested that the typical sheath potential on the divertor surface can trap sputtered Li + ions, which were previously reported as ~ 60% of total sputtered Li species from Li targets (Allain and Ruzic in Nucl Fusion 42:202, 2002). Hence, our results for the sputtering yields of ejected ion species and their associated ion energies from a Li–O–H surface indicates that lithium sputtering is suppressed and impurity removal is enhanced due to the sheath potential at the divertor surface for fusion reactor applications.

Plasma-material interaction↗

Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump

The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun’s lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Finally, sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.

59 BASIC BIOLOGICAL SCIENCES↗

Validation of the strike point position estimation with the local expansion method for MAST upgrade on the DIII-D tokamak

A local expansion method has been proposed for estimating the strike point position for the advanced divertor configuration on the MAST Upgrade tokamak. The paper discusses the application and assesses the performance of the technique on a long-legged divertor plasma configuration on an operating device - the DIII-D tokamak. A comparison of the spatial location of the outer strike point estimated with the local expansion method against the plasma boundary reconstruction and divertor diagnostics on the DIII-D tokamak is reported. A good agreement with the equilibrium reconstruction and diagnostic data is achieved with respect to estimation of the spatial location of the outer strike point for the long-legged divertor plasma discharge.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Plasma shape and position control development for NSTX-U using the GSEvolve plasma simulator

NSTX-U discharges have been reproduced using the GSEvolve plasma simulator in order to improve their control and reduce oscillations during the plasma current (Ip) ramp-up phase, and with the ultimate goal of enabling reliable H-mode access with a double-null shape at high elongation, low internal inductance, and high plasma performance. The control objective is to eliminate undesired oscillations in the plasma shape and vertical position that start when the plasma diverts during the Ip ramp-up phase, and that happened recurrently during the first NSTX-U experimental campaign. Model-based control solutions have been developed, including alternative H-mode access recipes and a Multi-Input Multi-Output (MIMO) decoupling controller. These solutions have demonstrated their capability to reduce or eliminate the aforementioned oscillations in GSEvolve simulations, enabling reproducible H-mode access. The results of this work aim to inform NSTX-U experimental operations on potential control developments to maximize its scientific output, and highlight the powerful capabilities of high-fidelity control-simulation frameworks like GSEvolve.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Coexistence of positive and negative exchange bias effect in Pr-doped NdCrO 3 samples

Positive and negative exchange bias effects are observed in Nd 1-x Pr x CrO 3 (0.00 ≤ x ≤ 1.00) polycrystalline samples. The shift of hysteresis loops, either opposing or following the direction of the field cooling, depends on the concentration of praseodymium. The temperature dependence of magnetization reveals a magnetic transition at T ≈ 220 K likely ascribed to the N é el temperature of Cr 3+ magnetic moments. The non-Kramer Pr 3+ ion seems to play an important role in the magnetic properties of this compound. In the range 0.00 ≤ x ≤ 0.60, all samples presented a decrease in the magnetization below TN and a clear compensation point. Pr-rich samples (x ≥ 0.70) show a paramagnetic-like behavior down to low temperatures. We report the most impressive result is the relation between reversal magnetization and the signal of exchange bias effect which seems be tuned by the Pr-doping.

36 MATERIALS SCIENCE↗

Learning constitutive relations using symmetric positive definite neural networks

In this work, we present a new neural-network architecture, called the Cholesky-factored symmetric positive definite neural network (SPD-NN), for modeling constitutive relations in computational mechanics. Instead of directly predicting the stress of the material, the SPD-NN trains a neural network to predict the Cholesky factor of the tangent stiffness matrix, based on which the stress is calculated in incremental form. As a result of this special structure, SPD-NN weakly imposes convexity on the strain energy function, satisfies the second order work criterion (Hill's criterion) and time consistency for path-dependent materials, and therefore improves numerical stability, especially when the SPD-NN is used in finite element simulations. Depending on the types of available data, we propose two training methods, namely direct training for strain and stress pairs and indirect training for loads and displacement pairs. We demonstrate the effectiveness of SPD-NN on hyperelastic, elasto-plastic, and multiscale fiber-reinforced plate problems from solid mechanics. The generality and robustness of SPD-NN make it a promising tool for a wide range of constitutive modeling applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Anti-symmetric and positivity preserving formulation of a spectral method for Vlasov-Poisson equations

We analyze the anti-symmetric properties of a spectral discretization for the one-dimensional Vlasov-Poisson equations. The discretization is based on a spectral expansion in velocity with the symmetrically weighted Hermite basis functions, central finite differencing in space, and an implicit Runge Kutta integrator in time. The proposed discretization preserves the anti-symmetric structure of the advection operator in the Vlasov equation, resulting in a stable numerical method. We apply such discretization to two formulations: the canonical Vlasov-Poisson equations and their continuously transformed square-root representation. The latter preserves the positivity of the particle distribution function. We derive analytically the conservation properties of both formulations, including particle number, momentum, and energy, which are verified numerically on the following benchmark problems: manufactured solution, linear and nonlinear Landau damping, two-stream instability, bump-on-tail instability, and ion-acoustic wave.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗