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At least 109 records · Page 6

On the Effectiveness of Neural Operators at Zero-Shot Weather Downscaling [SWR-25-20]

Code repository for the experiments performed in the paper: On the Effectiveness of Neural Operators at Zero-Shot Weather Downscaling (https://doi.org/10.1017/eds.2025.11) Overall, our work investigates the zero-shot downscaling potential of neural operators. To summarize, our contributions are: 1. We provide a comparative analysis based on two challenging weather downscaling problems, between various neural operator and non-neural-operator methods with large upsampling factors (e.g., 8x and 15x) and fine grid resolutions (e.g., 2 km × 2 km wind speed). 2. We examine whether neural operator layers provide unique advantages when testing downscaling models on upsampling factors higher than those seen during training, i.e., zero-shot downscaling. Our results instead show the surprising success of an approach that combines a powerful transformer-based model with a parameter-free interpolation step at zero-shot weather downscaling. 3. We find that this Swin-Transformer-based approach mostly outperforms all neural operator models in terms of average error metrics, whereas an enhanced super-resolution generative adversarial network (ESRGAN)-based approach is better than most models in capturing the physics of the system, and suggests their use in future work as strong baselines. However, these approaches still do not capture variations at smaller spatial scales well, including the physical characteristics of turbulence in the HR data. This suggests a potential for improvement in transformer or GAN-based methods and neural-operator-based methods for zero-shot weather downscaling.

Sinha, Saumya [National Renewable Energy Laborator↗

Strictly Enforcing Invertibility and Conservation in CNN-Based Super Resolution for Scientific Datasets

Abstract Recently, deep convolutional neural networks (CNNs) have revolutionized image “super resolution” (SR), dramatically outperforming past methods for enhancing image resolution. They could be a boon for the many scientific fields that involve imaging or any regularly gridded datasets: satellite remote sensing, radar meteorology, medical imaging, numerical modeling, and so on. Unfortunately, while SR-CNNs produce visually compelling results, they do not necessarily conserve physical quantities between their low-resolution inputs and high-resolution outputs when applied to scientific datasets. Here, a method for “downsampling enforcement” in SR-CNNs is proposed. A differentiable operator is derived that, when applied as the final transfer function of a CNN, ensures the high-resolution outputs exactly reproduce the low-resolution inputs under 2D-average downsampling while improving performance of the SR schemes. The method is demonstrated across seven modern CNN-based SR schemes on several benchmark image datasets, and applications to weather radar, satellite imager, and climate model data are shown. The approach improves training time and performance while ensuring physical consistency between the super-resolved and low-resolution data. Significance Statement Recent advancements in using deep learning to increase the resolution of images have substantial potential across the many scientific fields that use images and image-like data. Most image super-resolution research has focused on the visual quality of outputs, however, and is not necessarily well suited for use with scientific data where known physics constraints may need to be enforced. Here, we introduce a method to modify existing deep neural network architectures so that they strictly conserve physical quantities in the input field when “super resolving” scientific data and find that the method can improve performance across a wide range of datasets and neural networks. Integration of known physics and adherence to established physical constraints into deep neural networks will be a critical step before their potential can be fully realized in the physical sciences.

54 ENVIRONMENTAL SCIENCES↗

Adaptive optics for optical microscopy [Invited]

Optical microscopy is widely used to visualize fine structures. When applied to bioimaging, its performance is often degraded by sample-induced aberrations. In recent years, adaptive optics (AO), originally developed to correct for atmosphere-associated aberrations, has been applied to a wide range of microscopy modalities, enabling high- or super-resolution imaging of biological structure and function in complex tissues. Here, we review classic and recently developed AO techniques and their applications in optical microscopy.

59 BASIC BIOLOGICAL SCIENCES↗

Field-resolved space–time characterization of few-cycle structured light pulses

Accompanied by the rapid development of ultrafast laser platforms in recent decades, the spatiotemporal manipulation of ultrashort laser pulses has attracted much attention due to the potential for cutting-edge applications of structured light, including optical tweezers, optical communications, super-resolution imaging, time-resolved spectroscopy in molecules and quantum materials, and strong-field physics. Today, techniques capable of characterizing the full spatial, temporal, and polarization state properties of structured light are strongly desired. Here, we demonstrate a technique, termed 3D TIPTOE, for characterizing structured mid-infrared waveforms, which uses only a two-dimensional silicon-based image sensor as both the detector and the nonlinear medium. By combining the advantages of the sub-cycle time resolution afforded by nonlinear excitation and the spatial resolution inherent to the two-dimensional sensor, the 3D TIPTOE technique allows full characterization of structured electric fields, significantly reducing the complexity of detection compared to other techniques. The validity of the technique is established by measuring both few-cycle Bessel–Gaussian pulses and radially polarized femtosecond vector beams.

Liu, Yangyang (ORCID:0000000335205332)↗

Metaoptics Enabled Multifunctional Imaging

Despite the fact that most microorganisms occupy two- and three-dimensional space in heterogeneous arrangements and in proximity to other microorganisms of different species, much of our current knowledge about their metabolic processes is derived from homogenizing, then analyzing, the chemical content of cultures containing a single microbial species. This project addressed this fundamental dichotomy by developing a set of optical imaging principles combining multiple new technologies. The imaging strategies developed in this project combine metaoptics structures with active in situ nanoscale control of the chemical environment and applied them to a microbial system, Myxococcus xanthus, with particular relevance to the DoE mission. The combination of metaoptical architectures and nanoscale control over the molecular environment enables: (a) precise control over the electromagnetic (EM) field at length scales smaller than the wavelength of light; (b) control of the interaction of the EM field with critical molecular systems in DOE relevant microbes; (c) control over the chemical environment – especially the presence and quantity of reactive oxygen species (ROS) that can affect redox homeostasis; and (d) the ability to ask new kinds of questions not accessible to ‘omics’ approaches or standard methods of biological imaging. These capabilities are applicable to detailed studies of metabolic pathways in microbes and to lignocellulosic biomass deconstruction. To accomplish these objectives, we pursued two over-arching technical goals: (1) the development of new metaoptics-enabled approaches to imaging and spectroscopic characterization; and (2) the development of tools to control the chemical environment of a microbial sample with nanometer-scale precision. Goal 1 was addressed through the design, fabrication, and characterization of new metasurfaces capable of super-resolution imaging through extreme confinement of the optical field. Goal 2 was addressed by controlling the redox potential on the nanoscale in microbial communities and characterizing their effect on intrinsic bacterial fluorophores which act as molecular sentinels and through characterization of soluble factors secreted by Myxococcus xanthus by confocal Raman imaging. The optical imaging/sensing approaches developed here make it possible to use these powerful new imaging and sensing modalities in metabolic studies by making it possible to visualize and track the spatial and temporal expression patterns of natural or engineered pathways in microorganisms.

09 BIOMASS FUELS↗

In planta single-molecule imaging and holographic force spectroscopy to study real-time, multimodal turnover dynamics of polysaccharides and associated carbohydrate metabolites

Cellular production of polysaccharides from simple sugar molecules serves critical roles in a variety of metabolic processes essential to the survival of every living organism. In the context of photosynthetically fixed carbon, cell wall polysaccharides synthesis is particularly of interest for increased biomass accumulation for human food, animal feed, and bioenergy related applications. Despite a long history of research in plant cell biology, our understanding of in planta cell wall biosynthesis and its regulation is far from complete due to lack of a comprehensive microscopy toolkit that encompass the multiple spatial and temporal scales in which cell wall polysaccharides fibrils are synthesized and assembled into intricate cell wall networks. In this project, a multidisciplinary team of scientists from Rutgers University, Vanderbilt University, and Oak Ridge National Laboratory carried out innovative multimodal, multiscale microscopy studies of cell wall synthesis using single-molecule force-spectroscopy, super-resolution fluorescence microscopy, and in vivo live cell imaging. Our novel multimodal and holistic imaging approach revealed plant cell wall polysaccharides synthesis processes in unprecedented detail across multiple spatiotemporal scales, from a single-molecule to a single-cell. Besides, the team has made technical and scientific innovations across multiple research fields—microscopy, bioengineering, single-molecule biophysics, and plant biology, etc.—to accomplish the goals. The results from this project will greatly advance the mechanistic and holistic understanding of in planta cell wall synthesis, which will accelerate the development of better transgenic crops for bioenergy applications. Moreover, the new toolbox, combining powerful advanced microscopy assays with cell/protein engineering, will have broader impacts on molecular and cellular biology fields by paving the way for studying cellular processes occurring across multiple physical scales with multimodal microscopy methodologies.

59 BASIC BIOLOGICAL SCIENCES↗

Single-molecule imaging of lignocellulose deconstruction by SCATTIRSTORM microscopy

The goal of this project is to build a multimodal optical microscope to measure the binding, processive degradation, and pausing behaviors of cellulases as they interact with and degrade both synthetic and naturally occurring lignocellulosic walls. To achieve this, we will use high spatio-temporal single-molecule imaging to track cellulases, while visualizing specific molecular components of cellulose, lignin and hemicellulose, that make up their lignocellulose substrate. The microscope will combine Interferometric Scattering (iSCAT), which provides unprecedented spatiotemporal resolution; Total Internal Reflection Fluorescence (TIRF), which provides single-molecule resolution of multiple fluorophore-labeled molecules; and Stochastic Reconstruction (STORM), which allows for three-dimensional super-resolution imaging of intact plant cell walls during degradation. Initial studies will investigate cellulase dynamics on in vitro-assembled cell wall analogs, and later work will progress to using native plant cell walls.

09 BIOMASS FUELS↗

Selection of Global Climate Model Data for Downscaling With Generative Machine Learning and Use in the Power Planning for Alignment of Climate and Energy Systems Project

The range of results from climate models and scenarios is important to the understanding of uncertainty in power planning analysis. A U.S. Department of Energy-funded analytic project called Power Planning for Alignment of Climate and Energy Systems is developing data and analytic methods to reflect the effects of climate change on key variables for power system planning, as part of the Grid Modernization Lab Consortium. This project will select and prepare global climate model results for use in power system planning models. A related report (Evaluation of Global Climate Models for Use in Energy Analysis) assesses the performance of various global climate models from the Coupled Model Intercomparison Project Phase 6 data archive for their historical skill with respect to energy system performance and for their future projections under multiple climate change scenarios. Building from that report, we describe the selection of a climate scenario (Shared Socioeconomic Pathway [SSP] 2-4.5) and five climate models: TaiESM1, EC-Earth3-CC, GFDL-CM4, EC-Earth3-Veg, and MPI-ESM1-2-HR. We describe the model selection criteria, which were based on the quality of the match between model results under historical conditions and on the representation of the range of future values for several variables. These results will be downscaled via an open-source generative machine learning method called Super-Resolution for Renewable Energy Resource Data with Climate Change Impacts.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

ESMs Latent Space Exploration for Uncertainty Quantification and Spatiotemporal Downscaling

This final report for DOE Award DE-SC0023044 presents advances in two key areas of climate modeling: (1) representative climate model selection and (2) Earth System Model (ESM) downscaling using hybrid AI methods. The first section introduces a reordered, three-stage workflow to select representative GCM runs that more effectively balance historical skill with ensemble spread, validated across Texas, Bihar, and New York. The second section introduces two novel super-resolution frameworks, ViSIR and ViFOR, that integrate Vision Transformers with sinusoidal and Fourier-based implicit neural representations. These models achieve state-of-the-art reconstruction accuracy for ESM variables including surface temperature and heat fluxes. The report includes detailed methodology, benchmarks, and results, demonstrating significant gains in uncertainty quantification, spatial fidelity, and scalability for climate-impact studies.

54 ENVIRONMENTAL SCIENCES↗

Downscaled Earth System Model Data for Resilient Energy System Planning

The second-generation Sup3rCC dataset provides high-resolution meteorological data generated through the downscaling of multiple earth system models (ESMs) from the Coupled Model Intercomparison Project Phase 6 (CMIP6). This downscaling is performed through application of a generative machine learning approach called Super-Resolution for Renewable Resource Data (sup3r). This dataset builds on the first-generation Sup3rCC data by applying improved bias correction methods and adding downscaled precipitation to the output variables. In this presentation, we explore the output characteristics of the dataset and various validation analyses. We also present and discuss plans for the integration of this data into power system planning models using a decision-making under deep uncertainty (DMDU) methodology.

97 MATHEMATICS AND COMPUTING↗

Development of high throughput light-sheet fluorescence lifetime imaging microscopy for 3D functional imaging of metabolic pathways in plant and microorganisms (Final Technical Report)

This research program will enable new biochemical contrast in the nanosecond lifetime domain through use of the recently demonstrated electro-optic fluorescence lifetime imaging technique (EO-FLIM) for wide-field lifetime imaging. The Stanford/Stanford Linear Accelerator Center multidisciplinary collaboration -- physics, applied physics, and structural biology -- will develop a light-sheet fluorescence lifetime imaging microscope for functional studies of microbial and plant metabolic pathways and dynamic interactions between plants and microorganisms in the rhizosphere. The proposed approach overcomes the imaging time bottleneck associated with existing fluorescence lifetime imaging methods. Initial demonstrations have shown a factor of 100,000 improvement in photon throughput compared to existing methods. High photon efficiency allowed the first wide-field fluorescence lifetime imaging of single molecules. Recent work has improved the technique’s repetition rate to enable compatibility with mode-locked lasers and demonstrated the combination of wide-field fluorescence lifetime imaging with super-resolution localization microscopy, observations of single molecule dynamics, and observation of donor lifetime quenching in single-molecule imaging. These results were achieved on standard camera sensors and would not have been possible with other wide-field approaches. The throughput and photon economy of the EO-FLIM method enables new BER-relevant imaging opportunities. In particular, scanned single- and two-photon light-sheet excitation will be used to achieve volumetric imaging with time-domain contrast.

47 OTHER INSTRUMENTATION↗

Deconstruction by C. thermocellum —from microbe mediated to dynamic redistribution of cellulosomes

Clostridium thermocellum is one of the most efficient microorganisms for the deconstruction of cellulosic biomass. To achieve this high level of cellulolytic activity, C. thermocellum uses large multienzyme complexes known as cellulosomes to break down complex polysaccharides, notably cellulose, found in plant cell walls. The attachment of bacterial cells to the nearby substrate via the cellulosome has been hypothesized to be the reason for this high efficiency. The region lying between the cell and the substrate has shown great variation and dynamics that are affected by the growth stage of cells and the substrate used for growth. Here, we used both super-resolution imaging and machine-learning approaches to study the distribution of C. thermocellum cellulosomes at different stages of growth. We show that C. thermocellum initially retains its cellulosomes primarily on the cell surface but then relocates large cellulosome clusters to the interface with biomass, therefore depleting its cell surface of cellulosomes. These results indicate dynamic redistribution of cellulosomes during growth, with a functional shift toward substrate-associated degradation later during growth on biomass.

09 BIOMASS FUELS↗

In situ Detection of Plasma Induced Surface Interaction based on Deep Learning based Visual Diagnostics (Technical Report)

It is characteristic for many plasma devices to undergo plasma-material interaction leading to surface erosion. These processes, often not easily detectable, lead to changes in device performance and lifespan. State-of-the-art lifetime tests and wear experiments require over 1000s hours. A self-consistent model for accurately predicting the erosion's effects is not available. In situ detection of these processes is not a trivial task since the surface variations at the early stages have a micron scale. Such limitations not only restrict testing and prediction capabilities but also slow the development of new thrusters and limit mission duration. To address these challenges, an in-situ diagnostic for real-time erosion assessment has been developed, aiming to expedite lifetime testing and broaden experimental campaigns. Several works were dedicated to real-time and in situ monitoring of material erosion during plasma exposure using laser holography, microscopy, and with telemicroscopes. However, the applicability of these approaches is limited due to complexity, cost and less flexibility as they often require placing diagnostic equipment inside the vacuum chamber. In collaboration with Princeton Collaborative Research Facility (PCRF), Princeton Plasma Physics Laboratory (PPPL), a new diagnostic approach is developed, where geometry modifications to the ceramic channel walls were introduced that would result in accelerated channel erosion. We employed Long-distance microscope (LDM) imagery, combined with Deep-Learning based Shape from focus or depth from focus (DFF or SFF) approach, that provides an accessible and cost-effective solution. LDM employs focus variation techniques to continuously capture multiple images of the target object at distinct focal planes. DFF, an optical focus variation method, generates a 3D topographical surface depth map from a sequence of variably focused images. Combined with the developed diagnostic, this approach offers a controllable means to study erosion under accelerated conditions. In this work, we develop Neural Network-based DFF algorithm applicable for LDM data to quantitatively evaluate plasma induced surface modification from LDM data. Next, we develop Deep Learning-based super-resolution depth map image reconstruction technique to increase the resolution of depth maps obtained from DFF algorithm to improve the accuracy of erosion measurements. Thirdly, we develop several image processing techniques to remove noise and improve the quality of depth map image. Here we report the results of initial tests for this approach. An experimental setup designed and built in PPPL was employed that consists of a 3-cm gridded ion source that produces a neutralized argon beam with energies up to 600 eV. A hexagonal boron nitride (h-BN) ceramic target, designed based on computational predictions, was used. Tests were conducted to reconstruct the complex geometry of the target under the lighting conditions of the operated ion source.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High-Resolution Meteorology with Climate Change Impacts from Global Climate Model Data Using Generative Machine Learning

As renewable energy generation increases, the impacts of weather and climate on energy generation and demand become critical to the reliability of the energy system. However, these impacts are often overlooked. Global climate models (GCMs) can be used to understand possible changes to our climate, but their coarse resolution makes them difficult to use in energy system modelling. Here we present open-source generative machine learning methods that produce meteorological data at a nominal spatial resolution of 4 km at an hourly frequency based on inputs from 100 km daily-average GCM data. These methods run 40 times faster than traditional downscaling methods and produce data that have high-resolution spatial and temporal attributes similar to historical datasets. We demonstrate that these methods can be used to downscale projected changes in wind, solar and temperature variables across multiple GCMs including projections for more frequent low-wind and high-temperature events in the Eastern United States.

climate change↗

Imaging a terahertz superfluid plasmon in a two-dimensional superconductor

The superconducting gap defines the fundamental energy scale for the emergence of dissipationless transport and collective phenomena in a superconductor. In layered high-temperature cuprate superconductors, in which the Cooper pairs are confined to weakly coupled two-dimensional (2D) copper–oxygen (CuO 2 ) planes, terahertz (THz) spectroscopy at subgap millielectronvolt (meV) energies has provided crucial insights into the collective superfluid response perpendicular to the superconducting layers. However, within the CuO 2 planes, the collective superfluid response manifests as plasmonic charge oscillations at energies far exceeding the superconducting gap, obscured by strong dissipation. Here, in this study, we present spectroscopic evidence of a below-gap, 2D superfluid plasmon in few-layer Bi 2 Sr 2 CaCu 2 O 8+x and spatially resolve its deeply subdiffractive THz electrodynamics. By placing the superconductor in the near field of a spintronic THz emitter, we reveal this distinct resonance—absent in bulk samples and observed only in the superconducting phase—and determine its plasmonic nature by mapping the geometric anisotropy and dispersion. Crucially, these measurements offer a direct view of the momentum-dependent and frequency-dependent superconducting transition in two dimensions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering

Nanoscopic imaging of cell metabolism is hindered by the incompatibility of small metabolites with fluorescent dyes and the limited resolution of imaging mass spectrometry. We present ultrasensitive reweighted visible stimulated Raman scattering (URV-SRS), a label-free vibrational nanoscopy technique that enables multiplexed detection of metabolic nanostructures within cells. We developed an extensively chirped spectral focusing visible SRS microscope that achieves a detection limit of 4,000 molecules and introduced a self-supervised learning-based denoiser to robustly suppress non-independent SRS noise by over 7.2 dB. The instrumentation-based signal enhancement and computation-based noise suppression synergistically improved the detection sensitivity by 50 times over near-infrared SRS. Leveraging this enhanced sensitivity, we further pushed the resolution to nanoscopic levels by introducing Fourier reweighting to amplify sub-100 nm spatial frequencies previously overwhelmed by noise. Validated by Fourier ring correlation, URV-SRS achieves a lateral resolution of 86 nm in cellular imaging. Here, we applied URV-SRS to elucidate the reprogramming of metabolic nanostructures associated with virus replication in Vero E6 host cells and to compositionally delineate subcellular fatty acid synthesis in engineered Escherichia coli, demonstrating its capability towards nanoscopic spatial metabolomics.

59 BASIC BIOLOGICAL SCIENCES↗

Sneaking in SpyCatcher using cell penetrating peptides for in vivo imaging

Abstract In vivo imaging of protein complexes is a powerful method for understanding the underlying biological function of these key biomolecules. Though the engineering of small, high affinity nanobodies have become more prevalent, the off-rates of these tags may result in incomplete or partial labeling of proteins in live cells. The SpyCatcher003 and SpyTag split protein system allow for irreversible, covalent binding to a short target peptide unlike nanobody-affinity based probes. However, delivering these tags into a cell without disrupting its normal function is a key challenge. Cell penetrating peptides (CPPs) are short peptide sequences that facilitate the transduction of otherwise membrane-impermeable ‘cargo’ , such as proteins, into cells. Here we report on our efforts to engineer and characterize CPP-SpyCatcher003 fusions as modular imaging probes. We selected three CPPs, CUPID, Pentratin, and pVEC, to engineer fusion protein probes for superresolution microscopy, with the aim to eliminate prior permeabilization treatments that could introduce imaging artifacts. We find that fusing the CPP sequences to SpyCatcher003 resulted in dimer and multimer formation as determined by size exclusion chromatography, dynamic light scattering, and SDS resistant dimers on SDS-PAGE gels. By isolating and labeling the monomeric forms of the engineered protein, we show these constructs retained their ability to bind SpyTag and all three CPP sequences remain membrane active, as assessed by CD spectroscopy in the presence of SDS detergent. Using fluorescence and super resolution Lattice structured illumination microscopy (Lattice SIM) imaging we show that the CPPs did not enhance uptake of SpyCatcher by E. coli, however with Caulobacter crescentus cells, we show that Penetratin, and to a lesser degree CUPID, does enhance uptake. Our results demonstrate the ability of the CPP-SpyCatcher003 to label targets within living cells, providing the groundwork for using split protein systems for targeted in vivo imaging.

59 BASIC BIOLOGICAL SCIENCES↗