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DOE OSTI2025

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗

DOE OSTI2018

Deformation analysis of SiC-SiC channel box for BWR applications

Silicon carbide fiber-reinforced silicon carbide matrix (SiC-SiC) composites are being considered as components in light water reactor cores to improve accident tolerance, including channel boxes and fuel cladding. In the nuclear reactor environment, core components like a channel box will be exposed to neutron and other radiation damage and temperature gradients. To ensure reliable and safe operation of a SiC-SiC channel box, it is important to assess its deformation behavior under in-reactor conditions including the expected neutron flux and temperature distributions. In particular, this work has evaluated the effect of non-uniform dimensional changes caused by spatially varying neutron flux and temperatures on the deformation behavior of the channel box over the course of one year. These analyses have been performed using the fuel performance modeling code BISON and the commercial finite element analysis code Abaqus, based on fast flux and temperature boundary conditions that have been calculated using the neutronics and thermal-hydraulics codes Serpent and CTF, respectively. The dependence of dimensions and thermophysical properties on fast flux and temperature has been incorporated into the material models. These initial results indicate significant bowing of the channel box with a lateral displacement greater than 6.5 mm. The channel box bowing behavior is time dependent and driven by the temperature dependence of the SiC irradiation-induced swelling and the neutron flux/fluence gradients. The bowing behavior gradually recovers during the course of the operating cycle as the swelling of the SiC-SiC material saturates. Furthermore, the bending relaxation due to temperature gradients does not fully recover and residual bending remains after the swelling saturates in the entire channel box.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2019

Collision system and beam energy dependence of anisotropic flow fluctuations

New measurements of elliptic flow from two- and four-particle correlations are used to investigate flow fluctuations in collisions of U+U at √ s NN = 193 GeV, Cu+Au at √ s NN = 200 GeV and Au+Au at several beam energies. These measurements highlight the dependence of these fluctuations on the event shape, system size and beam energy and indicate a dominant role for initial-state-driven fluctuations. These measurements could provide further constraints for initial-state models, as well as for precision extraction of the temperature-dependent specific shear viscosity η/s( T ).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

The BEST framework for the search for the QCD critical point and the chiral magnetic effect

The Beam Energy Scan Theory (BEST) Collaboration was formed with the goal of providing a theoretical framework for analyzing data from the Beam Energy Scan (BES) program at the relativistic heavy ion collider (RHIC) at Brookhaven National Laboratory. The physics goal of the BES program is the search for a conjectured QCD critical point as well as for manifestations of the chiral magnetic effect. We describe progress that has been made over the previous five years. This includes studies of the equation of state and equilibrium susceptibilities, the development of suitable initial state models, progress in constructing a hydrodynamic framework that includes fluctuations and anomalous transport effects, as well as the development of freezeout prescriptions and hadronic transport models. Lastly, we address the challenge of integrating these components into a complete analysis framework. This document describes the collective effort of the BEST Collaboration and its collaborators around the world.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Measurements of mixed harmonic cumulants in Pb–Pb collisions at √ s NN = 5.02 TeV

Correlations between moments of different flow coefficients are measured in Pb–Pb collisions at √ s NN = 5.02 TeV recorded with the ALICE detector. These new measurements are based on multiparticle mixed harmonic cumulants calculated using charged particles in the pseudorapidity region |η| < 0.8 with the transverse momentum range 0.2 < p T < 5.0 GeV/c. The centrality dependence of correlations between two flow coefficients as well as the correlations between three flow coefficients, both in terms of their second moments, are shown. In addition, a collection of mixed harmonic cumulants involving higher moments of v 2 and v 3 is measured for the first time, where the characteristic signature of negative, positive and negative signs of four-, six- and eight-particle cumulants are observed, respectively. The measurements are compared to the hydrodynamic calculations using iEBE-VISHNU with AMPT and TRENTo initial conditions. It is shown that the measurements carried out using the LHC Run 2 data in 2015 have the precision to explore the details of initial-state fluctuations and probe the nonlinear hydrodynamic response of v 2 and v 3 to their corresponding initial anisotropy coefficients and ε 2 and ε 3 . These new studies on correlations between three flow coefficients as well as correlations between higher moments of two different flow coefficients will pave the way to tighten constraints on initial-state models and help to extract precise information on the dynamic evolution of the hot and dense matter created in heavy-ion collisions at the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Beam energy dependence of the linear and mode-coupled flow harmonics in Au+Au collisions

The linear and mode-coupled contributions to higher-order anisotropic flow are presented for Au+Au collisions at √ S NN = 27, 39, 54.4, and 200 GeV and compared to similar measurements for Pb+Pb collisions at the Large Hadron Collider (LHC). The coefficients and the flow harmonics' correlations, which characterize the linear and mode-coupled response to the lower-order anisotropies, indicate a beam energy dependence consistent with an influence from the specific shear viscosity (η/s). In contrast, the dimensionless coefficients, mode-coupled response coefficients, and normalized symmetric cumulants are approximately beam-energy independent, consistent with a significant role from initial-state effects. These measurements could provide unique supplemental constraints to (i) distinguish between different initial-state models and (ii) delineate the temperature (T) and baryon chemical potential (μ B ) dependence of the specific shear viscosity η/s(T, μ B ).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Characterizing the initial state and dynamical evolution in XeXe and PbPb collisions using multiparticle cumulants

For the first time, correlations among mixed-order moments of two or three flow harmonics —( v n k , v m l ) and ( v n k , v m l , v p q ), with k, l, and q denoting the respective orders—are measured in xenon–xenon (XeXe) collisions and compared with lead–lead (PbPb) results, providing a novel probe of collective behavior in heavy ion collisions. These measurements compare a nearly spherical, doubly-magic 208 Pb nucleus to a triaxially deformed 129 Xe nucleus, emphasizing the sensitivity to initial-state geometry fluctuations arising from nuclear deformation. The dependence of these results (v n , n = 2 , 3 , 4 ) on the shape and size of the nuclear overlap region is studied. Comparisons between v 2 , v 3 , and v 4 demonstrate the importance of v 3 and v 4 in exploring the nonlinear hydrodynamic response of the quark-gluon plasma (QGP) to the initial spatial anisotropy. The results constrain initial-state model parameters that influence the evolution of the QGP. The CMS detector was used to collect XeXe and PbPb data at nucleon-nucleon center-of-mass energies of S N N = 5.44 and 5.36 TeV, respectively. Correlations are extracted using multiparticle mixed-harmonic cumulants (up to eight-particle cumulants) with charged particles in the pseudorapidity range |η| < 2.4 and transverse momentum range 0.5 < p T < 3 GeV/c.

CMS↗

DOE OSTI2021

Ultrafast Carrier–Lattice Interactions and Interlayer Modulations of Bi 2 Se 3 by X-ray Free-Electron Laser Diffraction

We report as a 3D topological insulator, bismuth selenide (Bi 2 Se 3 ) has potential applications for electrically and optically controllable magnetic and optoelectronic devices. Understanding the coupling with its topological phase requires studying the interactions of carriers with the lattice on time scales down to the sub-picosecond regime. Here we investigate the ultrafast carrier-induced lattice contractions and interlayer modulations in Bi 2 Se 3 thin films by time-resolved diffraction using an X-ray free-electron laser. The lattice contraction depends on the carrier concentration and is followed by an interlayer expansion accompanied by oscillations. Using density functional theory (DFT) and the Lifshitz model, the initial contraction can be explained by van der Waals force modulation of the confined free carrier layers. Our theory suggests that band inversion, related to a topological phase transition, is modulated by the expansion of the interlayer distance. These results provide insights into the topological phase control by light-induced structural change on ultrafast timescales.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2020

Patterning Metal Grids for GaAs Solar Cells with Cracked Film Lithography: Quantifying the Cost/Performance Tradeoff

We introduce cracked film lithography (CFL) as a way to reduce the cost of III–V photovoltaics (PV). We spin-coat nanoparticle suspensions onto GaAs thin-film device stacks. The suspensions dry in seconds, forming crack networks that we use as templates through which to electroplate the solar cells’ front metal grids. For the first time, we show that heating the crack template allows it to flow and refill cracks, which decreases crack footprint and improves final grid transmittance. We demonstrate 24.7%-efficient single-junction GaAs solar cells using vacuum-free CFL grids. These devices are only 1.7% (absolute) less efficient than the baseline grids patterned by photolithography with the loss mostly resulting from the reduced transparency of the CFL pattern. Additional optimization could decrease this difference. Initial cost modeling suggests that CFL is more scalable than photolithography: In particular, CFL’s lower materials and equipment costs could greatly reduce the levelized cost of electricity of III–V PV at scale, a potential step toward terrestrial deployment.

14 SOLAR ENERGY↗

DOE OSTI2019

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here in this paper, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box–tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate ‘discriminator’ structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Reproducibility of real-time time-dependent density functional theory calculations of electronic stopping power in warm dense matter

Real-time time-dependent density functional theory (TDDFT) is widely considered to be the most accurate available method for calculating electronic stopping powers from first principles, but there have been relatively few assessments of the consistency of its predictions across different implementations. This problem is particularly acute in the warm dense regime, where computational costs are high and experimental validation is rare and resource intensive. We report a comprehensive cross-verification of stopping power calculations in conditions relevant to inertial confinement fusion conducted using four different TDDFT implementations. We find excellent agreement among both the post-processed stopping powers and relevant time-resolved quantities for alpha particles in warm dense hydrogen. We also analyze sensitivities to a wide range of methodological details, including the exchange-correlation model, pseudopotentials, initial conditions, observable from which the stopping power is extracted, averaging procedures, projectile trajectory, and finite-size effects. We show that among these details, pseudopotentials, trajectory-dependence, and finite-size effects have the strongest influence, and we discuss different strategies for controlling the latter two considerations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Overview of Liquid-Metal PFC R&D at the University of Illinois Urbana-Champaign

The design and implementation of future flowing liquid-lithium plasma-facing components (LLPFCs) will be dependent on several factors. Of course, one of the most important is the need to be able to deal with high heat fluxes incident on the surface of the LLPFCs, but there are also several other important liquid-metal behaviors that have been identified for their critical impact on the feasibility of a LLPFC. One of these is the ability to constantly wet 100% of the plasma-facing component area and the best way to achieve that. Another key point is knowing and understanding the erosion and corrosion of the surfaces subject to a flowing liquid-lithium system and the ability for hydrogen and helium uptake by the system. The Center for Plasma Material Interactions (CPMI) has been tasked with looking at these various issues. The Mock-up Entry module for EAST device was used to investigate wetting and erosion effects and to design a suitable distribution and collection system with a liquid-lithium loop. The vapor shielding effects of lithium on the surface were also modeled and studied. A model coupling CRANE, an open-source global reaction network solver, and Zapdos, a plasma transport solver, is being developed to better understand the dynamics of the vapor cloud. Experiments on the Magnum-PSI at the Dutch Institute for Fundamental Energy Research have been carried out to study the vapor shielding effect and obtain experimental benchmarks to verify the model. Also, initial experiments using the Hybrid Illinois Device for Research and Applications have been performed to understand the pumping effects of lithium on helium. Experiments with a drop of liquid lithium (~100 mg) into a helium plasma have shown the ability of lithium to take out the cold recycling helium gas as well as hydrogen and oxygen impurity gases. The improvement in plasma performance was significant, and further understanding of this effect will have impacts on how future LLPFCs will be designed. Further investigation into the exact mechanism for helium pumping by lithium needs to be performed in the future. Finally, this paper presents a summary of the results obtained at the CPMI.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Computational budget optimization for Bayesian parameter estimation in heavy-ion collisions

Abstract Bayesian parameter estimation provides a systematic approach to compare heavy-ion collision models with measurements, leading to constraints on the properties of nuclear matter with proper accounting of experimental and theoretical uncertainties. Aside from statistical and systematic model uncertainties, interpolation uncertainties can also play a role in Bayesian inference, if the model’s predictions can only be calculated at a limited set of model parameters. This uncertainty originates from using an emulator to interpolate the model’s prediction across a continuous space of parameters. In this work, we study the trade-offs between the emulator (interpolation) and statistical uncertainties. We perform the analysis using spatial eccentricities from the T R ENTo model of initial conditions for nuclear collisions. Given a fixed computational budget, we study the optimal compromise between the number of parameter samples and the number of collisions simulated per parameter sample. For the observables and parameters used in the present study, we find that the best constraints are achieved when the number of parameter samples is slightly smaller than the number of collisions simulated per parameter sample.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Modulation of ENSO teleconnections over North America by the Pacific decadal oscillation

In this study, we investigate whether the Pacific decadal oscillation (PDO) can enhance or diminish El Niño Southern Oscillation (ENSO) temperature and precipitation teleconnections over North America using five single model initial-condition large ensembles (SMILEs). The use of SMILEs facilitates a statistically robust comparison of ENSO events that occur during different phases of the PDO. We find that a positive PDO enhances winter and spring El Niño temperature and precipitation teleconnections and diminishes La Niña teleconnections. A negative PDO has the opposite effect. The modulation of ENSO by the PDO is mediated by differences in the location and strength of the Aleutian Low and Pacific Jet during ENSO events under different phases of the PDO. This modulation is a simple combination of the individual effects of the PDO and ENSO over North America. Finally, we show that ENSO and the PDO can be used to evaluate the likelihood of the occurrence of temperature and precipitation anomalies in different regions, but cannot be used as a deterministic predictor of these anomalies due to the large variability between individual events.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Changing windstorm characteristics over the US Northeast in a single model large ensemble

Abstract Extreme windstorms pose a significant hazard to infrastructure and public safety, particularly in the highly populated US Northeast (NE). However, the influence climate change and changing land use will have on these events remains unclear. A large ensemble generated using the Max-Planck Institute (MPI) Earth system model is used to generate projections of NE windstorms under different shared socioeconomic pathways (SSPs) and to attribute changes to projected land use land cover (LULC) change, externally forced changes and internal climate variability. To reduce the influence of coarse grid cell resolution and uncertainties in surface roughness lengths, windstorms are identified using simultaneous widespread exceedance of local 99th percentile 10 m wind speeds (U 99 ). Projected declines in forest cover in the NE and the resulting reductions in surface roughness length under SSP3-7.0 lead to projections of large increases in U 99 and derived windstorm intensity and scale. However, these projected changes in regional LULC under SSP3-7.0 are unprecedented in a historical context and may not be realistic. After corrections are applied to remove the influence of LULC on wind speeds, regionally averaged U 99 exhibit declines for most of the single model initial-condition large ensemble (SMILE) members which are broadly proportional to the radiative forcing and global air temperature increase in the SSPs, with a median value of −0.15 ms −1 °C −1 . While weak cyclones are projected to decline in frequency in the NE, intense cyclones and the resulting windstorms and indices of socioeconomic loss do not. Where present, significant trends in these loss indices are positive, and some MPI SMILE members generate future windstorms that are unprecedented in the historical period.

Coburn, Jacob (ORCID:0000000309538117)↗

DOE OSTI2023

3D structure of anisotropic flow in small collision systems at energies available at the BNL Relativistic Heavy Ion Collider

Here, we present (3 + 1)-dimensional [(3 + 1)D] dynamical simulations of asymmetric nuclear collisions at the BNL Relativistic Heavy Ion Collider (RHIC). Employing a dynamical initial state model coupled to (3 + 1)D viscous relativistic hydrodynamics, we explore the rapidity dependence of anisotropic flow in the RHIC small system scan at 200 GeV center-of-mass energy. We calibrate parameters to describe central 3 He + Au collisions and make extrapolations to d + Au and p + Au collisions. Our calculations demonstrate that approximately 50% of the v 3 (p T ) difference between the measurements by the STAR and PHENIX Collaborations can be explained by the use of reference flow vectors from different rapidity regions. This emphasizes the importance of longitudinal flow decorrelation for anisotropic flow measurements in asymmetric nuclear collisions, and the need for (3 + 1)D simulations. We also present results for the beam energy dependence of particle spectra and anisotropic flow in d + Au collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Three-Stage Adjusted Regression Forecasting for Software Defect Prediction

In this paper, a three-stage adjusted regression forecasting model is proposed to forecast the local regression model [6]. This is a growth curve approximation model that predicts the parameters for a future linear model based on a sliding window of previous linear models. The three stages of the model are as follows: • Initial fit: train regression models on a sliding window of the date and record model coefficients. • Prediction: fit new regression models to the coefficient lists and predict the value of the next coefficient. • Error correction: correct coefficient prediction error using the residual of the last point of the coefficient list and moving average. The resulting model from the multi-stage process is a forecast of the local regression model that represents the future window of data and is referred to as the predicted line. Results suggest the three-stage model demonstrates better prediction capability compared to existing solutions.

Pritchard, Shadow↗

DOE OSTI2024

Thermal Management System of an Outer-Rotor-Motor-Based Traction Drive With Integrated Power Electronics in its Central Cavity

Increasing power densities of electric vehicle traction drive systems necessitates combining the electric motor and the power electronics into one unit. A compact, integrated traction drive unit with fewer components also drives production costs down, enabling wider adoption of electric vehicles. However, the integration of power electronics in the electric machine is associated with challenges of designing an effective thermal management solution for the combined traction drive system. This paper focuses on the thermal management approach selected for Oak Ridge National Laboratory’s outer-rotor-motor-based integrated traction drive and evaluates its potential performance. The outer-rotor-motor configuration provided an opportunity for integration of the six-phase inverter in the available space in the central cavity of the internal stator. A cylindrical inverter enclosure with integrated coolant (water-ethylene glycol) channels in its walls was designed to enable heat removal from the power electronics. Numerical thermal-fluid modeling and initial channel/fin optimization results for the cylindrical heat sink are presented here. As permanent magnets are integrated in a high-speed (20 000 RPM) outer rotor, forced air convection provides cooling for the magnets. The magnets were segmented axially to mitigate the eddy current losses. Heat generated in the stator windings and laminations is removed by water-ethylene glycol coolant circulating in interpolar T-shape ceramic heat exchangers inserted between windings. General design concepts and numerical thermal-fluid simulations illustrating the electric motor thermal management solution are also presented.

Kekelia, Bidzina↗