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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Signal sequences target enzymes and structural proteins to bacterial microcompartments and are critical for microcompartment formation

ABSTRACT Spatial organization of pathway enzymes has emerged as a promising tool to address several challenges in metabolic engineering, such as flux imbalances and off-target product formation. Bacterial microcompartments (MCPs) are a spatial organization strategy used natively by many bacteria to encapsulate metabolic pathways that produce toxic, volatile intermediates. Several recent studies have focused on engineering MCPs to encapsulate heterologous pathways of interest, but how this engineering affects MCP assembly and function is poorly understood. In this study, we investigated the role of signal sequences, short domains that target proteins to the MCP core, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterized two novel Pdu signal sequences on the structural proteins PduM and PduB, which constitute the first report of metabolosome signal sequences on structural proteins rather than enzymes. We then explored the role of enzymatic and structural Pdu signal sequences on MCP assembly by deleting their encoding sequences from the genome alone and in combination. Deleting enzymatic signal sequences decreased the MCP formation, but this defect could be recovered in some cases by overexpressing genes encoding the knocked-out signal sequence fused to a heterologous protein. By contrast, deleting structural signal sequences caused similar defects to knocking out the genes encoding the full-length PduM and PduB proteins. Our results contribute to a growing understanding of how MCPs form and function in bacteria and provide strategies to mitigate assembly disruption when encapsulating heterologous pathways in MCPs. IMPORTANCE Spatially organizing biosynthetic pathway enzymes is a promising strategy to increase pathway throughput and yield. Bacterial microcompartments (MCPs) are proteinaceous organelles that many bacteria natively use as a spatial organization strategy to encapsulate niche metabolic pathways, providing significant metabolic benefits. Encapsulating heterologous pathways of interest in MCPs could confer these benefits to industrially relevant pathways. Here, we investigate the role of signal sequences, short domains that target proteins for encapsulation in MCPs, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterize two novel signal sequences on structural proteins, constituting the first Pdu signal sequences found on structural proteins rather than enzymes, and perform knockout studies to compare the impacts of enzymatic and structural signal sequences on MCP assembly. Our results demonstrate that enzymatic and structural signal sequences play critical but distinct roles in Pdu MCP assembly and provide design rules for engineering MCPs while minimizing disruption to MCP assembly.

Johnson, Elizabeth R. (ORCID:0000000179236881)↗
DOE OSTI2025

Zinc isotope constraints on the cycling of carbon in the Bermuda mantle source

Volatile recycling and storage in the mantle transition zone (MTZ) is important for the refertilization of the upper mantle and is associated with the generation of high-µ (HIMU, where µ is 238 U/ 204 Pb) mantle. One way to probe the MTZ and the processes associated with mantle convection is to sample lavas that originate from the shallow mantle and were contaminated by upwelling from the MTZ, such as at the previously proposed shallow plume of Bermuda. Here we present the first δ 66 Zn isotopic compositions of Bermuda silica-undersaturated and silica-saturated lavas to explore the origin of the carbon-rich lithologies and the genesis of the large seamount found in the western North Atlantic Ocean. Contrasting with global δ 66 Zn data sets, our results (δ 66 Zn between 0.24 ± 0.04 and 0.41 ± 0.04) do not support direct sampling of recycled marine carbonates in the Bermuda HIMU mantle. Instead, we show that δ 66 Zn fractionation toward higher values is associated with magmatic processes and incorporation of carbon sourced from deep fluids associated with the formation of carbonatites. These carbon-rich fluids are likely sourced from the metasomatic reactions between the subducted cold slab of the Iapetus oceanic lithosphere ca. 500 Ma and the thickened continental lithospheric mantle of Pangea. Melting of this metasomatized mantle was triggered by the arrival of the Farallon slab to the eastern North American margin in the late Cenozoic via shallow convection.

Mazza, Sarah E. [Smith College, Northampton, MA (U↗
DOE OSTI2020

Three Artificial Spintronic Leaky Integrate-and-Fire Neurons

We report that due to their non-volatility and intrinsic current integration capabilities, spintronic devices that rely on domain wall (DW) motion through a free ferromagnetic track have garnered significant interest in the field of neuromorphic computing. Although a number of such devices have already been proposed, they require the use of external circuitry to implement several important neuronal behaviors. As such, they are likely to result in either a decrease in energy efficiency, an increase in fabrication complexity, or even both. To resolve this issue, we have proposed three individual neurons that are capable of performing these functionalities without the use of an external circuitry. To implement leaking, the first neuron uses a dipolar coupling field, the second uses an anisotropy gradient, and the third uses shape variations of the DW track.

neural network crossbar↗
DOE OSTI2021

Design of a Robust Memristive Spiking Neuromorphic System with Unsupervised Learning in Hardware

Spiking neural networks (SNN) offer a power efficient, biologically plausible learning paradigm by encoding information into spikes. The discovery of the memristor has accelerated the progress of spiking neuromorphic systems, as the intrinsic plasticity of the device makes it an ideal candidate to mimic a biological synapse. Despite providing a nanoscale form factor, non-volatility, and low-power operation, memristors suffer from device-level non-idealities, which impact system-level performance. To address these issues, this article presents a memristive crossbar-based neuromorphic system using unsupervised learning with twin-memristor synapses, fully digital pulse width modulated spike-timing-dependent plasticity, and homeostasis neurons. Additionally, the implemented single-layer SNN was applied to a pattern-recognition task of classifying handwritten-digits. The performance of the system was analyzed by varying design parameters such as number of training epochs, neurons, and capacitors. Furthermore, the impact of memristor device non-idealities, such as device-switching mismatch, aging, failure, and process variations, were investigated and the resilience of the proposed system was demonstrated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Single-node Partitioned-Memory for Huge Graph Analytics: Cost and Performance Trade-offs

Nonvolatile memory NVDIMMs, available as Intel Optane, are less expensive than DRAM and bring large byte-addressable storage within reach to many applications. Evaluations on graph analytics have shown promising performance only when DRAM is used as a hardware cache (Memory mode). An open question is whether graph applications can exploit Optane and DRAM directly (AppDirect mode) and achieving better-than-DRAM average bandwidth and run times. We evaluate Optane as a volatile pool on two large-scale graph applications with very different computational patterns, Grappolo and Ripples. We show that AppDirect mode can deliver better-than-DRAM performance, by allocating data structures to Optane and DRAM according to their access characteristics, resulting in higher average memory bandwidth and lower average latency. Memory mode provides DRAM-competitive performance with capacity equal to persistent memory. We demonstrate occasional 4x improvement using the latest AppDirect option and frequently observe competitive performance between Optane AppDirect Memory modes and DRAM.

Ghosh, Sayan↗
DOE OSTI2023

Flexible and Effective Object Tiering for Heterogeneous Memory Systems

Computing platforms that package multiple types of memory, each with their own performance characteristics, are quickly becoming mainstream. To operate efficiently, heterogeneous memory architectures require new data management solutions that are able to match the needs of each application with an appropriate type of memory. As the primary generators of memory usage, applications create a great deal of information that can be useful for guiding memory tiering, but the community still lacks tools to collect, organize, and leverage this information effectively. To address this gap, this work introduces a novel software framework that collects and analyzes object-level information to guide memory tiering. Using this framework, this study evaluates and compares the impact of a variety of data tiering choices, including how the system prioritizes objects for faster memory as well as the frequency and timing of migration events. The results, collected on a modern Intel platform with conventional DRAM as well as non-volatile RAM, show that guiding data tiering with object-level information can enable significant performance and efficiency benefits compared to standard hardware- and software-directed data tiering strategies.

Kammerdiener, Brandon↗
DOE OSTI2021

Review—(Mn,Co) 3 O 4 -Based Spinels for SOFC Interconnect Coating Application

With the reduction of solid oxide fuel cell (SOFC) operating temperature to the range of 600 °C–800 °C, Cr-containing ferritic alloys have become the preferred interconnect material, which unfortunately are susceptible to continuous scale growth and Cr volatility at the SOFC operating temperatures. The (Mn,Co) 3 O 4 spinel system is widely regarded as the most effective coating for SOFC interconnect protection, due to its high thermal and electrical conductivity, adequate coefficient of thermal expansion, and excellent Cr blocking capability. This article reviews the physical and chemical properties of the (Mn,Co) 3 O 4 -based spinels; different types of coating precursors and deposition techniques; and the effects of spinel composition, quality and thickness on the coating performance. Furthermore, it is concluded that the spinel coating composition, quality, and thickness are more critical than the coating process in affecting the overall coating performance.

08 HYDROGEN↗
DOE OSTI2023

Methods—Meso-Scale Electrodes for Characterizing Diffusion-Reaction Properties of Redox-Active Organics in Viscous Electrolytes

Deep Eutectic Solvents (DESs) have recently gained interest as flow battery electrolytes. Their advantages include a wider electrochemical stability window compared to aqueous electrolytes, higher solubility for redox-active species, and negligible volatility. However, DESs are often highly viscous, and suffer from low ionic conductivities. This can make assessing redox kinetics difficult when attempting to determine their viability for energy storage. In classical voltammetric measurements, low ionic conductivity manifests as high solution resistance, thereby requiring "live" compensation of the electrolyte ohmic drop when performing fast-scan voltammetry. An uncompensated or inadequately-compensated ohmic drop leads to misinterpretation of the voltammetric behavior, e.g., assessing reversibility vs. irreversibility of a redox reaction. Here, we present micro-fabricated electrodes as facile "meso-scale" electrodes, which overcome these issues by nearly eliminating the ohmic drop while retaining uniformity of the current distribution over the electrode surface. Their use in precise transport-kinetics measurements is demonstrated using a redox-active organic, i.e., 4-Hydroxy-TEMPO in an aqueous medium and in ethaline, which is a viscous DES. This study provides a methodical approach to design and to implement voltammetry experiments using meso-scale electrodes leading to reliable measurements of diffusion-reaction properties of 4-Hydroxy-TEMPO.

25 ENERGY STORAGE↗
DOE OSTI2020

Optimization of Lithium Content and Sintering Additives in Tape Cast Lithium Garnet Electrolyte Sheets

The lithium garnet (LLZO) remains one of the most promising electrolyte materials for producing solid state batteries. Tape casting is one method for producing the thin ceramic electrolyte layer required for a high-performance solid state battery. Processing of LLZO is complicated by several factors including lithium volatilization, abnormal grain growth and phase instability. Many of these issues are exacerbated in tape cast sheets by the sheets' higher surface area to volume ratio, when compared to pellet processing methods. Here, we report on an environmentally friendly aqueous tape casting process for LLZO using methylcellulose as a binder and compare final sheet properties to other, solvent-based, options. Solids loading, binder content, dispersant composition, and wetting agent type are varied to improve ease of casting and enhance properties of the as-cast tape. Lithium content in sintered LLZO sheets is controlled by the inclusion of excess Li 2 CO 3 as lithium source in the ceramic tape itself and by a novel method of producing a lithium-saturated furnace atmosphere. Sintering time and temperature are optimized, and rapid thermal processing is investigated as a method of reducing lithium loss. Al 2 O 3 and MgO are examined for use as sintering additives. Characterization of LLZO sheets is performed with XRD, EIS and SEM. Li 2 CO 3 and sintering additive levels are optimized for ionic conductivity and density. The optimization effort improved the conductivity and density of 100µm thick sintered sheets to greater than 3x10 -4 S/cm conductivity and 90% density.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Evaluating Contributions of Pitch-Carbon Coating to Improved Stability of Si Anodes Through Voltage-Resolved Multi-Phase Characterization

Silicon nanoparticles have emerged as a promising alternative to graphite to improve the energy density of next-generation lithium-ion battery anodes. Nano-sized Si domains facilitate rapid ion transport and minimize particle-scale mechanical degradation, but also exhibit increased (electro)chemical reactivity with Li-ion electrolyte components due to their high surface area. We have previously demonstrated that surface modification of Si nanoparticles with pitch-carbon is an effective strategy to reduce these parasitic reactions. In the present work, we holistically evaluate the mechanistic contribution of pitch-carbon coating to the observed stability improvement over uncoated Si. We utilize coupled in situ and ex situ methods to probe changes to solid-surface, volatile headspace, and gas-phase chemistry occurring during initial cycling. Measurements taken at targeted potentials associated with electrolyte species reduction enables the decoupling of specific reaction pathways tied to interfacial stability. Further, we demonstrate the non-trivial role of gas reconsumption in dictating the nature of the passivating surface layer evolved on both uncoated and pitch-coated Si. This multi-phase analysis offers insights into the mechanism of effective surface passivation, which may be applied to inform future Si material development.

ENERGY STORAGE↗
DOE OSTI2022

Uranium Dust Cloud Combustion: Burning Characteristics and Absorption Spectroscopy Measurements

This study characterized uranium metal dust cloud combustion using absorption spectroscopy, imaging, and broadband emission measurements. Other metals were similarly combusted to establish correlations between results from this study and those found in the literature. It was determined that the burn temperature of uranium was limited to the volatilization temperature of uranium dioxide. Combustion behavior was similar to that of other refractory metals in terms of burn time and the observation of exploding particle behavior.

42 ENGINEERING↗
DOE OSTI2022

Assessment of Spoilage Microbiota of Rainbow Trout (Oncorhynchus mykiss) during Storage by 16S rDNA Sequencing

Due to the high contents of protein and fat in rainbow trout, it is highly susceptible to spoilage, which limits the storage and transportation processes. Exploring the spoilage microbial community during rainbow trout storage is essential to develop an effective preservation method. Here, the changes in the total bacterial colony and total volatile base nitrogen (TVB-N) during the storage of rainbow trout were investigated. Storage at 0 °C can effectively slow down the spoilage process with bacterial counts and TVB-N contents decreased from 8.7 log CFU/g and 18.7 mg/100 g obtained at 4 °C to 5.6 log CFU/g and 14.5 mg/100 g, respectively. 16S rDNA high-throughput sequencing results showed that the diversity of microbial genera decreased during storage. Acinetobacter, Pseudomonas, and Shewanells gradually became the dominant spoilage genera with contents of 59.9%, 18.6%, and 1.7%, respectively, in the late stage of storage. The spoilage abilities of bacteria belonging to the Pseudomonas and Shewanells genera were analyzed. Shewanella sp. S5-52 showed the highest level of TVB-N content (100.6 mg/100 g) in sterile fish juice, indicating that it had a strong spoilage ability. This study confirmed the dominant spoilage bacterial genera and evaluated the spoilage abilities of isolated strains during the storage of rainbow trout, which laid the foundation for further investigation of the spoilage mechanism of rainbow trout and other aquatic products.

Du, Guangqing↗
DOE OSTI2025

Real-Time Dispatcher for a Distributed Energy Resource Power Plant to Provide Grid Services [SWR-25-17]

This software dispatches the aggregated power of a distributed energy resource (DER) plant located on an electrical distribution network. It is designed to provide the following services to the grid in real-time: (i) voltage support of the distribution network, (ii) virtual power plant at the substation with power factor support, and (iii) operating reserves for automatic generator control for the transmission system. This dispatcher integrates with the local power plant controller and utilizes the battery energy storage system (BESS) to smooth the volatile net power output from the DERs. It can also integrate with a day-ahead scheduler to strategically charge and discharge.

Comden, Joshua [National Renewable Energy Laborato↗
DOE OSTI2020

Floods due to Atmospheric Rivers along the U.S. West Coast: The Role of Antecedent Soil Moisture in a Warming Climate

Precipitation extremes are projected to become more frequent along the U.S. West Coast due to increased atmospheric river (AR) activity, but the frequency of less intense precipitation events may decrease. Antecedent soil moisture (ASM) conditions can have a large impact on flood responses, especially if prestorm precipitation decreases. Taken together with increased antecedent evaporative demand due to warming, this would result in reduced soil moisture at the onset of extreme precipitation events. In this work, we examine the impact of ASM on AR-related floods in a warming climate in three basins that form a transect along the U.S. Pacific Coast: the Chehalis River basin in Washington, the Russian River basin in Northern California, and the Santa Margarita River basin in Southern California. Additionally, we ran the Distributed Hydrology Soil Vegetation Model (DHSVM) over the three river basins using forcings downscaled from 10 global climate models (GCMs). We examined the dynamic role of ASM by comparing the changes in the largest 50, 100, and 150 extreme events in two periods, 1951–2000 and 2050–99. In the Chehalis basin, the projected fraction of AR-related extreme discharge events slightly decreases. In the Russian basin, this fraction increases, however, and more substantially so in the Santa Margarita basin. This is due to increases in AR-related extreme precipitation events, as well as the fact that the relationship of extreme precipitation to extreme discharge is strengthened by projected increases in year-to-year volatility of annual precipitation in California, which increases the likelihood of concurrent occurrence of large storms and wet ASM conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

UMap: An application-oriented user level memory mapping library

Exploiting the prominent role of complex memories in exascale node architecture, the UMap page fault handler offers new capabilities to access large memory-mapped data sets directly. UMap provides flexible configuration options to customize page handling to each application, including analysis of massive observational and simulation data sets. The high-performance design features I/O decoupling, dynamic load balancing, and application-level controls. Page faults triggered by application threads and processes accessing data mapped to a UMapp’ed region are handled via the Linux userfaultfd protocol, an asynchronous message-oriented kernel-user communication mechanism that avoids the context switch penalty of traditional signal fault handlers. UMap is fully open source. In this paper, we give an overview of the UMap library architecture, its extensible plugin architecture, and the use/performance of UMap in emerging heterogeneous memory hierarchies such as near-node Non-volatile Memory (NVM) and network attached memories. We highlight new capabilities in two pagefault management plugins, the NetworkStore and SparseStore. We demonstrate the integration between UMap and multiple ECP products including Caliper, Metall, ZFP, Mochi, and Ripples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A control-oriented combustion model framework for compression ignition engines operating on low-reactivity fuel

This work focuses on zero-dimensional modeling of the heat release rate in a compression ignition engine operating on gasoline-like fuels. Due to the properties of gasoline, such as high volatility and longer ignition delay than diesel, the injection strategies can vary significantly from the operation with conventional diesel fuel. Different injection strategies are commonly used to achieve varying degrees of in-cylinder stratification in order to shape the combustion event and maximize efficiency. The proposed zero-dimensional combustion model was developed to account for the different stages in combustion caused by the fuel stratification. As the ignition delay model is an integral part of the entire combustion process and significantly affects the prediction accuracy, special attention has been paid to local phenomena influencing ignition delay. A one-dimensional spray model by Musculus and Kattke was employed in conjunction with a Lagrangian tracking approach in order to estimate the local air–fuel ratio within the spray tip, as a proxy for reactivity. The local air–fuel ratio, in-cylinder temperature and pressure were used in an integral fashion to estimate the ignition delay. Heat release rates were modeled using first-order non-linear differential equations. The proposed combustion model was validated against experimental data of a heavy-duty compression ignition engine with up to three injection events at mostly 1038 r/min and 14 bar brake mean effective pressure. Further validation of the model was carried out at other engine loads and speeds. Model prediction errors in CA50 of less than 1 °CA across all conditions were found. Modeling results of other combustion metrics such as combustion duration and indicated mean effective pressure are also highly satisfactory. In addition, the model has been shown to be capable of estimating the ringing intensity for most conditions.

Pamminger, Michael↗
DOE OSTI2022

Effects of stratification and charge cooling on combustion in a gasoline direct-injection compression ignition (GDCI) engine

With the development of low temperature engine combustion strategies, performance of gasoline-type fuels under compression ignition conditions has attracted extensive research interest. Meanwhile, for the sake of co-optimization of engines and fuels for future ground transportation, identification and evaluation of general fuel properties should be a core research priority instead of endless testing of specific fuels. In this study, the roles of fuel octane sensitivity in characterizing the ignition performance of gasoline surrogates have been systematically investigated under typical gasoline direct ignition compression ignition (GDCI) engine conditions using 3D combustion CFD simulation, especially considering the subsequent in-cylinder charge stratification and charge cooling. Two different operating conditions, high boost pressure low boost temperature (beyond-RON) case and low boost pressure high boost temperature (beyond-MON) case, were considered. By comparing with our previous zero-dimensional chemical kinetic study of gasoline surrogates in advanced compression ignition (ACI) engines, the effects of stratification and charge cooling on the combustion processes are investigated. It is found that different fuel octane sensitivities lead to slight difference in equivalence ratio stratification and charge cooling due to differences in volatility. However, fuel reactivity is still the more dominant factor than the stratification and charge cooling effects in determining combustion phasing. The present results help to justify the P-T domain framework for engine autoignition analysis of overlapping pressure-temperature trajectory with ignition delay iso-contour. Here, the results also provide useful guidance to the understanding of GCI combustion process, and to the evaluation of controlling fuel properties and the selection of alternative fuels in GCI engines.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

Modeling the impact of the fuel injection strategy on the combustion and performance characteristics of a heavy-duty GCI engine

Gasoline compression ignition (GCI) is a promising strategy to achieve high thermal efficiency and low emissions with limited modifications to the conventional diesel engine hardware. It is a partially premixed concept, which derives its superiority from higher volatility and longer ignition delay of gasoline-like fuels combined with higher compression ratio typical of diesel engines. Here, the present study investigates the combustion process in a GCI engine operating with different injection strategies using computational fluid dynamics (CFD). Simulations are carried out on a single cylinder of a multi cylinder heavy-duty compression ignition engine, which operates at a compression ratio of 17:1 and an engine speed of 1038 rev/min. Two different injection strategies viz., late injection (LI), and early pilot injection (EP) are investigated to understand their impact on combustion and performance of the engine. Renormalized group (RNG) k-ε model is used to describe in-cylinder turbulence and KH RT model is used to simulate the fuel spray breakup. The developed CFD methodology is validated against relevant experimental data under a wide range of operating conditions for each injection strategy. The developed CFD methodology was found to capture the engine combustion behavior quite well. Based on the validated CFD model, the differences in the progress of combustion event for the two injection strategies is highlighted. It was found that a larger pilot fuel mass fraction results in a steeper rise in the initial heat release rate which in turn influences the transition to mixing controlled combustion. In line with the experimental data, the study showed that the late pilot injection strategy with three injection pulses, results in higher performance compared to the other conditions.

33 ADVANCED PROPULSION SYSTEMS↗