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At least 343 records · Page 19

Engineering Forisome Scaffolds: Elucidating Spatial Self-Assembly Patterning of Bio-inorganic Complexes

Organisms can synthesize biomaterials incorporating an array of naturally occurring elements while overcoming challenges and insults. Although, it is known that most cellular biomaterials are synthesized in specialized cellular compartments, there are knowledge gaps about how organic/inorganic biomaterial synthesis is orchestrated inside cells. In addition, there is great potential in understanding how individual monomers can self-assembly into organized patterns to form responsive biomaterials. Forisomes are a natural responsive biomaterial found in legume plants that serve as a plug sieve element in the plant phloem that undergo anisotropic conformational changes by rapid (<1 s) ATP-independent from condensed spindle to plug-like form, triggered by the influx of Ca 2+ . Addressing principles of forisome synthesis and assembly will determine how biomaterials containing inorganic elements self-assemble and conduct chemical modification to produce biomaterials or undergo biomineralization. We employ transcription and translation (TXTL) using cell-free expression systems for forisome monomer expression, self-assembly, and pattern probing. We conducted experiments to precisely control forisome proteins synthesis of various monomers SEO1, SEO2, SEO3, and SEO4 to explore self- assembly. We demonstrate forisome self-assembly of the SEO monomers is possible and indicate unique monomer fluorescent labeling patterns that require additional analysis. We investigated locations and linkers for adding tetracysteine tag fluorophore probes to determine impacts of self-assembly and anisotropic conformational changes.

42 ENGINEERING↗

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics↗

Disentangling the Impacts of Microtopography and Shrub Distribution on Snow Depth in a Subarctic Watershed: Toward a Predictive Understanding of Snow Spatial Variability

Snow plays a critical role in carbon cycling, vegetation dynamics, and permafrost hydrology at high latitudes by influencing surface energy exchange. Predicting snow distribution patterns is essential for understanding the evolution of Arctic ecosystems, yet scaling process-level knowledge to landscape predictions remains challenging. Here, we analyze snow depth (2019 and 2022), terrain elevation, and vegetation height from a watershed on the Seward Peninsula, Alaska, to examine how topography and shrubs shape snow redistribution across spatial scales. We find that snow depth is strongly coupled to terrain at scales below ∼60 m but becomes increasingly decoupled at larger scales. The topographic model of snow depth variation, which transforms terrain data to align with these scale-dependent snow patterns, is well correlated with local snow depth variations (linear fit R 2 > 0.5 for 85% of 100-m patches). A machine learning reconstruction of shrub canopy snow trapping reveals a simple exponential relationship between canopy structure and snow accumulation ( R 2 = 0.59), highlighting the combined influence of topography and vegetation on snow distribution. Together, these empirical relationships capture much of the observed snow variability in the watershed ( R 2 = 0.49, root mean square error (RMSE) = 30 cm), though systematic limitations persist in areas of strong scour and at coarser scales where wind-terrain interactions are more complex. These findings provide a framework for more efficient snow depth prediction and offer insights to improve snow-vegetation feedback representation in Earth System Models.

54 ENVIRONMENTAL SCIENCES↗

Vegetation heterogeneity reflects soil thermal state and surface soil displacement in a thawing permafrost landscape

Thawing permafrost has the potential to dramatically alter the physical and ecological structure of northern landscapes. Warming of the Arctic and subsequent degradation of permafrost have created a need to assess the stability and movement of soils on hillslopes and the potential impacts on ecosystem structure. In this work, we explore the relationships among vegetation heterogeneity, soil temperature, and soil surface displacements observed from 2019 to 2022 in a watershed in the discontinuous permafrost region on the Seward Peninsula of Alaska. Vegetation heterogeneity was measured as the standard deviation (SD) of the normalized difference vegetation index (NDVI) from 3 m PlanetScope satellite imagery around each soil temperature and active layer thickness observation. Locations of observations were clustered into three soil thermal groups, warm, intermediate, and cold, based on soil temperature and active layer thickness. Average annual horizontal surface displacements were significantly lower for soils within the warm thermal group (median = 0.033 m yr −1 ) compared to soils within the cold thermal group (median = 0.090 m yr −1 ; p < 0.001). Conversely, vegetation heterogeneity was significantly higher in the warm (median = 0.014 SD NDVI; p = 0.002) and intermediate (median = 0.015 SD NDVI; p = 0.002) groups compared with the cold thermal group (median = 0.012 SD NDVI), suggesting a warming-induced shift in vegetation community complexity. Because of the observed associations of ground surface displacement rates and vegetation heterogeneity with soil thermal state, we hypothesize that warming soil conditions induce changes in the rates and patterns of hillslope erosion due to an increase in surface movement as near-surface permafrost thaws, followed by a decrease as the permafrost table deepens and excess ice content diminishes. The transition to warm soils promotes surface ecosystem transformation, shifting the dominant vegetation at the site, given the warming climatic conditions of the region. We integrated our observations of soil temperature, vegetation heterogeneity, and soil surface displacements into a conceptual model that describes the co-evolution of hillslopes and vegetation in warming permafrost environments, which is currently unrepresented in earth system models.

54 ENVIRONMENTAL SCIENCES↗

Using a Genetic Algorithm to Optimize Configurations in a Data-Driven Application

Users of highly-configurable software systems often want to optimize a particular objective such as improving a functional outcome or increasing system performance. One approach is to use an evolutionary algorithm. However, many applications today are data-driven, meaning they depend on inputs or data which can be complex and varied. Hence, a search needs to be run (and re-run) for all inputs, making optimization a heavy-weight and potentially impractical process. In this paper, we explore this issue on a data-driven highly-configurable scientific application. We build an exhaustive database containing 3,000 configurations and 10,000 inputs, leading to almost 100 million records as our oracle, and then run a genetic algorithm individually on each of the 10,000 inputs. We ask if (1) a genetic algorithm can find configurations to improve functional objectives; (2) whether patterns of best configurations over all input data emerge; and (3) if we can we use sampling to approximate the results. We find that the original (default) configuration is best only 34% of the time, while clear patterns emerge of other best configurations. Out of 3,000 possible configurations, only 112 distinct configurations achieve the optimal result at least once across all 10,000 inputs, suggesting the potential for lighter weight optimization approaches. We show that sampling of the input data finds similar patterns at a lower cost.

Sinha, Urjoshi↗

Intercalated chalcogenides Fe 1/4 TaS 2 and Fe 1/3 TaS 2 under extreme pressure—temperature conditions

Intercalation is an important strategy for enhancing functionality in complex chalcogenides. This is because layered materials can be endowed with intriguing properties by filling the van der Waals gap with various ions and molecules, which, in addition to their unique chemistry, break symmetry in new ways. In order to explore the properties of intercalated metal dichalcogenides under extreme pressure-temperature conditions, we combine diamond anvil cell techniques, Raman scattering spectroscopy, magnetic susceptibility, and first-principles calculations to reveal the pressure–temperature phase diagram of Fe 1/3 TaS 2 . This system hosts a compression-driven structural phase transition to a polar state as well as remnant charge density wave signatures deriving from the host lamella of the 2H-parent compound. We also explore the role of different A-site patterns and determine that, by comparison, Fe 1/4 TaS 2 is soft and flexible due to the lower metal density inside the van der Waals gap. These findings open the door to entirely new states of matter with exciting property combinations, including metallicity, polarity, chirality, and altermagnetism – depending upon the conditions – that can support a wide range of spintronics and phononics applications.

Materials science↗

Real-time neutron multiplicity and source localization for criticality safety during fuel debris removal

Advancing neutron detection and analysis techniques for complex radiation environments is an ongoing focus in nuclear instrumentation and monitoring. This proposal presents research and development of a generalized real-time neutron monitoring and analysis system, applicable to any detector capable of producing time-tagged neutron count data. While the work is demonstrated using the Neutron Multiplication Analysis Detector (NoMAD), a modular 15-tube helium-3 (He-3) array, due to its availability, spatial resolution, and flexible deployment, the methods developed are extensible to other systems, including organic scintillators and fast digital detectors. This research investigates two complementary analytical techniques for real-time characterization of neutron emitting sources: neutron multiplicity estimation based on the Hage-Cifarelli formalism and spatial localization using supervised machine learning applied to spatial count rate patterns. These methods are designed to operate under dynamic, evolving conditions such as fuel debris retrieval or reactor startup, where neutron-emitting material geometries may be partially unknown or changing over time. By integrating statistical neutron emission data with spatial localization, this research aims to develop and evaluate methods for real time neutron monitoring, source characterization, and material verification. Key contributions include implementation of a low-latency data pipeline for continuous neutron multiplicity analysis, development and validation of machine learning models for spatial inference, and experimental evaluation of system performance under variable measurement conditions. The outcomes are intended to support applications in nuclear safeguards, verification, emergency response, and reactor startup.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

On differentiable local bounds preserving stabilization for Euler equations

This work presents the design of nonlinear stabilization techniques for the finite element discretization of Euler equations in both steady and transient form. Implicit time integration is used in the case of the transient form. A differentiable local bounds preserving method has been developed, which combines a Rusanov artificial diffusion operator and a differentiable shock detector. Nonlinear stabilization schemes are usually stiff and highly nonlinear. This issue is mitigated by the differentiability properties of the proposed method. Moreover, in order to further improve the nonlinear convergence, we also propose a continuation method for a subset of the stabilization parameters. The resulting method has been successfully applied to steady and transient problems with complex shock patterns. Numerical experiments show that it is able to provide sharp and well resolved shocks. Furthermore, the importance of the differentiability is assessed by comparing the new scheme with its non-differentiable counterpart. Numerical experiments suggest that, for up to moderate nonlinear tolerances, the method exhibits improved robustness and nonlinear convergence behavior for steady problems. Additionally, in the case of transient problem, we also observe a reduction in the computational cost.

42 ENGINEERING↗

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data

The dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D fast Fourier transforms, correlation, and pair distribution functions are explored using the unsupervised linear unmixing, demonstrating the presence of static ordered and dynamic disordered phases and establishing their time dynamics. Here, the deep learning (DL)-based workflow is developed to analyze detailed particle dynamics and explore the evolution of local geometries. Finally, we use a combination of DL feature extraction and mixture modeling to define particle neighborhoods free of physics constraints, allowing for a separation of possible classes of particle behavior and identification of the associated transitions. Overall, this work establishes the workflow for the analysis of the self-organization processes in complex systems from observational data and provides insight into the fundamental mechanisms.

36 MATERIALS SCIENCE↗

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

ABSTRACT The Shox2 homeodomain transcriptional regulator is known for its critical functions during mouse embryogenesis, enabling accurate development of limbs, craniofacial structures, neural populations and the cardiac conduction system. At the genomic level, the Shox2 gene is flanked by an extensive gene desert, a continuous non-coding genomic region spanning over 500 kilobases that contains a multitude of evolutionarily conserved elements with predicted cis -regulatory activities. However, the transcriptional enhancer potential of the vast majority of these elements in combination with the biological necessity of the gene desert have not yet been explored. Using transgenic reporter assays in mouse embryos to validate an extensive set of stringent epigenomic enhancer predictions, we identify several novel gene desert enhancers with distinct tissue-specific activities in Shox2 expressing tissues. 4C-seq chromatin conformation capture further uncovers a repertoire of gene desert enhancers with overlapping activities in the proximal limb, in a compartment essential for Shox2 -mediated stylopod formation. Leveraging CRISPR/Cas9 to delete the gene desert region contained in the Shox2 topologically associated domain (TAD), we demonstrate that this complex cis -regulatory platform is essential for embryonic survival and required for control of region-specific Shox2 expression in multiple developing tissues. While transcription of Shox2 in the embryonic limb is only moderately affected by gene desert loss, Shox2 expression in craniofacial and cardiac domains is nearly abolished. In particular, Shox2 transcripts in the sinus venosus (SV) encompassing the sinoatrial node (SAN) were depleted in embryos lacking the gene desert, likely accounting for the embryonic lethality due to Shox2 -dependency of the SAN pacemaker. Finally, we discover a 1.5kb SV enhancer within the deleted gene desert region, which may act as a genomic module controlling the development of the cardiac conduction system. In summary, our results identify a gene desert indispensable for pleiotropic patterning and highlight the importance of these extensive regulatory landscapes for embryonic development and viability.

Abassah-Oppong, Samuel↗

Optimal carbon storage reservoir management through deep reinforcement learning

Model-based optimization plays a central role in energy system design and management. The complexity and high-dimensionality of many process-level models, especially those used for geosystem energy exploration and utilization, often lead to formidable computational costs when the dimension of decision space is also large. This work adopts elements of recently advanced deep learning techniques to solve a sequential decision-making problem in applied geosystem management. Specifically, a deep reinforcement learning framework was formed for optimal multiperiod planning, in which a deep Q-learning network (DQN) agent was trained to maximize rewards by learning from high-dimensional inputs and from exploitation of its past experiences. To expedite computation, deep multitask learning was used to approximate high-dimensional, multistate transition functions. Both DQN and deep multitask learning are pattern based. As a demonstration, the framework was applied to optimal carbon sequestration reservoir planning using two different types of management strategies: monitoring only and brine extraction. Both strategies are designed to mitigate potential risks due to pressure buildup. Results show that the DQN agent can identify the optimal policies to maximize the reward for given risk and cost constraints. Finally, experiments also show that knowledge the agent gained from interacting with one environment is largely preserved when deploying the same agent in other similar environments.

15 GEOTHERMAL ENERGY↗

Machine Learning Models for Mapping Groundwater Pollution Risk: Advancing Water Security and Sustainable Development Goals in Georgia, USA

The widespread use of pesticides, such as atrazine and malathion, in agricultural systems raises significant concerns regarding the contamination of groundwater, which serves as a critical resource for drinking water. This study applies machine learning techniques to predict the concentrations of atrazine and malathion in groundwater across Georgia, USA, using 2019 data. A Random Forest classifier was employed to integrate various environmental and demographic factors, including pesticide application rates, precipitation, lithology, and population density, to predict pesticide contamination in groundwater. The models demonstrated high training accuracies of 100% and moderate average testing accuracy of 55% for atrazine and 60% for malathion across five iterations. The low test accuracy of the model, ranging from 50% to 75%, is likely due to overfitting, which can be attributed to the small dataset size and the complex nature of pesticide-contamination patterns, making it challenging for the model to generalize to unseen data. Feature importance analysis revealed that average pesticide usage emerged as the most influential factor for atrazine, while aquifer lithology and precipitation played crucial roles in both models. These results provide valuable insights into the dynamics of pesticide contamination, highlighting areas at greater risk of contamination. The findings underscore the importance of integrating environmental, geological, and agricultural variables for more effective groundwater management and sustainable agricultural practices, contributing to the protection of water resources and public health.

54 ENVIRONMENTAL SCIENCES↗

Designing Energy-Efficient Quantum Computers Through Prediction and Reduction of Cooling Requirements for Cryogenic Electronics

Quantum computing has been identified as a “wild card” by the International Energy Agency in predicting future global data center energy usage. This is primarily because both uncertainty in the extent to which quantum computing will be adopted, and uncertainty in the power consumption of individual quantum data centers. Unlike the classical counterparts, quantum computers need to be maintained at near absolute zero, requiring energy-intensive cryogenic cooling systems. Therefore, as quantum computers scale up from existing 50 qubit technology demonstrations to the 10,000 to 100,000 qubit systems that will be able to solve complex problems, the energy consumption of both the electronics and the required cooling systems will also increase. To predict this scaling, this work analyzes the energy requirements for both computation and cooling of quantum hardware. We show that the energy requirements for cooling of quantum computers is determined by several computing system parameters, including the number and type of physical qubits, the operating temperature, the packaging efficiency of the system, and the split between circuits operating at cryogenic temperatures and those operating at room temperature. The energy requirements can then be found based on thermal system parameters such as cooling efficiency and cryostat heat transfer. Analysis of these parameters shows that the energy required for cooling is significantly larger than that required for computation, a reversal from energy usage patterns seen in conventional computing. The results and discussions provide a road-map for creating energy efficient quantum computers through the selection of computer architectures and cryogenic system configurations that minimize cooling requirements.

energy efficiency↗

Role of uncertainties in protecting ecological resources during remediation and restoration

Cleanup of contaminated waste sites is a National priority to protect human health and the environment, while restoring land to productive uses. While there are uncertainties with under standing risk to individuals from exposure, the aim of this study was to focus on uncertainties and complexities for ecological systems, complicated by hundreds of species occupying any remediation site which participate in multiple-interacting food webs. The ability to better predict the effectiveness of remediation in fostering future ecosystems might facilitate remedy selection and improve strategic environmental management. This investigation examined (1) uncertainties in ecosystem processes, (2) uncertainties in exposure from contamination before remediation, and (3) uncertainties during remediation. Two Department of Energy sites Hanford Site and Savannah River Site were used as case studies to illustrate how the uncertainties affect eco-receptors. Several types of ecological, physical, and human dimension uncertainties are defined. Ecological uncertainties include temporal, spatial, individual, developmental, and exogenous types. Physical uncertainties are weather-related, watershed variations, slope/aspect, soil/sediment structure and form, unforeseen events, and temporal patterns. Human dimension uncertainties include current land use, future land use, extractive and non-extractive recreation. The effects of remedial strategies varied between the two sites because Hanford is a primarily arid shrub-steppe ecotype, while Savannah River is a wet forest ecotype. Defining the associated ecological sensitivities and uncertainties and providing examples might help policy-makers, managers, planners, and contractors to be aware of issues to consider throughout planning, remediation, and restoration. Adding ecological uncertainty analysis to risk evaluations and remediation planning is analogous to using safety factors in human health risk assessment.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Long-term climate change and periodic environmental extremes threaten food and fuel security and global crop productivity. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation—knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass ( Panicum virgatum ). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

09 BIOMASS FUELS↗

Machine Learning Classification Strategy to Improve Streamflow Estimates in Diverse River Basins in the Colorado River Basin

Streamflow in the Colorado River Basin (CRB) is significantly altered by human activities including land use/cover alterations, reservoir operation, irrigation, and water exports. Climate is also highly varied across the CRB which contains snowpack-dominated watersheds and arid, precipitation-dominated basins. Recently, machine learning methods have improved the generalizability and accuracy of streamflow models. Previous successes with LSTM modeling have primarily focused on unimpacted basins, and few studies have included human impacted systems in either regional or single-basin modeling. We demonstrate that the diverse hydrological behavior of river basins in the CRB are too difficult to model with a single, regional model. We propose a method to delineate catchments into categories based on the level of predictability, hydrological characteristics, and the level of human influence. Lastly, we model streamflow in each category with climate and anthropogenic proxy data sets and use feature importance methods to assess whether model performance improves with additional relevant data. Overall, land use cover data at a low temporal resolution was not sufficient to capture the irregular patterns of reservoir releases, demonstrating the importance of having high-resolution reservoir release data sets at a global scale. On the other hand, the classification approach reduced the complexity of the data and has the potential to improve streamflow forecasts in human-altered regions.

54 ENVIRONMENTAL SCIENCES↗

Evaluating the effects of heatwave events on hydrological processes in the contiguous United States (2003–2022)

Extreme heat and drought conditions are affecting water availability in many regions worldwide, leading to negative impacts on human societies, agriculture, and ecosystems. However, current research lacks comprehensive spatiotemporal analysis examining the interplay between multiple hydrological factors and heatwave events, especially in the context of climate change. This research broadly pertains to understanding the dynamics of hydrological factors and their potential responses to heatwave during warm seasons across the contiguous United States for the period from 2003 to 2022. Utilizing data from the Global Land Data Assimilation System (GLDAS), we analyzed surface runoff, evapotranspiration (ET), precipitation, Groundwater Storage (GWS), Root Zone Soil Moisture (RZSM), and Total Water Storage (TWS) to discern annual patterns and the impacts of heatwave. Further, the spatial patterns of heatwave highlighted a higher occurrence in the western, central, and northeastern U.S., with longer average durations in the western and south-central regions. These events are predominantly dry, characterized by low Relative Humidity (RH), except in the southeastern U.S., where heatwave coincide with high RH levels. Post-heatwave analysis indicated a reduction in GWS, TWS, RZSM, and ET, alongside an increase in surface runoff, RH, and precipitation. An in-depth examination of rainfall and temperature dynamics during heatwave revealed weak correlations between rainfall and temperature, as well as between rainfall and heatwave duration, highlighting the complex nature of these interactions. The study also found an enhanced probability of rainfall following heatwave, particularly in the eastern regions, drawing attention to the potential for increased flood risks post-heatwave. Our findings contribute to the growing body of knowledge on the impacts of heatwave on hydrological factors, providing valuable insights for climate change adaptation and water resource management strategies.

54 ENVIRONMENTAL SCIENCES↗

Improving CLM5.0 Biomass and Carbon Exchange Across the Western United States Using a Data Assimilation System

The Western United States is dominated by natural lands that play a critical role for carbon balance, water quality, and timber reserves. This region is also particularly vulnerable to forest mortality from drought, insect attack, and wildfires, thus requiring constant monitoring to assess ecosystem health. Carbon monitoring techniques are challenged by the complex mountainous terrain, thus there is an opportunity for data assimilation systems that combine land surface models and satellite-derived observations to provide improved carbon monitoring. Here, we use the Data Assimilation Research Testbed to adjust the Community Land Model (CLM5.0) with remotely sensed observations of leaf area and above-ground biomass. The adjusted simulation significantly reduced the above-ground biomass and leaf area, leading to a reduction in both photosynthesis and respiration fluxes. The reduction in the carbon fluxes mostly offset, thus both the adjusted and free simulation projected a weak carbon sink to the land. This result differed from a separate observation-constrained model (FLUXCOM) that projected strong carbon uptake to the land. Simulation diagnostics suggested water limitation had an important influence upon the magnitude and spatial pattern of carbon uptake through photosynthesis. We recommend that additional observations important for water cycling (e.g., snow water equivalent, land surface temperature) be included to improve the veracity of the spatial pattern in carbon uptake. Furthermore, the assimilation system should be enhanced to maximize the number of the simulated state variables that are adjusted, especially those related to the recommended observed quantities including water cycling and soil carbon.

54 ENVIRONMENTAL SCIENCES↗