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At least 1,675 records · Page 93

Sequence length scaling in vision transformers for scientific images on frontier

Vision Transformers (ViTs) are pivotal for foundational models in scientific imagery, including Earth science applications, due to their capability to process large sequence lengths. While transformers for text have inspired scaling sequence lengths in ViTs, adapting these for ViTs introduces unique challenges. We develop distributed sequence parallelism for ViTs, enabling them to handle up to 1M tokens. Our approach, leveraging DeepSpeed-Ulysses and Long-Sequence-Segmentation with model sharding, is the first to apply sequence parallelism in ViT training, achieving a 94% batch scaling efficiency on 2,048 AMD-MI250X GPUs. Evaluating sequence parallelism in ViTs, particularly in models up to 10B parameters, highlighted substantial bottlenecks. We countered these with hybrid sequence, pipeline, and flash attention strategies, to scale beyond single GPU memory limits. Our method significantly enhances climate modeling accuracy by 20% in temperature predictions, marking the first training of a vision transformer model to convergence with a sequence length of 188K tokens, using full self-attention.

Tsaris, Aristeidis (aris) [ORNL] (ORCID:0000000277↗

Opinion: Lighting Research During and After the Pandemic

For many lighting researchers, the recent restrictions related to COVID-19 have paused most in-person laboratory or field experiments. In certain countries, regulatory institutions have allowed such experiments to resume but issued safety recommendations like pre-checking participants for disease symptoms and excluding those that are especially vulnerable. To avoid potential complications and delays, researchers are likely to resort to other research designs that enable remote research — eliminating the need for the experimenter and subjects to be in the same room. While unanticipated, this shift to remote research methods is an opportunity to revisit and further develop remote experimental techniques, which can have beneficial long-lasting implications on lighting research during and after the pandemic. Perhaps the most common type of remote research is online experiments; which can greatly benefit from improved techniques to allow for greater control or characterization of experimental conditions, like those proposed by Villa and Labayrade . These techniques require validation specific to the type of response collected and context, e.g. space type and attributes. New research techniques continue to emerge and will enable remote collection of objective measures such as gaze direction and high dynamic range images (HDRIs) without specialized equipment. In fact, many of these methods and techniques are commonly used in other disciplines, like vision science and psychology, and can be adapted for lighting research. Not all lighting studies can be conducted online, but in the age of ubiquitous and connected technologies, there is a largely missed opportunity to utilize crowdsourced responses to lighting conditions in real environments where people live and go about their daily lives without the research being limited to a certain time and laboratory locations. For instance, outdoor street luminaires can be rated by passersby using ecological momentary assessments on mobile phones. While this approach does not provide laboratory-level control over experimental conditions, it can provide more contextual responses resulting from ‘normal’ dynamic gaze, behavior, and interactions. Further, it can also reduce bias related to the experimental setting. Further development of remote research methods and their use in lighting research can improve the quality of lighting research. Given that sample sizes in most lighting research are relatively small, remote research can substantially increase sample sizes, reduce research costs, and shorten study duration, all while reducing interaction between experimenter and subjects. Another benefit is reaching a wider audience and including under-represented individuals who typically are not reachable using common recruitment methods. The pandemic has set back our plans for in-lab experiments, but can it inspire us to think of new and creative ways to expand lighting research?

Abboushi, Belal K.↗

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture

Abstract Background Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate species or measure species-specific attributes in most multi-species systems. Anaerobic gut fungi (AGF) (Neocallimastigomycetes) are native to the rumen of large herbivores, where they exist as minority members among a wealth of prokaryotes. AGF have significant biotechnological potential owing to their diverse repertoire of potent lignocellulose-degrading carbohydrate-active enzymes (CAZymes), which indirectly bolsters activity of other rumen microbes through metabolic exchange. While decades of literature suggest that polysaccharide degradation and AGF growth are accelerated in co-culture with prokaryotes, particularly methanogens, methods have not been available to measure concentrations of individual species in co-culture. New methods to disentangle the contributions of AGF and rumen prokaryotes are sorely needed to calculate AGF growth rates and metabolic fluxes to prove this hypothesis and understand its causality for predictable co-culture design. Results We present a simple, microplate-based method to measure AGF and methanogen concentrations in co-culture based on fluorescence and absorbance spectroscopies. Using samples of < 2% of the co-culture volume, we demonstrate significant increases in AGF growth rate and xylan and glucose degradation rates in co-culture with methanogens relative to mono-culture. Further, we calculate significant differences in AGF metabolic fluxes in co-culture relative to mono-culture, namely increased flux through the energy-generating hydrogenosome organelle. While calculated fluxes highlight uncertainties in AGF primary metabolism that preclude definitive explanations for this shift, our method will enable steady-state fluxomic experiments to probe AGF metabolism in greater detail. Conclusions The method we present to measure AGF and methanogen concentrations enables direct growth measurements and calculation of metabolic fluxes in co-culture. These metrics are critical to develop a quantitative understanding of interwoven rumen metabolism, as well as the impact of co-culture on polysaccharide degradation and metabolite production. The framework presented here can inspire new methods to probe systems beyond AGF and methanogens. Simple modifications to the method will likely extend its utility to co-cultures with more than two organisms or those grown on solid substrates to facilitate the design and deployment of microbial communities for bioproduction and beyond.

59 BASIC BIOLOGICAL SCIENCES↗

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Abstract Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses

We currently understand the carbon cycle in methanogenic environments as trophic interactions revolving around interspecies H 2 transfer between organotrophs and methanogens. However, many H 2 -generating processes are thermodynamically sensitive to H 2 accumulation and can be inhibited by high H 2 concentrations produced by other metabolisms. To uncover how anaerobes combat this H 2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology – methanogenic bioreactors. Through analysis of 15 anaerobic digesters, we recover 1343 high-quality metagenome-assembled genomes (MAGs) and corresponding gene expression profiles for diverse uncultured lineages spanning 66 phyla and reconstruct their individual metabolic capacities. We discover that diverse uncultured organotrophic populations can drive H 2 -sensitive degradation through (i) metabolic coupling with concurrent H 2 -tolerant catabolism, (ii) unprecedented shifts from H 2 generation to CO 2 -reducing formate transfer and cytochrome/pili-mediated direct interspecies electron transfer for avoiding thermodynamic conflict, and (iii) integration of low-concentration O 2 as an ancillary thermodynamics-enhancing electron sink. Archaeal populations in situ support the above processes through novel metabolisms distinct from conventional methanogenesis – high-affinity H 2 oxidation driven by methyl-reducing methanogenesis and concomitant uptake of formate, electrons, and acetate from HS metabolism by Methanothrix. In total, synthesis of omics analyses and eco-thermodynamics reveals overlooked metabolic behavior and interactions of uncultured organisms that address a central issue in methanogenic carbon cycling, thermodynamic conflict among diverse concurrent metabolic processes.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

Background The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress. Results Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that anti- viral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities. Conclusions Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗

VQE method: a short survey and recent developments

Abstract The variational quantum eigensolver (VQE) is a method that uses a hybrid quantum-classical computational approach to find eigenvalues of a Hamiltonian. VQE has been proposed as an alternative to fully quantum algorithms such as quantum phase estimation (QPE) because fully quantum algorithms require quantum hardware that will not be accessible in the near future. VQE has been successfully applied to solve the electronic Schrödinger equation for a variety of small molecules. However, the scalability of this method is limited by two factors: the complexity of the quantum circuits and the complexity of the classical optimization problem. Both of these factors are affected by the choice of the variational ansatz used to represent the trial wave function. Hence, the construction of an efficient ansatz is an active area of research. Put another way, modern quantum computers are not capable of executing deep quantum circuits produced by using currently available ansatzes for problems that map onto more than several qubits. In this review, we present recent developments in the field of designing efficient ansatzes that fall into two categories—chemistry–inspired and hardware–efficient—that produce quantum circuits that are easier to run on modern hardware. We discuss the shortfalls of ansatzes originally formulated for VQE simulations, how they are addressed in more sophisticated methods, and the potential ways for further improvements.

Fedorov, Dmitry A. (ORCID:0000000316598580)↗

Prospects and applications of on-chip lasers

Abstract Integrated silicon photonics has sparked a significant ramp-up of investment in both academia and industry as a scalable, power-efficient, and eco-friendly solution. At the heart of this platform is the light source, which in itself, has been the focus of research and development extensively. This paper sheds light and conveys our perspective on the current state-of-the-art in different aspects of application-driven on-chip silicon lasers. We tackle this from two perspectives: device-level and system-wide points of view. In the former, the different routes taken in integrating on-chip lasers are explored from different material systems to the chosen integration methodologies. Then, the discussion focus is shifted towards system-wide applications that show great prospects in incorporating photonic integrated circuits (PIC) with on-chip lasers and active devices, namely, optical communications and interconnects, optical phased array-based LiDAR, sensors for chemical and biological analysis, integrated quantum technologies, and finally, optical computing. By leveraging the myriad inherent attractive features of integrated silicon photonics, this paper aims to inspire further development in incorporating PICs with on-chip lasers in, but not limited to, these applications for substantial performance gains, green solutions, and mass production.

Zhou, Zhican↗

An accumulation method for early fault warning and its application to wind turbine systems

Unexpected failures in engineering systems lead to expensive maintenance actions and should be avoided if at all possible. This is particularly true for wind turbine systems for which unexpected failures not only demand costly repairs but also cause long downtime. Motivated by this need, we present an accumulation method for fault early warning and failure anticipation. Here, our research shows that one critical element allowing the ability of early warning is to accumulate the small-magnitude symptoms resulting from gradual changes in an engineering system like wind turbines. Our idea is inspired by the classical cumulative sum method, or CUSUM, but we have to redesign the accumulation mechanism for tackling unique challenges in wind turbine data. The new accumulation method is applied to two real wind turbine datasets, one with gearbox failures and the other with generator failures, and demonstrates superior performance as compared with CUSUM.

17 WIND ENERGY↗

On the regeneration of fish scales: structure and mechanical behavior

Fish scales serve as a dermal armor that provides protection from physical injury. Owing to a number of outstanding properties, fish scales are inspiring new concepts for layered engineered materials and next-generation flexible armors. Although past efforts have primarily focused on the structure and mechanical behavior of ontogenetic scales, the structure–property relationships of regenerated scales have received limited attention. In the present study, common carp ( Cyprinus carpio ) acquired from the wild were held live in an aquatic laboratory at 10°C and 20°C. Ontogenetic scales were extracted from the fish for analysis, as well as regenerated scales after approximately 1 year of development and growth. Their microstructure was characterized using microscopy and Raman spectroscopy, and the mechanical properties were evaluated in uniaxial tension to failure under hydrated conditions. We note the strength, strain to fracture and toughness of the regenerated scales were significantly lower than those of ontogenetic scales from the same fish, regardless of the water temperature. Scales that regenerated at 20°C exhibited significantly higher strength, strain to fracture and toughness than those regenerated at 10°C. The regenerated scales exhibited a highly mineralized outer layer, but no distinct limiting layer or external elasmodine; they also possessed a significantly lower number of plies in the basal layer than the ontogenetic scales. The results suggest that a mineralized layer develops preferentially during scale regeneration with the topology needed for protection, prior to the development of other qualities.

59 BASIC BIOLOGICAL SCIENCES↗

Setup and verification of a SCALE/KENO platform for generic FHR benchmark calculations

The work presented in this article is preliminary to downstream analysis of a generic fluoride salt-cooled high-temperature reactor (gFHR) core performed by the University of Tennessee in collaboration with Kairos Power (KP). A Monte Carlo transport model of the publicly available gFHR equilibrium core is developed in SCALE/KENO with multigroup energy treatment. Several output quantities of interest are used to verify the simulations against a benchmark model developed by KP using the continuous energy Monte Carlo code Serpent 2. Good agreement is seen in flux and fission rate profiles with a maximum relative difference of 1.4% and 2.8% respectively. Furthermore, an effective multiplication factor bias of 44 pcm was observed between the two simulations. The fuel temperature reactivity coefficient calculated with SCALE is within uncertainty to the reference model. This verification acts as a publicly reproducible benchmark for the gFHR in SCALE/KENO. A simplified depletion model is also presented where a single fuel pebble is depleted to discharge burnup through the equilibrium core while the equilibrium core is assumed to be invariant. This method produces results that intercept the equilibrium core concentrations in every case, however, an interesting artifact of this particular depletion model is uncovered. The phenomenon is shown to be a fundamental feature of the differential rate equations and inspires questions about how this system behaves when the time evolution of the equilibrium core is considered. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

The fast neutron source at UTK: a project with Massimo Salvatores

This article is dedicated to the memory of Massimo Salvatores and offers an overview of the history of the design of the Fast Neutron Source (FNS) flexible experiment system at the University of Tennessee. Our collaboration with Massimo set much of the over-arching design goals and inspired the concept that we have today. The decision to design the FNS as a subcritical assembly rather than a critical one stems back to discussions with Massimo Salvatores and his advocacy for subcritical Accelerator Driven Systems (ADS) which coincides with lower licensing time, costs and greater safety for a university-operated nuclear experimental facility. The second contribution of Massimo to the design concept of the FNS was the direct instruction to design the FNS as an extremely flexible facility. This article provides an update on the current design concept and discusses the future innovations in design optimization of flexible, re-configurable nuclear experiments.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Cusp-artifacts in high order superresolution optical fluctuation imaging

Superresolution optical fluctuation imaging (SOFI) is a simple and affordable super-resolution imaging technique, and attracted a growing community over the past decade. However, the theoretical resolution enhancement of high order SOFI is still not fulfilled. In this study, we identify “cusp artifacts” in high order SOFI images, and show that the high-order cumulants, odd-order moments and balanced-cumulants (bSOFI) are highly vulnerable to cusp artifacts. Our study provides guidelines for developing and screening for fluorescence probes, and improving data acquisition for SOFI. The new insight is important to inspire positive utilization of the cusp artifacts.

47 OTHER INSTRUMENTATION↗

Coupling between plasmonic and photonic crystal modes in suspended three-dimensional meta-films

A complementary metal oxide semiconductor (CMOS) compatible fabrication method for creating three-dimensional (3D) meta-films is presented. In contrast to metasurfaces, meta-films possess structural variation throughout the thickness of the film and can possess a sub-wavelength scale structure in all three dimensions. Here we use this approach to create 2D arrays of cubic silicon nitride unit cells with plasmonic inclusions of elliptical metallic disks in horizontal and vertical orientations with lateral array-dimensions on the order of millimeters. Fourier transform infrared (FTIR) spectroscopy is used to measure the infrared transmission of meta-films with either horizontally or vertically oriented ellipses with varying eccentricity. Shape effects due to the ellipse eccentricity, as well as localized surface plasmon resonance (LSPR) effects due to the effective plasmonic wavelength are observed in the scattering response. The structures were modeled using rigorous coupled wave analysis (RCWA), finite difference time domain (Lumerical), and frequency domain finite element (COMSOL). The silicon nitride support structure possesses a complex in-plane photonic crystal slab band structure due to the periodicity of the unit cells. We show that adjustments to the physical dimensions of the ellipses can be used to control the coupling to this band structure. The horizontally oriented ellipses show narrow, distinct plasmonic resonances while the vertically oriented ellipses possess broader resonances, with lower overall transmission amplitude for a given ellipse geometry. We attribute this difference in resonance behavior to retardation effects. The ability to couple photonic slab modes with plasmonic inclusions enables a richer space of optical functionality for design of metamaterial-inspired optical components.

42 ENGINEERING↗

Orthogonal spatial coding with stimulated parametric down-conversion

Orthogonal optical coding is widely used in classical multi-user communication networks. Using the phase conjugation property of stimulated parametric down-conversion, we extend the current time-domain orthogonal optical coding scheme to the spatial domain to encode and decode image information. In this process, the idler beam inherits the complex conjugate of the field information encoded in the seed beam. An encoding phase mask introduced onto the input seed beam blurs the image transferred to the idler. The original image is restored by passing the coded transferred image through a corrective phase mask placed in the momentum space of the idler beam. We expect that this scheme can also inspire new techniques in secure image transmission, aberration cancellation, and frequency conversion imaging.

Xu, Yang↗

Combined speckle- and propagation-based single shot two-dimensional phase retrieval method

Single-shot two-dimensional (2D) phase retrieval (PR) can recover the phase shift distribution within an object from a single 2D x-ray phase contrast image (XPCI). Two competing XPCI imaging modalities often used for single-shot 2D PR to recover material properties critical for predictive performance capabilities are: speckle-based (SP-XPCI) and propagation-based (PB-XPCI) XPCI imaging. However, PR from SP-XPCI and PB-XPCI images are, respectively, limited to reconstructing accurately slowly and rapidly varying features due to noise and differences in their contrast mechanisms. Herein, we consider a combined speckle- and propagation-based XPCI (SPB-XPCI) image by introducing a mask to generate a reference pattern and imaging in the near-to-holographic regime to induce intensity modulations in the image. We develop a single-shot 2D PR method for SPB-XPCI images of pure phase objects without imposing restrictions such as object support constraints. It is compared against PR methods inspired by those developed for SP-XPCI and PB-XPCI on simulated and experimental images of a thin glass shell before and during shockwave compression. Reconstructed phase maps show improvements in quantitative scores of root-mean-square error and structural similarity index measure using our proposed method.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Tandem neural network-based controller for x-ray bimorph mirrors

Nanometer-scale shape control of x-ray mirrors is crucial for coherent x-ray beam experiments at low-emittance synchrotron beamline instruments. Piezoelectric bimorph mirrors offer adaptive control but are hindered by nonlinearities such as cross talk, creep, and hysteresis. To overcome these limitations, we present a novel feedback-free control solution, inspired by the proportional–integral–derivative (PID) scheme, driven by tandem neural networks (TNNs). Using task-specific datasets, the TNN-based system predicts actuator voltages with greater speed, accuracy, and stability than a single NN-based model. This approach is ideal for real-time applications, such as adapting beam focus to dynamic sample sizes while maintaining precise wavefront quality. Our findings highlight the potential of artificial intelligence in rapidly optimizing adaptive optics and managing nonlinear control systems.

Zhang, Runyu↗

Fast and accurate influenza forecasting in the United States with Inferno

Infectious disease forecasting is an emerging field and has the potential to improve public health through anticipatory resource allocation, situational awareness, and mitigation planning. By way of exploring and operationalizing disease forecasting, the U.S. Centers for Disease Control and Prevention (CDC) has hosted FluSight since the 2013/14 flu season, an annual flu forecasting challenge. Since FluSight’s onset, forecasters have developed and improved forecasting models in an effort to provide more timely, reliable, and accurate information about the likely progression of the outbreak. While improving the predictive performance of these forecasting models is often the primary objective, it is also important for a forecasting model to run quickly, facilitating further model development and improvement while providing flexibility when deployed in a real-time setting. In this vein I introduce Inferno, a fast and accurate flu forecasting model inspired by Dante, the top performing model in the 2018/19 FluSight challenge. When pseudoprospectively compared to all models that participated in FluSight 2018/19, Inferno would have placed 2nd in the national and regional challenge as well as the state challenge, behind only Dante. Inferno, however, runs in minutes and is trivially parallelizable, while Dante takes hours to run, representing a significant operational improvement with minimal impact to performance. Forecasting challenges like FluSight should continue to monitor and evaluate how they can be modified and expanded to incentivize the development of forecasting models that benefit public health.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗