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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 541 records · Page 30

Elucidating Abnormal Grain Growth in Thermomagnetic Processed Materials with Transfer Learning and Reinforcement Learning

The goal of this research program is to establish the mechanism governing local grain boundary motion, which is needed to design and process desirable microstructures for better performance, by identifying the relative contributions of grain boundary (GB) energy and mobility to grain growth. Classical models for grain growth assume that the primary mechanism for reducing the total interfacial energy is area reduction and that GB restructuring is not significant. This assumption implies that grain growth is locally driven by curvature. However, recent experimental observations using new non-destructive 3D x-ray diffraction microscopy techniques (3D-XRM) reveal that classic descriptors (i.e., curvature, number of neighbors, grain size) do not predict real grain growth. Instead, local GB motion appears to be governed by its energy relative to its neighbors such that low-energy boundaries replace those of higher energy. However, simulations that incorporate GB energy anisotropy still fail to reproduce these observations. These discrepancies suggest that the common assumption for grain growth theory must be re-examined to predict and, thus, control microstructure evolution in real polycrystals. A significant challenge to testing this assumption is due to anisotropic GB mobility. Mobility may cause abnormal grain growth or affect the final grain shapes or growth rate but its true contributions are unknown because it is difficult to measure. For example, observations in Fe have found that grains associated with high energy and high mobility boundaries tend to experience abnormal grain growth, whereas abnormal grain growth is associated with low energy and high mobility boundaries in alumina. As mobility and energy both control GB motion, it is challenging to isolate the local driving forces necessary to test the common assumption that the primary mechanism is area reduction. The novelty of this work is the use of machine learning tools to capture GB mobility and energy from 3D-XRM measurements in polycrystals to test the common assumption used in grain growth models. Machine learning can capture high-order correlations in dynamic systems like those found in the evolving GB topology. The PIs have developed a physics-regularized interpretable machine learning microstructure evolution (PRIMME) model that accurately replicates the grain growth behavior of its trained data set.

36 MATERIALS SCIENCE↗

National Energy Water Treatment & Speciation (NEWTS): A Water & Critical Mineral Database and Dashboard

The scarcity of water resources, the need for beneficial water reuse, and the challenges of wastewater treatment are becoming increasingly pressing in economic, social, and environmental domains. Addressing these concerns requires effective treatment strategies to manage wastewater streams and tackle environmental and economic issues. Furthermore, the recovery of critical minerals from the waste streams associated with energy production holds the promise of offsetting treatment costs and securing local sources of valuable minerals. However, relevant data on these waste streams are dispersed and challenging to locate. The process of ingesting such data into modeling software often involves multiple steps, requiring data restructuring to meet software-input requirements. The non-standardized reporting of water data makes data aggregation and reformatting a time-consuming process. Additionally, essential attributes necessary for modeling water treatment and mineral scale formation are frequently missing. Moreover, data gaps vary depending on the region of interest. Consequently, there is a pressing need for high-quality energy-water composition data that can be easily imported into water chemistry modeling software. To address this need, the National Energy Technology Laboratory has created the National Energy Water Treatment and Speciation (NEWTS) Database and Dashboard—a free online tool catering to community leaders and water researchers. NEWTS facilitates a comprehensive understanding of the composition of energy-related wastewater streams in the United States. The datasets provide detailed concentrations and speciation of major and minor aqueous compounds in energy-related wastewater streams, including power plant leachate, acid mine drainage, brackish water, and oil and gas produced water across the United States. Many of the aqueous species are critical minerals (Li, REEs) in high demand to modernize the world’s energy infrastructure. Many of the datasets also contain volumetric flow-rates needed to model the treatment and reuse scenarios in advanced aqueous chemistry software programs. The NEWTS Database and Dashboard offer public access to hitherto challenging-to-access datasets, presented in a standardized format that is tailored for easy input into aqueous chemistry modeling software. By performing the work needed to transform dispersed, disparate data sources into unified, model-ready datasets, NEWTS serves as an essential resource in advancing water treatment research and sustainable water resource management.

produced water management↗

The Concept and Role of Reference Architectures In NIF LRU Refurbishment Factories within LLNL

The National Ignition Facility (NIF) at Lawrence Livermore National Laboratory (LLNL) operates one of the most advanced laser systems in the world, relying on a vast number of optical components and Line Replaceable Units (LRUs) to maintain its functionality. Over time, these components degrade due to operational wear, necessitating refurbishment to sustain performance. However, many NIF LRU refurbishment factories have been “mothballed” or suffer from aging infrastructure, inconsistent work flows, and inefficiencies due to different approaches to production control and management. This paper explores the concept of reference architecture as a standardized framework to guide the redevelopment and restructuring of NIF LRU refurbishment factories. By establishing a common reference architecture, the refurbishment process can achieve reduced inefficiencies, produce quality products, and enhanced coordination across factories. This paper evaluates existing reference architectures, particularly those that integrate technical architecture, business architecture, customer context perspectives, and proposes tailored reference architecture for NIF LRU refurbishment factories.

42 ENGINEERING↗

Autonomous Fueling System for Heavy-Duty Fuel Cell Electric Trucks

The motivation for this project stemmed from the challenges associated with rapidly refueling heavy-duty hydrogen fuel cell electric trucks (FCETs). Current manual refueling processes for fast refueling involve large, heavy equipment (e.g., hoses three times heavier than standard) and pose ergonomic risks and potential for equipment damage. The goal was to develop and test an autonomous fueling system to improve ergonomics, enhance safety, increase equipment durability through design improvements, and potentially speed up the fueling process. This project aimed to add to the understanding of autonomous systems in the context of heavy-duty hydrogen refueling, evaluating the technical effectiveness of potential concepts. A successfully developed system would benefit the public by facilitating the adoption of zero-emission heavy-duty transport, reducing reliance on manual labor for a physically demanding task, and potentially improving the safety and efficiency of hydrogen refueling infrastructure. The major accomplishment during the project's active period was the completion of the system-level architecture task. This involved establishing a detailed list of system requirements covering interfaces, environmental conditions, regulatory compliance, industry standards, safety, security, performance capabilities, and optional features. Five key use cases for the autonomous system were also identified. However, due to internal restructuring at Nikola, the necessary resources could not be allocated to continue the project. Consequently, Nikola opted to discontinue the project. The award was mutually terminated by Nikola and the DOE.

08 HYDROGEN↗

Exploring Multilayer Network Models to Build a Scientific Basis for Integrated Deterrence: Final Report

The emerging multipolar international security environment represents a fundamental restructuring of global nuclear balance of power to include two nuclear peer competitors, growing non-peer nuclear threats, and concerns of nuclear latency from both allies and adversaries. Conflicts in the grey zone, cyber operations, mis- and disinformation campaigns, and emerging disruptive technologies like drones, and hypersonic missiles are becoming more prevalent. These present a risk of cross-domain and multi-domain conflicts that may not follow known escalatory patterns. In order to prepare for the new deterrence environment, it is critical to have quantitative and qualitative understandings of these cross-domain conflicts, their potential for escalation, and which systems they may impact. To that end, our team created a Multi-Layer Network (MLN) model of ‘integrated deterrence’ where instruments of national power are modeled as individual network graph layers that include efforts from all domains. We then evaluate the potential for escalation against escalation scenarios. Analysis of the escalation scenarios is then used to identify insights of potential risk and escalation within integrated deterrence.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

A Study of Emerging Ancillary Service Markets in Non-Restricted Regions of the Western Power Grid (CRADA Final Report)

Rising penetrations of renewable energy generation in the Western United States pose new requirements for ancillary services, which are the services required, in addition to energy service, in order to maintain the system reliability. This project combines the research capabilities of the National Renewable Energy Laboratory (NREL) and the University of Colorado at Boulder (CU-Boulder) to provide more accurate information to market participants and regulators about the present and future size and composition of ancillary service markets in the non-restructured regions of the West. This information would provide market participants and state and federal regulators with a more transparent view of future ancillary service markets, and allow for more efficient system planning in both the private and public sectors of the electricity market.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Core Model Proposal 382: Representing agricultural and food storage

Purpose: This Core Model Proposal develops data and methods to represent agricultural storage and the inter-period stockholding behavior for agricultural and food products in global economic and multisector dynamic modeling. In particular, the proposal aims to (1) restructure and rebalance the supply-utilization accounts to separate stock variations, opening stock, closing stock, and loss associated with stockholding behavior, (2) incorporate agricultural stockholding behavior as a technology of regional consumers who allocate regional supply to current consumption or future consumption (storage carried over to the next period), and (3) explore the sensitivity of the key factors introduced that determine stockholder’s responses.

99 GENERAL AND MISCELLANEOUS↗

Degradation science: Integrating modeling and experiments to predict localized corrosion processes (Annual Progress Report)

Additively manufactured (AM) eutectic high-entropy alloys (EHEAs), such as nano-lamellar AlCoCrFeNi 2.1 , have excellent strength, ductility, and wear resistance even at elevated temperatures, but their corrosion behavior in aggressive acids at different length scales remain poorly understood. This work investigates the corrosion behavior of laser powder bed–fused (L-PBF) AlCoCrFeNi 2.1 as a function of annealing temperatures, probing degradation mechanisms from nanoscopic to macroscopic length scales. The alloy is dual phase consisting of a ductile FCC L1 2 phase and a high-strength BCC B2 phase. Rapid solidification during L-PBF produces a far-from-equilibrium nano-lamellar structure with nearly homogeneous elemental distribution, which tends to evolve upon annealing toward Cr/Co/Fe-enriched FCC and Al/Ni-enriched B2. Three conditions were studied: as-printed, 600 °C/5 h, and 1000 °C/1 h, over which B2 lamellae coarsen, lamellar spacing increases, and elemental segregation becomes more prominent. Microstructure and chemistry were characterized by scanning electron microscopy (SEM) and energy-dispersive spectroscopy (EDS), while in-situ electrochemical atomic force microscopy (EC-AFM) was used to link early (<5 h) local dissolution to microstructure after exposure in sulfuric acid. EC-AFM highlights preferential dissolution of the BCC/B2 phase where the surrounding matrix is Cr-depleted and directly quantifies the dissolution rates within individual phases, tracks the transition from early nano-scale attack to partial repassivation, to correlate height differences with current and impedance responses. To monitor longer-term behavior (up to 96 h), ex-situ AFM, SEM, and confocal imaging were combined with conventional bulk electrochemical tests, bridging nanoscale observations to micro/meso-scale damage morphologies. At the meso-scale, the deepest dissolution channels align with the build-direction lamellae and melt-pool boundaries, indicating that printing directionality guides the propagation of these localized corrosion sites. Annealing modifies corrosion by restructuring BCC/FCC phase fractions, lamellar spacing, and Cr/Al segregation, thereby changing the cathode/anode ratio and passive film stability. The results clarify how as-printed and annealed nano-lamellar architectures differ in their susceptibility to selective dissolution; how elemental segregation competes with residual stresses along the build direction. With these insights, future work will use CALPHAD-guided alloy modification to stabilize higher Cr contents in the B2 phase while retaining a dominant FCC+B2/BCC microstructure, with the goal of designing mechanically robust, corrosion-resistant EHEAs for safety-critical applications to leverage the LLNL’s broader national and global security mission.

36 MATERIALS SCIENCE↗

Core Model Proposal #410: Updates to Socioeconomic and Macroeconomic Data, Processing Structure, and Visualization

This Core Model Proposal (CMP) comprehensively restructures and updates the macroeconomic and socioeconomic modules in gcamdata. It includes visualizations of key data inputs, accounting identities, and data flows in the context of GCAM-Macro-KLEM. Major improvements include: (1) updating the Penn World Table (PWT) to version 10 and incorporating a new source, the Global Macro Database (GMD); (2) updating the SSP socioeconomics database from version 3.0.1 to 3.2; (3) introducing SSP-specific differentiation of employment and labor force data; (4) improving data integration between national accounts (from PWT, GMD, and GTAP) and GDP/population data from external sources; and (5) general data cleaning and structural refinements. We document the data sources and key assumptions used throughout the processing. These updates establish the foundation for the forthcoming KLEAM version of GCAM-macro.

97 MATHEMATICS AND COMPUTING↗

Captan+X Data Converter Integration

Fermi National Accelerator Laboratory's CAPTAN (Compact And Programmable daTa Acquisition Node) series provides a flexible hardware platform for data acquisition across a range of experiments and facilities. The latest iteration, CAPTAN+X, is built around a Kintex-7 FPGA supporting four FPGA Mezzanine Card (FMC) connections. As part of a broader laboratory effort to bring facility systems under a Model-Based Systems Engineering (MBSE) framework, CAPTAN+X is one of several systems slated to be incorporated into this modeling environment in the near term. A necessary step toward that goal is incorporating the platform's core functionality, which centers on integration with the LXD31K4 FMC, a data converter module combining dual AD9652 analog-to-digital converters and dual AD9142A digital-to-analog converters. Achieving compatibility required resolving pin-mapping conflicts between the LXD31K4's High Pin Count connector and the CAPTAN+X's available pin types, adapting a Board Support Project originally written for an UltraScale-class evaluation board to the Kintex-7 architecture, replacing incompatible primitives, restructuring clock distribution, and manually configuring chip initialization in place of an unsupported soft-processor-based approach. Functional verification of the ADC and DAC channels, followed by closed-loop testing combining both converters with real-time filtering, confirmed correct operation of the integrated system. These results establish a working hardware and firmware baseline for the CAPTAN+X platform, positioning it for future inclusion in the laboratory's growing MBSE modeling effort.

Espinoza, David [Illinois U., Urbana (main)]↗

INFORMATION: Audit Report on "Accounting and Reporting for the American Recovery and Reinvestment Act by the Department of Energy's Funding Recipients"

The American Recovery and Reinvestment Act of 2009 (Recovery Act) was established to jumpstart the U.S. economy, create or save millions of jobs, and invest in the Nation's energy future. The Department of Energy received approximately $37 billion through the Recovery Act to support a variety of science, energy and environmental initiatives. The Office of Management and Budget (OMB) issued guidance for carrying out stimulus-related activities which requires, among other things, that recipients ensure funds provided by the Recovery Act are clearly distinguishable from non-Recovery Act funds in all reporting systems and that recipients' actions are transparent to the public. To meet these requirements, the Department's recipients must clearly and accurately track and report on 18 separate data elements. In addition, the Department was to develop and implement a process to ensure that recipient information reported to the public was free from material omissions and significant reporting errors. Our recent report (OAS-RA-10-01, October 2009) noted that the Department had developed a quality assurance process to facilitate the quarterly reviews of recipient data and planned to test it during the first quarterly reporting cycle. To determine whether the Department's quality assurance process was effective, we examined information reported by recipients of Departmental funding as of September 30, 2009. We also sought to determine whether the Department's prime contractors were prepared to track and report on Recovery Act activities. The Department had taken a number of actions designed to ensure the accuracy and transparency of reported Recovery Act results. This process identified potential anomalies with information reported by 1,113 of 2,038, or 55 percent of recipients. We view the Department's data quality assurance efforts as both timely and significant. As noted by our audit testing, however, opportunities exist to strengthen the process. In particular: (1) Site officials did not always ensure that anomalies, once identified during the quality assurance process, were actually resolved. For example, the Department's process identified that about 740 of the approximately 10,000 jobs reported in the first quarter of Fiscal Year 2010 as created/retained were for projects reported as having no funds spent. Although these problems were referred to site officials for follow-up and/or correction, the information was never actually changed; (2) The Department did not always utilize the correct basis when evaluating the accuracy of 'funds provided' data submitted by grant recipients. For example, in its analysis process, the Department used data reflecting 'funds obligated' rather than the correct amount of 'total grant awards'. This generated a number of potential false positives; and, (3) Duplicate reports by certain recipients, resulting in overstatements of as much as $137 million of the more than $18 billion obligated, were not corrected. We observed that the Department had taken prompt action to ensure that its prime facility management contractors could properly report Recovery Act information. Notably, the seven contractors in this category included in our review had modified their accounting systems, as necessary, to ensure that they could accurately track and report on Recovery Act activities. The systems at each of these entities had been restructured so that they: (i) could separate Recovery Act and non-Recovery Act funds; and, (ii) had adequate processing capacity to handle the projected increase in transactions. We found the Department's decision to limit its reviews to the four elements that it considered to be critical (award amount, invoiced amount, jobs created/retained, and project status) to be reasonable. We concluded, however, other elements or dependent relationships should not be completely excluded from review. Beyond its initial development and implementation of its quality assurance process, the Department had taken steps to improve its ability to ensure that Recovery Act information was both accurate and transparent to the public. Specifically, officials changed the quality assurance plan based on initial data reviews. Department officials also informed us that they are in the process of updating their quality assurance process to meet new OMB requirements. For example, recent guidance directed agencies to focus on certain data elements, such as award number and recipient name, during their quality assurance reviews. In addition, subsequent to our review, the Department added two more data elements and comparisons to its quarterly assurance process, including an analysis of costs/expenditures and a comparison of the recipient reported project status to the Department's data contained in its financial system.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

In Situ Studies of Surface Mobility on Noble Metal Model Catalysts Using STM and XPS at Ambient Pressure

High Pressure Scanning Tunneling Microscopy (HP-STM) and Ambient Pressure X-ray Photoelectron Spectroscopy were used to study the structural properties and catalytic behavior of noble metal surfaces at high pressure. HP-STM was used to study the structural rearrangement of the top most atomic surface layer of the metal surfaces in response to changes in gas pressure and reactive conditions. AP-XPS was applied to single crystal and nanoparticle systems to monitor changes in the chemical composition of the surface layer in response to changing gas conditions. STM studies on the Pt(100) crystal face showed the lifting of the Pt(100)-hex surface reconstruction in the presence of CO, H 2 , and Benzene. The gas adsorption and subsequent charge transfer relieves the surface strain caused by the low coordination number of the (100) surface atoms allowing the formation of a (1 x 1) surface structure commensurate with the bulk terminated crystal structure. The surface phase change causes a transformation of the surface layer from hexagonal packing geometry to a four-fold symmetric surface which is rich in atomic defects. Lifting the hex reconstruction at room temperature resulted in a surface structure decorated with 2-3 nm Pt adatom islands with a high density of step edge sites. Annealing the surface at a modest temperature (150 C) in the presence of a high pressure of CO or H 2 increased the surface diffusion of the Pt atoms causing the adatom islands to aggregate reducing the surface concentration of low coordination defect sites. Ethylene hydrogenation was studied on the Pt(100) surface using HP-STM. At low pressure, the lifting of the hex reconstruction was observed in the STM images. Increasing the ethylene pressure to 1 Torr, was found to regenerate the hexagonally symmetric reconstructed phase. At room temperature ethylene undergoes a structural rearrangement to form ethylidyne. Ethylidyne preferentially binds at the three-fold hollow sites, which are present on the Pt(100) hex reconstructed phase, but not the (100)-(1x1) surface. The increase in ethylene pressure caused the adsorbate interactions to dominate the crystal morphology and imposed a surface layer structure that matched the ethylidyne binding geometry. The STM results also showed that the surface was reversibly deformed during imaging due to increases in Pt mobility at high pressure. The size dependence on the activity and surface chemistry of Rh nanoparticles was studied using AP-XPS. The activity was found to increase with particle size. The XPS spectra show that in reaction conditions the particle surface has an oxide layer which is chemically distinct from the surface structure formed by heating in oxygen alone. This surface oxide which is stabilized in the catalytically active CO oxidation conditions was found to be more prevalent on the smaller nanoparticles. The reaction-induced surface segregation behavior of bimetallic noble metal nanoparticles was observed with APXPS. Monodisperse 15 nm RhPd and PdPt nanoparticles were synthesized with well controlled Rh/Pd and Pd/Pt compositions. In-situ XPS studies showed that at 300 C in the presence of an oxidizing environment (100 mTorr NO or O 2 ) the surface concentration of the more easily oxidized element (Rh in RhPd and Pd in PdPt) was increased. Switching the gas environment to more reducing conditions (100 mTorr NO and 100 mTorr CO) caused the surface enrichment of the element with the lowest surface energy in its metallic state. Using in-situ characterization, the redox chemistry and the surface composition of bimetallic nanoparticle samples were monitored in reactive conditions. The particle surfaces were shown to reversibly restructure in response to the gas environment at high temperature. The oxidation behavior of the Pt(110) surface was studied using surface sensitive in-situ characterization by APXPS and STM. In the presence of 500 mTorr O 2 and temperatures between 25 and 200 °C, subsurface oxygen was detected in the surface layer. STM images show that these conditions were found to cause a roughened surface decorated with 1 nm islands. The formation of this surface oxide is a high pressure phenomenon and was not detected in 50 mTorr O 2 . After forming the surface oxide at high pressure, its chemical activity was measured through the reaction with CO at low pressure while continuously monitoring the oxygen species with XPS. The subsurface oxygen was removed by CO oxidation at a comparable rate to the chemisorbed oxygen at 2 °C. Repeating the experiment at -3 °C reduced the reaction rate, but not the relative activity of the two chemical species suggesting that neither species is significantly more active for the CO oxidation reaction. These studies use molecular level surface characterization in the presence of gases to show the structural changes induced by gas adsorption at high pressure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimizing Performance of Combustion Chemistry Solvers on Intel's Many Integrated Core (MIC) Architectures

This work investigates novel algorithm designs and optimization techniques for restructuring chemistry integrators in zero and multidimensional combustion solvers, which can then be effectively used on the emerging generation of Intel's Many Integrated Core/Xeon Phi processors. These processors offer increased computing performance via large number of lightweight cores at relatively lower clock speeds compared to traditional processors (e.g. Intel Sandybridge/Ivybridge) used in current supercomputers. This style of processor can be productively used for chemistry integrators that form a costly part of computational combustion codes, in spite of their relatively lower clock speeds. Performance commensurate with traditional processors is achieved here through the combination of careful memory layout, exposing multiple levels of fine grain parallelism and through extensive use of vendor supported libraries (Cilk Plus and Math Kernel Libraries). Important optimization techniques for efficient memory usage and vectorization have been identified and quantified. These optimizations resulted in a factor of ~ 3 speed-up using Intel 2013 compiler and ~ 1.5 using Intel 2017 compiler for large chemical mechanisms compared to the unoptimized version on the Intel Xeon Phi. The strategies, especially with respect to memory usage and vectorization, should also be beneficial for general purpose computational fluid dynamics codes.

97 MATHEMATICS AND COMPUTING↗

An Integrated Framework for Memory-Centric Analysis: From Trace Collection to Co-Design

The memory wall phenomenon—where advances in processor performance significantly outpace those in memory subsystems—poses a fundamental challenge for contemporary computing systems. In memory-bound applications, memory subsystem behavior dominates performance, yet existing analysis approaches present significant limitations: detailed microarchitectural simulators require days to weeks to simulate modest workloads; hardware performance counters provide only aggregate statistics that obscure temporal and spatial access patterns; and scaled simulation approaches face challenges in capturing certain behaviors that emerge at larger scales. These limitations reflect a processor-centric design philosophy increasingly misaligned with memory-bound workloads where detailed understanding of memory access patterns, cache hierarchy interactions, and contention is critical for effective optimization. This paper presents an integrated framework for memory-centric analysis that enables effective hardware-software co-design. We describe practical trace collection techniques, including hardware-assisted processor tracing with minimal overhead and portable software-based instrumentation with statistical sampling. We present multi-perspective analysis methods that examine memory behavior from temporal, sequential, spatial, and relational viewpoints, revealing distinct optimization opportunities invisible in aggregate metrics. We detail an architectural modeling framework that uses sampled traces with temporal interpolation and confidence-based filtering to evaluate cache and memory configurations. Evaluation on representative benchmarks demonstrates that this framework achieves practical accuracy (L2 cache errors of 2.64\%, confidence-filtered L3 errors of 9.92\%, bandwidth errors of 7.33\%) while providing substantial speedup (26.8×) over cycle-accurate simulation, enabling rapid design space exploration. We demonstrate how this integrated framework enables systematic identification of both hardware optimizations (memory controller tuning, bank partitioning, NUMA configuration) and software optimizations (data layout restructuring, prefetching strategies, memory-aware scheduling). Through this comprehensive treatment of the memory-centric analysis pipeline—from trace collection through architectural modeling to co-design application—we provide researchers and practitioners with practical techniques for addressing memory bottlenecks in contemporary computing systems.

Gajaria, Dhruv Mayur↗

Unveiling a Drift Resistant Cryptotope within Marburgvirus Nucleoprotein Recognized by Llama Single-Domain Antibodies

Marburg virus (MARV) is a highly lethal hemorrhagic fever virus that is increasingly re-emerging in Africa, has been imported to both Europe and the US, and is also a Tier 1 bioterror threat. As a negative sense RNA virus, MARV has error prone replication which can yield progeny capable of evading countermeasures. To evaluate this vulnerability, we sought to determine the epitopes of 4 llama single-domain antibodies (sdAbs or VHH) specific for nucleoprotein (NP), each capable of forming MARV monoclonal affinity reagent sandwich assays. Here, we show that all sdAb bound the C-terminal region of NP, which was produced recombinantly to derive X-ray crystal structures of the three best performing antibody-antigen complexes. The common epitope is a trio of alpha helices that form a novel asymmetric basin-like depression that accommodates each sdAb paratope via substantial complementarity-determining region (CDR) restructuring. Shared core contacts were complemented by unique accessory contacts on the sides and overlooks of the basin yielding very different approach routes for each sdAb to bind the antigen. The C-terminal region of MARV NP was unable to be crystallized alone and required engagement with sdAb to form crystals suggesting the antibodies acted as crystallization chaperones. While gross structural homology is apparent between the two most conserved helices of MARV and Ebolavirus, the positions and morphologies of the resulting basins were markedly different. Naturally occurring amino acid variations occurring in bat and human Marburgvirus strains all mapped to surfaces distant from the predicted sdAb contacts suggesting a vital role for the NP interface in virus replication. As an essential internal structural component potentially interfacing with a partner protein it is likely the C-terminal epitope remains hidden or “cryptic” until virion disruption occurs. Conservation of this epitope over 50 years of Marburgvirus evolution should make these sdAb useful foundations for diagnostics and therapeutics resistant to drift.

60 APPLIED LIFE SCIENCES↗

Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing

Biological soil crusts (biocrusts) are microbial communities that are a feature of arid surface soils worldwide. In drylands where precipitation is pulsed and ephemeral, the ability of biocrust microbiota to rapidly initiate metabolic activity is critical to their survival. Community gene expression was compared after a short duration (1 h) wetting pulse in both intact and soils disturbed by chronic foot trampling. Across the metatranscriptomes the majority of transcripts were cyanobacterial in origin, suggesting that cyanobacteria accounted for the bulk of the transcriptionally active cells. Chronic trampling substantially altered the functional profile of the metatranscriptomes, specifically resulting in a significant decrease in transcripts for nitrogen fixation. Soil depth (biocrust and below crust) was a relatively small factor in differentiating the metatranscriptomes, suggesting that the metabolically active bacteria were similar between shallow soil horizons. The dry samples were consistently enriched for hydrogenase genes, indicating that molecular hydrogen may serve as an energy source for the desiccated soil communities. The water pulse was associated with a restructuring of the metatranscriptome, particularly for the biocrusts. Biocrusts increased transcripts for photosynthesis and carbon fixation, suggesting a rapid resuscitation upon wetting. In contrast, the trampled surface soils showed a much smaller response to wetting, indicating that trampling altered the metabolic response of the community. Finally, several biogeochemical cycling genes in carbon and nitrogen cycling were assessed for their change in abundance due to wetting in the biocrusts. Different transcripts encoding the same gene product did not show a consensus response, with some more abundant in dry or wet biocrusts, highlighting the challenges in relating transcript abundance to biogeochemical cycling rates. These observations demonstrate that metatranscriptome sequencing was able to distinguish alterations in the function of arid soil microbial communities at two varying temporal scales, a long-term ecosystems disturbance through foot trampling, and a short term wetting pulse. Thus, community metatranscriptomes have the potential to inform studies on the response and resilience of biocrusts to various environmental perturbations.

59 BASIC BIOLOGICAL SCIENCES↗

A review of the shear rheology of carbon black suspensions

The microstructural link to the rheology of carbon black suspensions has recently become clear as a result of advances in computational and experimental methods. This understanding reveals the important role of the restructuring, build-up, and break-up of carbon black agglomerates in simple shear, rationalized by a dimensionless balance of the hydrodynamic forces acting to break the agglomerates apart against the cohesive forces holding them together (i.e., the Mason number). The Mason number not only can predict the origin of reversible thixotropy seen in carbon black suspensions observed at higher shear intensities, but can also be used to rationalize the evolution of microstructure at lower shear intensities. This review focuses on carbon black suspension behavior, but the insights derived from carbon black suspensions are broadly applicable to a diverse class of soft matter including colloidal gels relevant to a variety of applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗