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At least 361 records · Page 20

Comparison of DeePMD, MTP, GAP, ACE and MACE Machine‐Learned Potentials for Radiation‐Damage Simulations: A User Perspective

Accurate and efficient interatomic potentials are essential for molecular dynamics (MD) simulations of radiation damage, gas diffusion, and phase stability in complex ceramics such as LiAlO 2 , especially under extreme conditions relevant to tritium production. Here, we evaluate the performance of six machine-learned interatomic potentials (MLIPs), moment tensor potential (MTP), Gaussian approximation potential, deep potential (DeePMD), atomic cluster expansion (ACE), message-passing ACE (multilayer atomic cluster expansion (MACE) pretrained) and MACE (trained from-scratch), all trained on the same density functional theory dataset with inclusion of tritium. The MLIPs are benchmarked against traditional Buckingham and ReaxFF potentials in terms of energy accuracy, density predictions, thermal equilibration behavior, threshold displacement energy (E d ), tritium diffusivity, and computational cost. Among the models, MTP shows the best overall balance between efficiency and accuracy, with low force and energy errors and realistic E d values for Li and Al. The ACE and MACE (pretrained and trained from scratch) models exhibit high E d (>200 eV) and unphysical pair interactions. DeePMD underestimates Ed due to overly repulsive behavior even at equilibrium distances. All models over-estimate tritium diffusion but the pretrained MACE model behaves well during tritium-diffusion simulations up to 500 K, maintaining diffusivities in the physically consistent 10 −11 m 2 /s range. Finally, we quantify the computational cost of each potential in large-scale atomic/molecular massively parallel simulator, finding that only MTP is more efficient than traditional empirical potentials, while others are significantly more expensive. These findings explain the trade-offs between accuracy and computational cost in MLIP development and provide essential guidance for use in high-throughput radiation damage and gas diffusion simulations in nuclear ceramics.

74 ATOMIC AND MOLECULAR PHYSICS↗

Full radiator-perturber interaction in computer simulations of hydrogenic spectral line broadening by plasmas

Spectral line broadening by plasmas can be computed by solving the equation of motion for the dipole of the radiating system perturbed by a fluctuating potential obtained from computer simulations. Such calculations have relied on the multipole expansion of the radiator-plasma interaction often keeping only the dipole term. With increasing density, however, higher multipoles as well as plasma perturbers overlapping the bound electron wave functions are expected to become important. For hydrogenic systems, the atomic matrix elements of the full Coulomb and screened Coulomb interactions are given by analytical formulas. Using these results, a computer simulation approach that accounts for the full radiator-plasma interaction is developed. One benefit is the removal of inherent strong collision divergences in the multipole expansion approximation. Furthermore, it yields the plasma polarization shift produced by perturbers penetrating the wave function of the radiator bound electrons. Here, the model was applied to hydrogenic argon Ly-α , Ly- β , and Ly-$\gamma$ spectral lines in a dense argon plasma at free electron densities of 10 24 or 10 25 cm ⁻3 and temperature of $800$ $eV$ relevant to plasma diagnostic techniques for inertial confinement fusion implosions.

74 ATOMIC AND MOLECULAR PHYSICS↗

Shallow soils are warmer under trees and tall shrubs across Arctic and Boreal ecosystems

Soils are warming as air temperatures rise across the Arctic and Boreal region concurrent with the expansion of tall-statured shrubs and trees in the tundra. Changes in vegetation structure and function are expected to alter soil thermal regimes, thereby modifying climate feedbacks related to permafrost thaw and carbon cycling. However, current understanding of vegetation impacts on soil temperature is limited to local or regional scales and lacks the generality necessary to predict soil warming and permafrost stability on a pan-Arctic scale. Here we synthesize shallow soil and air temperature observations with broad spatial and temporal coverage collected across 106 sites representing nine different vegetation types in the permafrost region. We showed ecosystems with tall-statured shrubs and trees (> 40 cm) have warmer shallow soils than those with short-statured tundra vegetation when normalized to a constant air temperature. In tree and tall shrub vegetation types, cooler temperatures in the warm season do not lead to cooler mean annual soil temperature indicating that ground thermal regimes in the cold-season rather than the warm-season are most critical for predicting soil warming in ecosystems underlain by permafrost. Our results suggest that the expansion of tall shrubs and trees into tundra regions can amplify shallow soil warming, and could increase the potential for increased seasonal thaw depth and increase soil carbon cycling rates and lead to increased carbon dioxide loss and further permafrost thaw.

54 ENVIRONMENTAL SCIENCES↗

Time propagation of electronic wavefunctions using nonorthogonal determinant expansions

The use of truncated configuration interaction in real-time time-dependent simulations of electron dynamics provides a balance of computational cost and accuracy, while avoiding some of the failures associated with real-time time-dependent density functional theory. However, low-order truncated configuration interaction also has limitations, such as overestimation of polarizability in configuration interaction singles, even when perturbative doubles are included. Increasing the size of the determinant expansion may not be computationally feasible, and so, in this work, we investigate the use of nonorthogonality in the determinant expansion to establish the extent to which higher-order substitutions can be recovered, providing an improved description of electron dynamics. Model systems are investigated to quantify the extent to which different methods accurately reproduce the (hyper)polarizability, including the high-harmonic generation spectrum of H 2 , water, and butadiene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

N-jettiness beam functions at N3LO

We present the first complete calculation for the quark and gluon N -jettiness ( $$ {\mathcal{T}}_N $$ T N ) beam functions at next-to-next-to-next-to-leading order (N 3 LO) in perturbative QCD. Our calculation is based on an expansion of the differential Higgs boson and Drell-Yan production cross sections about their collinear limit. This method allows us to employ cutting edge techniques for the computation of cross sections to extract the universal building blocks in question. The class of functions appearing in the matching coefficents for all channels includes iterated integrals with non-rational kernels, thus going beyond the one of harmonic polylogarithms. Our results are a key step in extending the $$ {\mathcal{T}}_N $$ T N subtraction methods to N 3 LO, and to resum $$ {\mathcal{T}}_N $$ T N distributions at N 3 LL' accuracy both for quark as well as for gluon initiated processes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Probing configurational disorder in ZnGeN 2 using cluster-based Monte Carlo

ZnGeN 2 is sought as a semiconductor with comparable lattice constant to GaN and tunable band gap for integration in optoelectronic devices. Configurational disorder on the cation sublattice of ZnGeN 2 can strongly modify the electronic structure compared to the ordered material, and both ordered and disordered forms of ZnGeN 2 are candidates for light-emitting diodes and other emitters. The nonisovalent character of the disordered species (Zn 2+ and Ge 4+ ) subjects the cation ordering to strong short-range order effects. To model these effects, we use Monte Carlo (MC) simulations utilizing a cluster expansion to approximate formation enthalpy. Representative disordered configurations in 1024-atom supercells are relaxed in density functional theory calculations. From the MC structures, we extract a short-range order parameter (the N-cation coordination motif), and two long-range order parameters (Bragg-Williams and stretching parameters), and examine their correlations. We perform a thermodynamic integration to determine the mixing entropy and free energy. ZnGeN 2 exhibits a first-order phase transition with pronounced discontinuities in enthalpy and entropy, as well as in the structural order parameters. We discuss the relationship between the effective temperature used in the MC simulation and the growth temperatures in experiment in relation to the crossover from the nonequilibrium to the equilibrium growth regime. This work expands on current models of site disorder in ZnGeN 2 and provides atomic structure models with a systematic variation of the degree of cation disorder.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Crystal Structure Evolution of UCl 3 from Room Temperature to Melting

We report uranium trichloride (UCl 3 ) is actively researched to develop and improve applications ranging from molten salt reactors to actinide processing, including spent fuel reprocessing. Here, we report for the first time the crystal structure evolution between room temperature and melting point from in situ high-temperature neutron diffraction to quantify, for example, the thermal expansion of the hexagonal a and c lattice parameters. The results are compared with density functional theory calculations. The melting point of UCl 3 is determined by differential scanning calorimetry to be 1108.2 ± 0.2 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fluorescent toxins as ion channel activity sensors.

Voltage gated ion channels (VGICs) shape the electrical character of cells by undergoing structural changes in response to membrane depolarization. High-resolution techniques have provided a wealth of data on individual VGIC structures, but the conformational changes of endogenous channels in live cell membranes have remained unexplored. Here, we describe methods for imaging structural changes of voltage-gated K + channels in living cells, using peptidyl toxins labeled with fluorophores that report specific protein conformations. These Endogenous Voltage-sensor Activity Probes (EVAPs) enable study of both VGIC allostery and function in the context of endogenous live-cell membranes under different physiological states. In this chapter, we describe methods for the synthesis, imaging, and analysis of dynamic EVAPs, which can report K + channel activity in complex tissue preparations via 2-photon excitation microscopy, and environment-sensitive EVAPs, which report voltage-dependent conformational changes at the VGIC-toxin interface. The methods here present the utility of current EVAPs and lay the groundwork for the development of other probes that act by similar mechanisms. EVAPs can be correlated with electrophysiology, offering insight into the molecular details of endogenous channel function and allostery in live cells. This enables investigation of conformational changes of channels in their native, functional states, putting structures and models into a context of live-cell membranes. The expansive array of state-dependent ligands and optical probes should enable probes more generally for investigating the molecular motions of endogenous proteins.

Stewart, Robert↗

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

59 BASIC BIOLOGICAL SCIENCES↗

Demonstrating SolarPILOT’s Python API Through Heliostat Optimal Aimpoint Strategy Use Case

SolarPILOT is a software package that generates solar field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. SolarPILOT was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL’s1 System Advisor Model (SAM) in a simplified format. Prior means for user interaction with SolarPILOT have included the application’s graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called “LK.” This paper presents a new, full-featured, Python-based application programmable interface (API) for SolarPILOT, which we hereafter refer to as CoPylot. CoPylot provides access to all SolarPILOT’s capabilities to generate and characterize power tower CSP systems seamlessly through Python. Supported capabilities include (i) creating and destroying a model instance with message reporting tools; (ii) accessing and setting any SolarPILOT variable including custom land boundaries for field layouts; (iii) programmatically managing receiver and heliostat objects with varied attributes for systems with multiple receiver or heliostat types; (iv) generating, assigning, and modifying solar field layouts including the ability to set individual heliostat locations, aimpoints, soiling rates, and reflectivity levels; (v) simulating solar field performance; (vi) returning detailed results describing performance of individual heliostats, the aggregate field, and receiver flux distribution; and, (vii) exporting Python-based model instances to multiple file formats. CoPylot enables Python users to perform detailed CSP tower analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. In addition to CoPylot’s functionality, Python users have access to the over 100,000 open-source libraries to develop, analyze, optimize, and visualize power tower CSP research. This enables CSP researchers to perform analysis that was previously not possible through SolarPILOT’s existing interfaces. This paper discusses the capabilities of CoPylot and presents a use case wherein we demonstrate optimal solar field aiming strategies.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Demonstrating SolarPILOT's Python API Through Heliostat Optimal Aimpoint Strategy Use Case: Preprint

SolarPILOT is a software package that generates heliostat field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. SolarPILOT was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL's System Advisor Model (SAM) in a simplified format. Prior means for user interaction with SolarPILOT have included the application's graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called "LK." This paper presents a new, full-featured Python-based application programmable interface (API) for SolarPILOT, which we hereafter refer to as CoPylot. CoPylot provides access to all SolarPILOT's capabilities to generate and characterize power tower CSP systems seamlessly through Python. Supported capabilities include (i) creating and destroying a model instances with message reporting tools; (ii) accessing and setting any SolarPILOT variable including custom land boundaries for field layout; (iii) programmatically managing receiver and heliostat objects with varied attributes for systems with multiple receiver or heliostat types; (iv) generating, assigning, and modifying heliostat field layouts including the ability to set individual heliostat locations, aimpoints, soiling rates, and reflectivity levels; (v) simulating heliostat field performance; (vi) returning detailed results describing performance of individual heliostats, the aggregate field, and receiver flux; and, (vii) exporting Python-based model instances to multiple file formats. CoPylot enables Python users to perform detailed tower CSP analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. In addition to CoPylot's functionality, Python users have access to the over 100,000 open-source libraries to develop, analyze, optimize, and visualize CSP tower research.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Iron Economy Management

Marine algae are responsible for half of the world's primary productivity, but this critical carbonsink is often constrained by insufficient iron. One species of marine algae, Dunaliella tertiolecta, isremarkable for its ability to maintain photosynthesis and thrive in low-iron environments. A relatedspecies, Dunaliella salina Bardawil, shares this attribute but is an extremophile found in hypersaline environments. To elucidate how algae manage their iron requirements, we produced highquality genome assemblies and transcriptomes for both species to serve as a foundation for acomparative multi-omics analysis. We identified a host of iron-uptake proteins in both species,including a massive expansion of transferrins and a novel family of siderophore-iron uptakeproteins. Complementing these multiple iron-uptake routes, ferredoxin functions as a large ironreservoir that can be released by induction of flavodoxin. Proteomic analysis revealed reducedinvestment in the photosynthetic apparatus coupled with remodeling of antenna proteins bydramatic iron-deficiency induction of TIDI1, a light harvesting complex protein found also in otherchlorophytes. These combinatorial iron scavenging and sparing strategies make Dunaliellaunique among photosynthetic organisms

iron homeostasis, phytoplankton, Iron starvation i↗

Crystallographic Insight of Reduced Lattice Volume Expansion in Mesoporous Cu 2+ -Doped TiNb 2 O 7 Microspheres during Li + Insertion

TiNb 2 O 7 represents a promising anode material for lithium-ion batteries (LIBs), but its practical applications are currently hampered by the non-negligible volumetric expansion and contraction during the charge/discharge process and the sluggish ion/electron kinetics. Here a combination technique is reported by systematically optimizing the porous and spherical morphology, crystal structure, and surface decoration of mesoporous Cu 2+ -doped TiNb 2 O 7 microspheres to enhance the electrochemical Li + storage performance and stability simultaneously. The Cu 2+ dopants preferentially replace Ti 4+ in crystal lattices, which decreases the Li + diffusion barrier and increases the electronic conductivity, as confirmed by density functional theory (DFT) calculation and demonstrated by diverse electrochemical characterizations. The successful Cu 2+ doping significantly reduces the lattice expansion coefficient from 7.26% to 4.61% after Li + insertion along the b-axis of TiNb 2 O 7 , as visualized from in situ and ex situ XRD analysis. The optimal 5% Cu 2+ -doped TiNb 2 O 7 with surface coating of N-doped carbon exhibits significantly enhanced specific capacity and rate and cyclic performances in both half- and full-cell configurations, demonstrating an excellent electrochemical behavior for fast-charging LIB applications.

36 MATERIALS SCIENCE↗

Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows

Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a “user guide” for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure–property relationships in soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of downhole pressure and fluid-access on the effectiveness of wellbore cement expansion additives

Autogenous shrinkage of wellbore cement widely impairs zonal isolation. MgO-based cement expansion additives (CEAs) can mitigate this shrinkage, or even impart net expansion, by creating porosity through displacive crystal growth-processes. However, both MgO hydration and autogenous shrinkage behaviour depend strongly on stress state. Evaluation of CEA performance in wellbore cements therefore requires testing under elevated pressures representative for subsurface environments. We report experiments addressing the chemical and bulk volume changes that occur in cement hydrating at 10 MPa confining pressure and 90 °C. Volumetric response was investigated as function of MgO concentration, external water supply, and pore pressure decrease through water consumption during reaction. Results show the bulk expansion achieved using MgO-based CEAs diminishes markedly with increasing effective confining pressure or, equivalently, upon restricting fluid supply. This reduced expansion-potential under pressure has profound implications for slurry design, notably regarding CEA-concentrations required to counteract micro-annulus formation while maintaining low cement permeability.

36 MATERIALS SCIENCE↗

Remote Sensing of Multitemporal Functional Lake‐To‐Channel Connectivity and Implications for Water Movement Through the Mackenzie River Delta, Canada

The Mackenzie River Delta in Canada is a mediator of hydrological transport between the expansive Mackenzie River watershed and the Beaufort Sea. Within the delta, lakes frequently act as water and sediment traps, limiting or delaying the movement of material to the coastal ocean. The degree to which this filtering takes place depends on the ease with which sediment-laden water is transported from distributary channels into deltaic lakes, referred to as functional lake-to-channel connectivity, which varies both spatially and temporally. Tracking of connectivity has previously been limited to either small regions of the delta or has focused on a snapshot of connectivity at a single instance in time. Here we describe an algorithm that uses Landsat imagery to track summertime functional lake-to-channel connectivity of 10,362 lakes between 1984 and 2022 on an image-by-image basis. We calculate a total average connected lake area of 1400.7 km 2 during the 2 weeks after peak discharge, 763.6 km 2 higher than previous estimates, suggesting a larger influence of connected lakes on water movement through the delta than previously estimated. We also identify water level thresholds that lead to the initiation of high sediment river water movement into 5,989 lakes (908 lakes with uncertainty ≤±0.5 m), and identify an additional 2899 lakes whose connectivity does not vary at all. As the Arctic hydrological cycle responds to climate change, this work lays a foundation for tracking the movement of water, and the matter it carries, from the Mackenzie River watershed to the Beaufort Sea.

47 OTHER INSTRUMENTATION↗

Proton isovector helicity PDF at NNLO and the twist-3 moment $\tilde{d}$ 2 from lattice QCD at physical quark masses

We present a lattice quantum chromodynamics calculation of the 𝑥-dependent isovector quark helicity parton distribution function (PDF) of the proton in the large momentum effective theory (LaMET) framework. Through operator product expansion (OPE) we also extract the $\tilde{d}$ 2 moment of the twist-3 PDF 𝑔 𝑇 ⁡(𝑥) for the first time in the $\overline{MS}$ scheme, which is proportional to the average color Lorentz force experienced by the quark in the proton. This calculation is performed on a lattice of spacing 𝑎 =0.076 fm at physical quark masses. The quasi-PDF matrix elements are measured in proton states boosted to momenta 𝑃 𝑧 ={0,0.25,1.02,1.53} GeV. We first extract the lowest few helicity PDF moments from the renormalization-group (RG) invariant ratios of the matrix elements with OPE. Combined with the matrix elements relevant for 𝑔 𝑇 ⁡(𝑥), we obtain $\tilde{d}$$^{u-d}_2$⁡(2 GeV) =0.0024⁢(46) at next-to-leading order in $\overline{MS}$. Then, the helicity quasi-PDF matrix elements are renormalized in the hybrid scheme with linear renormalon resummation and Fourier transformed to the 𝑥-space after an asymptotic extrapolation. The quasi-PDF is perturbatively matched to the $\overline{MS}$ PDF with RG and threshold resummations at next-to-leading power and next-to-next-to-leading logarithmic accuracies. After resummations, we determine the PDF in the region 𝑥 ∈[0.25,0.75]. The end-point regions are then parametrized, combined with the LaMET prediction at moderate 𝑥, and fitted to the short-distance matrix elements in coordinate space.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗