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At least 451 records · Page 25

High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

There is increasing interest in harnessing the functional diversity of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Understanding the response of communities to stimulation, including flanking taxa, presents important opportunities for optimizing remediation approaches. We used high-density PhyloChip microarray analysis to comprehensively determine community membership and abundance patterns amongst a suite of samples from U(VI) bioremediation experiments. Samples were unstimulated or collected during Fe(III) and sulfate reduction from an acetate-augmented aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Results showed the greatest diversity in abundant SRB lineages was present in naturally-reduced sediment. Desulfuromonadales and Desulfobacterales were consistently identified as the dominant Fe(III)- and sulfate-reducing bacteria (IRB and SRB) throughout acetate amendment experiments. Stimulated communities also exhibited a high degree of functional redundancy amongst enriched flanking members. Not surprisingly, competition for both sulfate and iron was evident amongst abundant taxa, but the distribution and abundance of these ancillary SRB (Peptococcaceae, Desulfovibrionales and Syntrophobacterales), and lineages containing IRB (excluding Desulfobacteraceae) was heterogeneous amongst sample types. Interesting, amongst the most abundant taxa, particularly during sulfate reduction, were Epsilonproteobacteria that perform microaerobic or nitrate-dependant sulfur oxidation, and a number of bacteria other than Geobacteraceae that may enzymatically reduce U(VI). Finally, in depth community probing with PhyloChip determined the efficacy of experimental approaches, notably revealing striking similarity amongst stimulated sediment (from drill cores and in-situ columns) and groundwater communities, and demonstrating that sediment-packed in-situ (down-well) columns served as an ideal method for subsurface biostimulation.

54 ENVIRONMENTAL SCIENCES↗

NPQ (T) : a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem-II-associated antenna complexes: New, rapid probe of non-photochemical quenching

In photosynthesis, light energy is absorbed by light-harvesting complexes and used to drive photochemistry. However, a fraction of absorbed light is lost to non-photochemical quenching (NPQ) that reflects several important photosynthetic processes to dissipate excess energy. Currently, estimates of NPQ and its individual components (q E , q I , q Z and q T ) are measured from pulse-amplitude-modulation (PAM) measurements of chlorophyll fluorescence yield and require measurements of the maximal yield of fluorescence in fully dark-adapted material (F m ), when NPQ is assumed to be negligible. Unfortunately, this approach requires extensive dark acclimation, often precluding widespread or high-throughput use, particularly under field conditions or in imaging applications, while introducing artefacts when F m is measured in the presence of residual photodamaged centres. To address these limitations, we derived and characterized a new set of parameters, NPQ (T) , and its components that can be (1) measured in a few seconds, allowing for high-throughput and field applications; (2) does not require full relaxation of quenching processes and thus can be applied to photoinhibited materials; (3) can distinguish between NPQ and chloroplast movements; and (4) can be used to image NPQ in plants with large leaf movements. Finally, we discuss the applications benefits and caveats of both approaches.

chlorophyll fluorescence↗

Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity

Notch receptor activation initiates cell fate decisions and is distinctive in its reliance on mechanical force and protein glycosylation. The 2.5-angstrom-resolution crystal structure of the extracellular interacting region of Notch1 complexed with an engineered, high-affinity variant of Jagged1 (Jag1) reveals a binding interface that extends ~120 angstroms along five consecutive domains of each protein. O-Linked fucose modifications on Notch1 epidermal growth factor–like (EGF) domains 8 and 12 engage the EGF3 and C2 domains of Jag1, respectively, and different Notch1 domains are favored in binding to Jag1 than those that bind to the Delta-like 4 ligand. Jag1 undergoes conformational changes upon Notch binding, exhibiting catch bond behavior that prolongs interactions in the range of forces required for Notch activation. In conclusion, this mechanism enables cellular forces to regulate binding, discriminate among Notch ligands, and potentiate Notch signaling.

60 APPLIED LIFE SCIENCES↗

Autonomy and Complexity at Sandia Executive Summary of Academic Alliance Workshop on Autonomy and Complex Systems.

Sandia has identified autonomy as a strategic initiative and an important area for providing national leadership. A key question is, “How might autonomy change how we think about the national security challenges we address and the kinds of solutions we deliver?” Three workshops at Sandia early in 2017 brought together internal stakeholders and potential academic partners in autonomy to address this question. The first focused on programmatic applications and needs. The second explored existing internal capabilities and research and development needs. This report summarizes the outcome of the third workshop, held March 3, 2017 in Albuquerque, NM, which engaged Academic Alliance partners in autonomy efforts at Sandia by discussing research needs and synergistic areas of interest within the complex systems and system modeling domains, and identifying opportunities for partnering on laboratory directed and other joint research opportunities.

42 ENGINEERING↗

Recordation of Buildings 9207 and 9210: The Oak Ridge National Laboratory Biology Complex, Located at the Y-12 National Security Complex, Oak Ridge, Tennessee

In the summer of 2018, Cultural Resource Analysts, Inc. (CRA) prepared this recordation package for two World War II-era buildings (Buildings 9207 and 9210) located within what is now known as the Y-12 National Security Complex (Y-12) in Oak Ridge, Tennessee. This recordation also briefly addresses Buildings 9767-6, 9767-7, and 9207A: two small utilities buildings and an annex to Building 9207, each of which was constructed in the 1960s. Completed at the request of UT-Battelle, LLC (UT-B) on behalf of the U.S. Department of Energy (DOE), this document has been prepared to document the history and current conditions of Buildings 9207 and 9210, which had previously been determined eligible for listing in the National Register of Historic Places (NRHP).

99 GENERAL AND MISCELLANEOUS↗

Closing the Loop between In Situ Stress Complexity and EGS Fracture Complexity

We present an agent-guided approach to CAD geometry decomposition that automates hex/hybrid meshing with graph neural networks (GNNs) to accelerate next-generation ModSim workflows. Our end-to-end pipeline (i) reduces 3D boundary-representation (B-Rep) models to a 2D chordal axis skeleton (CAT) and then to a 1D bipartite graph of surface and curve nodes, (ii) assigns per node labels as Cubit® WebCut actions, (iii) trains a multi-action GNN under supervised learning, and (iv) predicts five surface-node and three curve-node actions on out-of-distribution test geometries. Each graph node carries geometric, topological, and meshing attributes drawn from the B-Rep “skin” and CAT “skeleton,” with two-way mappings across 3D↔2D↔1D representations to maintain traceability back to 3D CAD. The supervised learning model exhibits stable convergence of the binary cross-entropy loss and achieves 98.7% accuracy on unseen lattice models. To operationalize decision-making, we rank predicted commands by geometric significance and prototyped the agent-guided workflow through the Cubit® Meshing PowerTool GUI. As a stretch goal, we explore reinforcement learning (RL) to reduce or remove label requirements and to learn policies for action sequences that maximize total reward (e.g., size of hex-meshable regions and resulting hex mesh quality). When all-hex meshing is not feasible, the agent assists in producing hybrid meshes—prioritizing hex in critical regions and transitioning to tetrahedral elements (tets) elsewhere—maintaining fidelity while ensuring robustness. The overarching objective is to replace manual, heuristics-based decomposition with data-driven, reproducible automation, cutting meshing turnaround time by orders of magnitude. We anticipate direct impact on simulation workflows through intelligent, scalable decomposition of complex CAD models into hex-meshable subdomains.

42 ENGINEERING↗

Final Report for Closing the Loop Between In Situ Stress Complexity and EGS Fracture Complexity

Characterizing in situ stress is essential in Enhanced Geothermal System (EGS) for both risk assessment and operation design. Standard stress measurement techniques such as diagnostic fracture injection tests (DFITs) require creating hydraulic fractures and apply analytical methods such as the G -function analysis to estimate the stress. These classical approaches rely on several assumptions, including but not limited to: (i) the induced fracture is planar and persistent, and (ii) the fracture plane is normal to the minimum horizontal stress. However, these assumptions may not hold in EGS environments like Utah FORGE, where thermo-hydro-mechanical (THM) coupling, wellbore deviation, and rock heterogeneity can alter the local stress condition and consequently lead to fracture complexities in both near-well and far-field regions.

15 GEOTHERMAL ENERGY↗

Gas-Phase Dimerization of Ethylene under Mild Conditions Catalyzed by MOF Materials Containing (bpy)Ni II Complexes

NU-1000-(bpy)Ni II , a highly porous MOF material possessing well-defined (bpy)Ni II moieties, was prepared through solvent-assisted ligand incorporation (SALI). Treatment with Et 2 AlCl affords a single-site catalyst with excellent catalytic activity for ethylene dimerization (intrinsic activity for butenes that is up to an order of magnitude higher than the corresponding (bpy)NiCl 2 homogeneous analogue) and stability (can be reused at least three times). The high porosity of this catalyst results in outstanding levels of activity at ambient temperature in gas-phase ethylene dimerization reactions, both under batch and continuous flow conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluating the WFIP2 updates to the HRRR model using scanning Doppler lidar measurements in the complex terrain of the Columbia River Basin

The wind-energy (WE) industry relies on numerical weather prediction (NWP) forecast models as foundational or base models for many purposes, including wind-resource assessment and wind-power forecasting. During the Second Wind Forecast Improvement Project (WFIP2) in the Columbia River Basin of Oregon and Washington, a significant effort was made to improve NWP forecasts through focused model development, to include experimental refinements to the High Resolution Rapid Refresh (HRRR) model physics and horizontal grid spacing. In this study, the performance of an experimental version of HRRR that includes these refinements is tested against a control version, which corresponds to that of the operational HRRR run by National Oceanic and Atmospheric Administration/National Centers for Environmental Protection at the outset of WFIP2. Furthermore, the effects of horizontal grid resolution were also tested by comparing wind forecasts from the HRRR (with 3-km grid spacing) with those from a finer-resolution HRRR nest with 750-m grid spacing. Model forecasts are validated against accurate wind-profile measurements by three scanning, pulsed Doppler lidars at sites separated by a total distance of 71 km. Model skill and improvements in model skill, attributable to physics refinements and improved horizontal grid resolution, varied by season, by site, and during periods of atmospheric phenomena relevant to WE. In general, model errors were the largest below 150 m above ground level (AGL). Experimental HRRR refinements tended to reduce the mean absolute error (MAE) and other error metrics for many conditions, but degradation in skill (increased MAE) was noted below 150 m AGL at the two lowest-elevation sites at night. Finer resolution was found to produce the most significant reductions in the error metrics.

17 WIND ENERGY↗

Southeast Regional CO 2 Utilization and Storage Acceleration Partnership (SECARB-USA): Preliminary Regional Assessment of Potential Storage Complexes, Including Capacities and Costs, Based on Application of NRAP and SCO2T (Deliverable 3.3) Storage Complexes

The Recipient will assist with the field validation of one or more risk assessment toolsets through: 1) collaborative research; 2) sharing of relevant datasets, information, and technical insights from field efforts; and 3) other modeling and simulation toolsets as they are developed. Collaborative research could include, but is not limited to: 1) demonstrating use of field data for improved leakage pathway characterization, uncertainty reduction, and risk management and uncertainty workflows; 2) testing and validation of a specific National Risk Assessment Partnership (NRAP) tool using site specific data; and 3) improved modeling or reduced-order modeling of geophysical monitoring.

42 ENGINEERING↗