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DOE OSTI2026

Improving 3D reconstruction quality for root phenotyping: assessing the impact of camera calibration and imaging parameters

Arate 3D reconstruction is essential for high-throughput plant phenotyping, particularly for studying complex structures such as root systems. While photogrammetry and Structure from Motion (SfM) techniques have become widely used for 3D root imaging, the camera settings used are often underreported in studies, and the impact of camera calibration on model accuracyccu remains largely underexplored in plant science. In this study, we systematically evaluate the effects of focus, aperture, exposure time, and gain settings on the quality of 3D root models made with a multi-camera scanning system. We show through a series of experiments that calibration significantly improves model quality, with focus misalignment and shallow depth of field (DoF) being the most important factors affecting reconstruction accuracy. Our results further show that proper calibration has a greater effect on reducing noise than filtering it during post-processing, emphasizing the importance of optimizing image acquisition rather than relying solely on computational corrections. This work improves the repeatability and accuracy of 3D root imaging for phenotyping pipelines by giving useful calibration guidelines. This leads to better trait quantification for use in crop research and plant breeding in downstream analysis.

3D reconstruction↗

DOE OSTI2020

Contrast analysis in two-beam laser interference lithography

Interference lithography enables large area, sub-µm, periodic patterning without photomasks or projection lithography tools. We show that optical contrast, which is the fundamental design variable of interference lithography, enforces coupled constraints on source coherence, beam pointing stability, field size, polarization state, and the intensity balance between beams. The analysis enables selection and alignment tolerance of components to meet a specific design requirement. In particular, the analysis reveals that grating beam splitters are significantly less sensitive to beam pointing and polarization misalignment than plate beam splitters.

Miller, David B. (ORCID:0000000207755284)↗

DOE OSTI2025

Birefringence axis rotation and nonlinear response of a side-hole fiber pressure sensor

The pressure-induced birefringence of side-hole fibers has been widely explored for hydrostatic pressure measurement. Here, this paper studies the effects of the initial birefringence of a side-hole fiber on the pressure response of polarimetric sensors based on side-hole fibers. A mathematical model, where the stress field induced by the pressure is assumed to be uniform in the core region of the fiber, was established to calculate the birefringence and optical axis rotation as a function of the differences between the two principal stress components of the stress field in the core region. Simulation results show that when there is misalignment between the initial birefringence axes and the principal axes of the stress field, pressure changes cause rotations of the birefringence axis, leading to complicated and nonlinear changes of birefringence as a function of pressure. Experiments were conducted using fiber-Bragg-grating-based resonators on side-hole fibers with different initial birefringence, and the results agree well with the simulation. The results underscore the importance of the control of magnitude and direction of the initial birefringence of the side-hole fiber and provide guidelines for the design and fabrication of side-hole fiber pressure sensors.

42 ENGINEERING↗

DOE OSTI2025

Chasing ghosts: characterization of artifact generation in coded aperture decoding due to experimental implementation

Coded aperture imaging is a form of lensless aperture imaging that projects multiple overlapping images of the source onto the detector, enhancing signal strength, which is advantageous for low-flux sources or high-resolution imaging. This technique requires decoding of the detector signal to reconstruct the original source, which involves convolving the detector data with the aperture pattern. When the signal is from a centered point source, the reconstructed source image is known as the point spread function (PSF). A clean PSF without artifacts is a Dirac delta function [Appl. Opt. 20, 1858 (1981)]. This paper examines the robustness of the decoding process against variations in experimental tolerances by analyzing artifact growth in the reconstructed PSF. We illustrate the effects of incorrect magnification, rotation, and detector size and find that aperture–detector rotational misalignment about the imaging axis is the most sensitive parameter, with significant artifact generation occurring with angular offsets of less than one degree. We discuss compensation methods for imperfect aperture placement, finding that small detector sizes produce uncompensatable artifact generation, and compare theoretical predictions with experimental PSF measurements of a rank , 6.8 mm thick (less than one mean free path) coded aperture with a 3.5 mm cell size, conducted at the MegaJOuLe Neutron Imaging Radiography dense plasma focus [IEEE Trans. Plasma Sci. 49, 3299 (2021)] using a 2.45 MeV neutron source. Based on our findings, we recommend using magnified coded apertures in the under-sampled regime, which allows for the inclusion of fiducial markers to characterize aperture–detector rotational offsets and the addition of mechanical coupling, where possible, to constrain rotational and magnification offsets.

Selwood, M. P. [Lawrence Livermore National Labora↗

DOE OSTI2020

Effect of tilt on circular zone plate performance

Fresnel zone plates are frequently used as focusing and imaging optics in x-ray microscopy, as they provide the ease of use of normal incidence optics. We consider here the effects of tilt misalignment on their optical performance, both in the thin optics limit and in the case of zone plates that are sufficiently thick so that volume diffraction effects come into play. Using multislice propagation, we show that simple analytical models describe the tilt sensitivity of thin zone plates and the thickness at which volume diffraction must be considered, and examine numerically the performance of example zone plates for soft x-ray focusing at 0.5 keV and hard x-ray focusing at 10 keV.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Crystal structure of an RNA/DNA strand exchange junction

Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types—an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5′/DNA-3′ strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

CHESS 2025: Crown polygons and extracted reflectance for field sampling sites

This dataset contains (1) crown polygons for each tree, meadow, and shrub site sampled in the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS) campaign (in geojson format, .geojson) and (2) extracted reflectance, uncertainty, and shade estimates for each crown polygon from the 2018 National Ecological Observatory Network (NEON) and 2025 CHESS campaigns. (in CSV format, .csv). Additional metadata are provided in a data dictionary describing column names and definitions (dd.csv), and in a file-level metadata file (flmd.csv). Crown polygons were manually delineated for each site in the 2025 campaign using a combination of field-collected GPS data (doi:10.15485/3022418), RGB (red, green, blue) and false color reflectance mosaics (doi:10.15485/3013535), and LiDAR-derived (Light Detection and Ranging) canopy height (CHM) and digital surface (DSM) models (DOI and citation to be added upon publication). Where there was misalignment between the spectrometer- and LiDAR-derived data products, polygons prioritized alignment with the spectrometer-derived data products. Polygons were delineated conservatively to only select pixels representative of vegetation samples collected in the field. Crown polygons for 2018 are published at (doi:10.15485/1618130) and were developed using the same protocol. For each polygon, all pixels from all flightlines were extracted where the pixel centroid was contained within the polygon. For each pixel, we extracted the surface reflectance, uncertainty, and shade estimates. Details on the extracted datasets are available at (doi:10.15485/3013527, doi:10.15485/3013535). CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004) and was funded by EMIT Extended Mission Phase E Science.

2018 NEON and 2025 CHESS Campaigns↗

DOE OSTI2021

A Multi-physics Computational Investigation of Droplet Pathogen Transport Eminating from Synthetic Coughs and Breathing

In response to the global SARS-CoV-2 transmission pandemic, Sandia National Laboratories Rapid Lab-Directed Research and Development (LDRD) COVID-19 initiative has deployed a multi-physics, droplet-laden, turbulent low-Mach simulation tool to model pathogen-containing water droplets that emanate from synthetic human coughing and breathing. The low-Mach turbulent Eulerian/point-particle Lagrangian methodology directly couples mass, momentum, energy, and species to capture droplet evaporation physics that supports the ability to distinguish between droplets that deposit and those that persist in the environment. Additionally, the cough mechanism is modeled as a pulsed-spray with a prescribed log-normal droplet size distribution. Simulations demonstrate direct droplet deposition lengths in excess of three meters while the persistence of a droplet nuclei entrained within a buoyant plume is noted. Including the effect of protective barriers demonstrates effective mitigation of large-droplet transport. For coughs into a protective barrier, jet impingement and large-scale re-circulation can drive droplets vertically and back towards the subject while supporting persistence of droplet nuclei. Simulations in quiescent conditions demonstrate droplet preferential concentrations due to the coupling between vortex ring shedding and the subsequent advection of a series of three-dimensional rings that tilt and rise vertically due to a misalignment between the initial principle vortex trajectory and gravity. These resolved coughing simulations note vortex ring formation, roll-up and breakdown, while entraining droplet nuclei for large distances and time scales.

42 ENGINEERING↗

DOE OSTI2024

Role of physics in physics-informed machine learning

Physical systems are characterized by inherent symmetries, one of which is encapsulated in the units of their parameters and system states. These symmetries enable a lossless order-reduction, e.g., via dimensional analysis based on the Buckingham theorem. Despite the latter's benefits, machine learning (ML) strategies for the discovery of constitutive laws seldom subject experimental and/or numerical data to dimensional analysis. We demonstrate the potential of dimensional analysis to significantly enhance the interpretability and generalizability of ML-discovered secondary laws. Our numerical experiments with creeping fluid flow past solid ellipsoids show how dimensional analysis enable both deep neural networks and sparse regression reproduce old results, e.g., Stokes law for a sphere, and generate new ones, e.g., an expression for an ellipsoid misaligned with the flow direction. Furthermore, our results suggest the need to incorporate other physics-based symmetries and invariances into ML-based techniques for equation discovery.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

SKS Polarization Anomalies Due to the Coriolis Force

The Earth’s Coriolis force has been well–known to impact surface waves and normal modes, which is essential to accurately interpret these waves. However, the Coriolis force on body waves has been assumed to be negligible and mostly ignored. It has been previously shown that the Coriolis force impacts polarizations of shear waves, whereas the wavefronts remain unaffected. We expand on the potential influences of Earth’s Coriolis force on shear–wave polarization measurements by conducting 3D numerical simulations for elastic waves generated by earthquake and explosive sources in a radially symmetric, and 3D mantle and crustal models. The Coriolis force can produce polarization anomalies of mantle shear waves up to 7° and core phases, such as SKS and SKKS, up to 4°. Uncorrected shear–wave polarizations due to the Coriolis force can cause an additional source of error (5°–10° in fast direction, and 0.2–0.3 s delay time depending on the method and seismic phase), inaccurate interpretation of station misalignments, and imprecise estimates of the core–mantle boundary topography. We show how to correct for the Coriolis force on teleseismic shear waves using 1D ray tracing for well–isolated phases. Here, we recommend the use of full waveform simulations to accurately account for earthquake sources parameters, poorly isolated phases that could include interfering phase arrivals within the measurement time window, and the effect of the Coriolis force on the polarizations of shear waves.

58 GEOSCIENCES↗

DOE OSTI2023

Spin-Polarization Simulations for the Future Circular Collider $E^+E^-$ using BMAD

The high precision measurement of the centre-of-mass energy in the Future Circular Collider e+e- (FCC-ee) at Z and W energies can be realized through resonant spin depolarization utilizing transversely polarized beams. This requires a guaranteed sufficiently-high spin polarization in the presence of lattice imperfections. Investigations of the impact of misalignments on the equilibrium polarization are conducted using analytical and Monte-Carlo spin simulations with Bmad. Potential optimization schemes to ensure high polarization using orbit bumps have been explored.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Space charge dominated momentum spread and compensation strategies in the post-linac section of Proton Improvement Plan-II at Fermilab

The upcoming Proton Improvement Plan-II (PIP-II), designated for enhancements to the Fermilab accelerator complex, features a new 800 MeV superconducting linac and a Beam Transfer Line (BTL) to transport the beam to the existing Booster synchrotron. To mitigate the space charge tune shift associated with a high intensity accumulated beam, the low emittance linac beam is used to paint the ring phase space both transversely and longitudinally. To prevent losses caused by particles injected outside the rf separatrix while painting longitudinal phase space, the momentum spread of the incoming beam should not exceed 2.1 x 10^-4. Detailed simulations showed that due to space charge, the rms momentum spread increases to 4 x 10^-4 while it is transported in the BTL --about twice the allowable limit. In this paper, we outline a mitigation strategy involving a debuncher cavity. We discuss location, operating frequency, and gap voltage under both nominal and perturbed beam conditions, specifically accounting for momentum jitter. The impact of cavity misalignments is also assessed. The paper concludes by recommending an optimized configuration.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Selected Field Measurement Topics [Slides]

Various measurements were conducted with a NaI FLIR IdentiFINDER2 to examine the effects of: the radiation scattering environment, hotspot misalignment effects, dead time, INL Coin, neutrons, and thermal variations. This brief study is by no means conclusive but it offers examples of how the conditions of the measurement can affect the result.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Exploratory Efforts to Constrain Geologic Material Properties from Remote Sensing Data: Joint Study (FY2020 Final Report)

Identification and characterization of underground events from surface or remote data requires a thorough understanding of the rock material properties. However, material properties usually come from borehole data, which is expensive and not always available. A potential alternative is to use topographic characteristics to approximate the strength, but this has never been done before quantitatively. Here we present the results from the first steps towards this goal. We have found that there are strong correlations between compressive and tensile strengths and slopes, but these correlations vary depending on data analysis details. Rugosity may be better correlated to strength than slope values. More comprehensive analyses are needed to fully understand the best method of predicting strength from topography for this area. We also found that misalignment of multiple GIS datasets can have a large influence on the ability to make interpretations. Lastly, these results will require further study in a variety of climatic conditions before being applicable to other sites.

58 GEOSCIENCES↗

DOE OSTI2020

Longitudinal space charge kick in Coherent Electron Cooling

In recent EIC Coherent electron Cooling (CeC) design, we adopted 591 MHz SRF LINAC to accelerate electron beam to certain energy(150 MeV, 54.1 MeV and 22.3 MeV). To reduce the energy spread caused by the RF curvature, a short bunch is preferred and results in high peak current. The longitudinal space charge kick will cause the energy spread increasing and lengthen the bunch length when through the R56 elements. This slippage of modulated microbunches may misalign with hadrons providing imprinting at kicker section. In this note, we will estimate this effect and discuss possible solution.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

The Distribution of U.S. Electric Utility Revenue Decoupling Rate Impacts from 2005 to 2017

Investments in energy efficiency and distributed generation reduce electric utility retail sales. Since electric utilities have historically collected a large portion of revenues from volumetric energy rates (¢/kWh), such reductions in sales can impact the utility’s ability to sufficiently recover non-production costs. Regulatory mechanisms that “decouple” utility revenues from sales were implemented to help make the utility indifferent to energy efficiency and distributed generation by ensuring the utility is able to collect an allowed level of revenue each year regardless of its sales. However, noticeable and consistent surcharges over time may create the perception of an incorrectly designed or implemented decoupling mechanism. To date, there are limited quantitative analyses of the rate adjustments due to decoupling mechanisms implemented among U.S. electric utilities (see Morgan, 2013). Given the recent rapid increase in distributed energy resource (DER) adoption in some states and utility service territories, consumers may be facing more prevalent and ongoing decoupling surcharges. This, in turn, may undermine stakeholder support for implementation of decoupling mechanisms and the associated utility support for energy efficiency and DERs. To determine the size of retail rate adjustments associated with decoupling mechanisms and whether they have a tendency towards bill surcharges or credits, we analyzed a large dataset of historical annual decoupling rate adjustments for 21 electric utilities in 11 states between 2005 and 2017. We found that decoupling mechanisms adjusted rates, both up and down, between rate cases, and the majority of those adjustments (54 percent) are small (within a range of -1 to 1 percent). However, we also found that 64 percent of the rate adjustment observations in our sample showed a positive rate adjustment. Importantly, once a surcharge is applied there is an 86 percent chance that there will be a surcharge in the next year as well. While our analysis did not seek to understand the root causes for such results, some possible factors include the accuracy of revenue requirement forecasts, emerging structural changes in customer use and production of energy, misaligned financial motivation, and other factors that influence sales (e.g., economic recession).

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

Exploratory Efforts to Constrain Geologic Material Properties from Remote Sensing Data: A Joint Study

42 ENGINEERING↗

DOE OSTI2022

Implementation and Results of Extended-MHD Post-processing of xRAGE Simulations

Magnetic fields are known to affect the evolution of conducting fluids via the J× B force, where J is the current density and B is the magnetic field. Typically, J× B in high energy density plasmas (HEDP) systems is considered small compared to the plasma pressure gradients. However, many experiments lie in a part of the parameter space where the plasma is indirectly affected via magnetization of the heat flux and charged particle transport. This is true even for initially unmagnetized plasmas, since misaligned density and temperature gradients can self-generate the so-called Biermann magnetic fields.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗