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At least 757 records · Page 42

Evolution of neuronal cell classes and types in the vertebrate retina

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

59 BASIC BIOLOGICAL SCIENCES↗

Metabolomics and the pig model reveal aberrant cardiac energy metabolism in metabolic syndrome

Abstract Although metabolic syndrome (MS) is a significant risk of cardiovascular disease (CVD), the cardiac response (MR) to MS remains unclear due to traditional MS models’ narrow scope around a limited number of cell-cycle regulation biomarkers and drawbacks of limited human tissue samples. To date, we developed the most comprehensive platform studying MR to MS in a pig model tightly related to human MS criteria. By incorporating comparative metabolomic, transcriptomic, functional analyses, and unsupervised machine learning (UML), we can discover unknown metabolic pathways connections and links on numerous biomarkers across the MS-associated issues in the heart. For the first time, we show severely diminished availability of glycolytic and citric acid cycle (CAC) pathways metabolites, altered expression, GlcNAcylation, and activity of involved enzymes. A notable exception, however, is the excessive succinate accumulation despite reduced succinate dehydrogenase complex iron-sulfur subunit b (SDHB) expression and decreased content of precursor metabolites. Finally, the expression of metabolites and enzymes from the GABA-glutamate, GABA-putrescine, and the glyoxylate pathways significantly increase, suggesting an alternative cardiac means to replenish succinate and malate in MS. Our platform discovers potential therapeutic targets for MS-associated CVD within pathways that were previously unknown to corelate with the disease.

59 BASIC BIOLOGICAL SCIENCES↗

Maximising the investment returns of a grid‐connected battery considering degradation cost

Energy storage systems (ESSs) are being deployed widely due to numerous benefits including operational flexibility, high ramping capability, and decreasing costs. This study investigates the economic benefits provided by battery ESSs when they are deployed for market‐related applications, considering the battery degradation cost. A comprehensive investment planning framework is presented, which estimates the maximum revenue that the ESS can generate over its lifetime and provides the necessary tools to investors for aiding the decision making process regarding an ESS project. The applications chosen for this study are energy arbitrage and frequency regulation. Lithium‐ion batteries are considered due to their wide popularity arising from high efficiency, high energy density, and declining costs. A new degradation cost model based on energy throughput and cycle count is developed for Lithium‐ion batteries participating in electricity markets. The lifetime revenue of ESS is calculated considering battery degradation and a cost–benefit analysis is performed to provide investors with an estimate of the net present value, return on investment and payback period. The effect of considering the degradation cost on the estimated revenue is also studied. The proposed approach is demonstrated on the IEEE Reliability Test System and historical data from PJM Interconnection.

25 ENERGY STORAGE↗

Twisted bilayer graphene as topological heavy fermion: II. Analytical approximations of the model parameters

The recently-introduced topological heavy fermion (THF) model [1] of twisted bilayer graphene (TBG) aims to reconcile the quantum-dot-like electronic structure of the latter observed by scanning tunneling microscopy, with its electron delocalization seen in transport measurements. The THF model achieves this by coupling localized (heavy) fermions with anomalous conduction electrons. Originally, the parameters of the THF model were obtained numerically from the Bistritzer–Macdonald (BM) model of TBG [1]. In this work, we derive analytical expressions for the THF model parameters as a function of the twist angle, the ratio between the tunneling amplitudes at the AA and AB regions (w 0 /w 1 ), and the screening length of the interaction potential. By numerically computing the THF model parameters across an extensive experimentally-relevant parameter space, we show that the resulting approximations are remarkably good, i.e., within the 30% relative error for almost the entire parameter space. At the single-particle level, the THF model accurately captures the energy spectrum of the BM model over a large phase space of angles and tunneling amplitude ratios. When interactions are included, we also show that the THF description of TBG is good around the magic angle for realistic values of the tunneling amplitude ratios (0.6 ≤ w 0 /w 1 ≤ 1.0), for which the hybridization between the localized and conduction fermions γ is smaller than the onsite repulsion of the heavy fermions U 1 (i.e., |γ| < U 1 ).

Approximation methods↗

Thermal mean-field theories

Several closely related ab initio thermal mean-field theories for fermions, both well-established and new ones, are compared with one another at the formalism level and numerically. The theories considered are Fermi–Dirac theory; thermal Hartree–Fock (HF) theory; two modifications of the thermal single-determinant and the first-order finite-temperature many-body perturbation theory based on a zero-temperature or thermal HF reference. Furthermore, thermal full-configuration-interaction theory is used as the benchmark.

74 ATOMIC AND MOLECULAR PHYSICS↗

Resistive hose modes in tokamak runaway electron beams II

Resistive hose instabilities of runaway electron (RE) beams immersed in resistive background plasmas are examined with analytic and numerical calculations. The RE beam-plasma equilibria considered are characteristic of the situation observed post-thermal quench in a tokamak disruption. An analytic linear dispersion relation is presented for the case of a uniform RE current density profile with a sharp boundary in cylindrical geometry. Initial value linear calculations for a more general profile in toroidal geometry find that reducing aspect ratio increases the resistive hose mode growth rates with fixed safety factor profile. Nonlinear calculations in cylindrical and toroidal geometry find that the resistive hose instability-driven fluctuations relax the gradient of the current density profile. In toroidal geometry, changes to the magnetic topology are observed as a result of the resistive hose activity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme’s reaction cycle. To examine positioning and motions and test catalytic proposals, we collected “room temperature” X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Here, ensemble analyses indicated limited change through KSI’s reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI’s general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure–function relationships, providing the basis for a new era of “ensemble–function” interrogation of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Conveyor-belt magneto-optical trapping of molecules

Abstract Laser cooling is used to produce ultracold atoms and molecules for quantum science and precision measurement applications. Molecules are more challenging to cool than atoms due to their vibrational and rotational internal degrees of freedom. Molecular rotations lead to the use of type-II transitions ( F ⩾ F ′ ) for magneto-optical trapping (MOT). When typical red detuned light frequencies are applied to these transitions, sub-Doppler heating is induced, resulting in higher temperatures and larger molecular cloud sizes than realized with the type-I MOTs most often used with atoms. To improve type-II MOTs, Jarvis et al (2018 Phys. Rev. Lett. 120 083201) proposed a blue-detuned MOT to be applied after initial cooling and capture with a red-detuned MOT. This was successfully implemented (Burau et al 2023 Phys. Rev. Lett. 130 193401; Jorapur et al 2024 Phys. Rev. Lett. 132 163403; Li et al 2024 Phys. Rev. Lett. 132 233402), realizing colder and denser molecular samples. Very recently, Hallas et al (2024 arXiv:2404.03636) demonstrated a blue-detuned MOT with a ‘1+2’ configuration that resulted in even stronger compression of the molecular cloud. Here, we describe and characterize theoretically the conveyor-belt mechanism that underlies this observed enhanced compression. We perform numerical simulations of the conveyor-belt mechanism using both stochastic Schrödinger equation and optical Bloch equation approaches. We investigate the conveyor-belt MOT characteristics in relation to laser parameters, g -factors and the structure of the molecule, and find that conveyor-belt trapping should be applicable to a wide range of laser-coolable molecules.

Li, Grace K. (ORCID:0000000277223355)↗

Beam breakup instability studies of powerful energy recovery linac for experiments

The maximum achievable beam current in an energy recovery linac (ERL) is often constrained by beam breakup (BBU) instability. Our previous research highlighted that filling patterns have a substantial impact on BBU instabilities in multipass ERLs. In this study, we extend our investigation to the eight-cavity model of the Powerful ERL for Experiment (PERLE). We evaluate its requirements for damping cavity higher order modes (HOMs) and propose optimal filling patterns and bunch timing strategies. Our findings reveal a significant new insight: while filling patterns are crucial, the timing of bunches also plays a critical role in mitigating HOM beam loading and BBU instability. This previously underestimated factor is essential for effective BBU control. We estimated the PERLE threshold current using both analytical and numerical models, incorporating the designed PERLE HOM dampers. During manufacturing, HOM frequencies are expected to vary slightly. Our study found no significant difference in BBU suppression for relative rms frequency jitters of 0.001, 0.002, and 0.005 for the same HOM. Introducing a jitter of 0.001 into our models, we found that the dampers effectively suppressed BBU instability, achieving a threshold current an order of magnitude higher than the design requirement. Our results offer new insights into ERL BBU beam dynamics and have important implications for the design of future ERLs. Published by the American Physical Society 2025

43 PARTICLE ACCELERATORS↗

Fourier Analyses of High-Order Continuous and Discontinuous Galerkin Methods

In this paper, we present a Fourier analysis of wave propagation problems subject to a class of continuous and discontinuous discretizations using high-degree Lagrange polynomials. This allows us to obtain explicit analytical formulas for the dispersion relation and group velocity and, for the first time to our knowledge, characterize analytically the emergence of gaps in the dispersion relation at specific wavenumbers, when they exist, and compute their specific locations. Wave packets with energy at these wavenumbers will fail to propagate correctly, leading to significant numerical dispersion. We also show that the Fourier analysis generates mathematical artifacts, and we explain how to remove them through a branch selection procedure conducted by analysis of eigenvectors and associated reconstructed solutions. The higher frequency eigenmodes, named erratic in this study, are also investigated analytically and numerically.

97 MATHEMATICS AND COMPUTING↗

Updraft Width Implications for Cumulonimbus Growth in a Moist Marine Environment

Abstract An idealized large-eddy simulation of a tropical marine cloud population was performed. At any time, it contained hundreds of clouds, and updraft width in shallow convection emerging from a subcloud layer appeared to be an important indicator of whether specific convective elements deepened. In an environment with 80%–90% relative humidity below the 0°C level, updrafts that penetrated the 0°C level were larger at and above cloud base, which occurred at the lifting condensation level near 600 m. Parcels rising in these updrafts appeared to emerge from boundary layer eddies that averaged ∼200 m wider than those in clouds that only reached 1.5–3 km height. The deeply ascending parcels (growers) possessed statistically similar values of effective buoyancy below the level of free convection (LFC) as parcels that began to ascend in a cloud but stopped before reaching 3000 m (nongrowers). The growers also experienced less dilution above the LFC. Nongrowers were characterized by negative effective buoyancy and rapid deceleration above the LFC, while growers continued to accelerate well above the LFC. Growers occurred in areas with a greater magnitude of background convergence (or weaker divergence) in the subcloud layer, especially between 300 m and cloud base, but whether the convergence actually led to eddy widening is unclear. Significance Statement Cumulonimbus clouds are responsible for many extreme weather phenomena and are important contributors to Earth’s energy balance. However, the processes leading to the growth of individual clouds are not completely understood nor well-represented in weather prediction models. We find that the clouds containing updrafts that start out wider at early stages of their life cycles grow taller, possibly because they are protected more from drier air outside the cloud than narrow clouds. In addition, this work shows how the initial width of clouds might be related to convergence in the lowest part of the atmosphere, at heights where clouds initially develop. However, meteorologists must be careful not to overinterpret these results because numerical simulations inherently include assumptions that may not reflect reality. This reinforces the need to also observe processes occurring at the scales of individual clouds.

54 ENVIRONMENTAL SCIENCES↗

Spectroscopic and Dynamical Studies of Highly Energized Small Polyatomic Molecules (End-of-Grant Report)

The aim of this research program has been to develop models for qualitative and quantitative understanding of complex processes in small molecules, such as vibronic coupling, predissociation, photodissociation, and isomerization. Simple models capture physical insights and lead to intuitive ideas that can enlighten a broad array of problems. Numerical fits can provide predictive power, but rarely impart insights into the underlying mechanisms responsible for the observed phenomena. This DOE supported program has prioritized a quantum mechanical understanding over a perfect numerical fit of spectra. Finding few-parameter models, when those parameters have physical meaning, allows the insights gained from one problem to be easily applied to related problems in other systems. The systems that have been under investigation include atmospherically relevant sulfur-containing compounds, various unimolecular dynamical processes of electronically excited acetylene, and the rovibrational dynamics of formaldehyde and SO 2 .

74 ATOMIC AND MOLECULAR PHYSICS↗

PHEV Distribution Grid Integration and Smart Systems Testing: Cooperative Research and Development Final Report

To continue NREL's mission, which includes preparing technologies and markets with "speed and scale," NREL researchers will collaborate with Toyota on plug-in electric vehicle technology. Toyota will provide a collection of plug-in hybrid electric vehicles ("PHEVs" [and ultimately including PEVs], collectively, the "Vehicles") to conduct infrastructure interaction testing at NREL facilities. NREL will use available resources in the Vehicle Testing and Integration Facility (VTIF), its staff parking garage with numerous commercial Electric Vehicle Supply Equipment ("EVSEs"), and its Energy Systems Integration Facility (ESIF) to safely execute research experiments that highlight potential distribution system power quality challenges related to plug-in electric vehicles. The expected outcome of this project is a better understanding of the correlation of individual vehicle power quality attributes to a system of vehicles on a distribution network. The data collected and the simulations conducted will be used to guide future experiments and project development that aid in the deployment of plug-in electric vehicles ("PEV").

24 POWER TRANSMISSION AND DISTRIBUTION↗

Godiva IV Shielding Benchmark Overview [Slides]

This presentation shows that Integral experiments increase the level of realism from that of data measurements. Further, Godiva IV is capable of intensities to activate foils. IER 498 uses a relative measurement to provide an intermediate level of realism. With reproducibility and room return management are key components. The test matrix put forward in CED-2 enables numerous cross-comparisons. IER 498 facilitates various additional works using a room return shield to isolate the source. IER 557 demonstrated burst reproducibility sufficient for IER 498.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed

The conversion of mercury (Hg) to monomethylmercury (MMHg) is a critical area of concern in global Hg cycling. Periphyton biofilms may harbor significant amounts of MMHg but little is known about the Hg-methylating potential of the periphyton microbiome. Therefore, we used high-throughput amplicon sequencing of the 16S rRNA gene, ITS2 region, and Hg methylation gene pair (hgcAB) to characterize the archaea/bacteria, fungi, and Hg-methylating microorganisms in periphyton communities grown in a contaminated watershed in East Tennes(see United States). Furthermore, we examined how nutrient amendments (nitrate and/or phosphate) altered periphyton community structure and function. We found that bacterial/archaeal richness in experimental conditions decreased in summer and increased in autumn relative to control treatments, while fungal diversity generally increased in summer and decreased in autumn relative to control treatments. Interestingly, the Hg-methylating communities were dominated by Proteobacteria followed by Candidatus Atribacteria across both seasons. Surprisingly, Hg methylation potential correlated with numerous bacterial families that do not contain hgcAB, suggesting that the overall microbiome structure of periphyton communities influences rates of Hg transformation within these microbial mats. To further explore these complex community interactions, we performed a microbial network analysis and found that the nitrate-amended treatment resulted in the highest number of hub taxa that also corresponded with enhanced Hg methylation potential. This work provides insight into community interactions within the periphyton microbiome that may contribute to Hg cycling and will inform future research that will focus on establishing mixed microbial consortia to uncover mechanisms driving shifts in Hg cycling within periphyton habitats.

59 BASIC BIOLOGICAL SCIENCES↗

Scaling Turbulent Combustion Fields in Explosions

We considered the topic of explosions from spherical high-explosive (HE) charges. We studied how the turbulent combustion fields scale. On the basis of theories of dimensional analysis by Bridgman and similarity theories of Sedov and Barenblatt, we found that all fields scaled with the explosion length scale r0. This included the blast wave, the mean and root mean squared (RMS) profiles of thermodynamic variables, combustion variables, velocities, vorticity, and turbulent Reynolds stresses. This was a consequence of the formulation of the problem and our numerical method, which both satisfied the similarity conditions of Sedov. We performed numerical simulations of 1 g charges and 1 kg charges; the solutions were identical (within roundoff error) when plotted in scaled variables. We also explored scaling laws related to three-phase pyrotechnic explosions. We show that although the scaling formally broke down, the fireball still essentially scaled with the explosion length scale r0. However, the discrete Lagrange particles (DLP) (phase 2) and the heterogeneous continuum model (HCM) of the DLP wakes (phase 3) did not scale with r0, and mean and RMS profiles could differ by a factor of 10 in some regions. This was because the DLP particles and wakes introduced an additional scale that broke the similarity conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Coreset Clustering on Small Quantum Computers

Many quantum algorithms for machine learning require access to classical data in superposition. However, for many natural data sets and algorithms, the overhead required to load the data set in superposition can erase any potential quantum speedup over classical algorithms. Recent work by Harrow introduces a new paradigm in hybrid quantum-classical computing to address this issue, relying on coresets to minimize the data loading overhead of quantum algorithms. We investigated using this paradigm to perform k-means clustering on near-term quantum computers, by casting it as a QAOA optimization instance over a small coreset. We used numerical simulations to compare the performance of this approach to classical k-means clustering. We were able to find data sets with which coresets work well relative to random sampling and where QAOA could potentially outperform standard k-means on a coreset. However, finding data sets where both coresets and QAOA work well—which is necessary for a quantum advantage over k-means on the entire data set—appears to be challenging.

42 ENGINEERING↗

First principles thermal transport modeling in GaN and related materials

Gallium nitride is a wide bandgap material utilized in a variety of technologies, including high-power electronics and light-emitting diodes, partly due to its favorable thermal properties. This chapter describes modern first-principles-based modeling of phonons and lattice thermal conductivity (k) of GaN, III-nitrides and related materials. In particular, we describe the theoretical underpinnings of calculating phonon dispersions, intrinsic phonon interactions, and other lattice dynamical properties from quantum perturbation theory and density functional theory (DFT) methods. Description of how these methods are then coupled with the Peierls-Boltzmann transport (PBT) equation to determine phonon distributions and lifetimes relevant for thermal transport is given. These theoretical and numerical methods have demonstrated quantitative accuracy and predictive power for calculating pristine k and defect-limited k from first principles for a variety of materials. We present a review of the literature utilizing DFT-PBT methods to understand novel k behaviors in III-nitrides and related materials.

Lindsay, Lucas↗