SEARCH · Engineering Papers

Results for “acquisition function”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8

All sources NASA NTRS DOE OSTI

DOE OSTI2021

Differential programming enabled functional imaging with Lorentz transmission electron microscopy

Abstract Lorentz transmission electron microscopy is an advanced characterization technique that enables the simultaneous imaging of both the microstructure and functional properties of materials. Information such as magnetization and electric potentials is carried by the phase of the electron wave, and is lost during image acquisition. Various methods have been proposed to retrieve the phase of the electron wavefunction using intensities of the acquired images, most of which work only in the small defocus limit. Imaging at strong defoci not only carries more quantitative phase information, but is essential to the study of weak magnetic and electrostatic fields at the nanoscale. In this work we develop a method based on differentiable programming to solve the inverse problem of phase retrieval. We show that our method maintains a high spatial resolution and robustness against noise even at the upper defocus limit of the microscope. More importantly, our proposed method can go beyond recovering just the phase information. We demonstrate this by retrieving the electron-optical parameters of the contrast transfer function alongside the electron exit wavefunction.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

SILIA: software implementation of a multi-channel, multi-frequency lock-in amplifier for spectroscopy and imaging applications

In this work, we describe a software implementation of a multi-channel, multi-frequency Lock-in Amplifier (SILIA) to extract modulated signals from noisy data distributed over multiple channels of arbitrary number and size. This software implementation emulates the functionality of a multi-channel, multi-frequency lock-in amplifier in a post-processing step following data acquisition. Unlike most traditional lock-in amplifiers, SILIA can work with any number of input channels and is especially useful to analyze data distributed over many channels. We demonstrate the versatility and performance for extracting weak signals in spectroscopy and fluorescence microscopy. We also discuss more general applications and exhibit a method to automatically estimate error from a lock-in result.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Development of Time Lapse VSP Integration Workflow: A Case Study at Farnsworth CO2-EOR Project

Abstract This study aims to develop a 4D Vertical Seismic Profile (VSP) integration workflow to improve the prediction of subsurface stress changes. The selected study site is a 5-spot pattern within the ongoing CO2-EOR operations at the Farnsworth Field Unit FWU in Ochiltree County, Texas. The specific pattern has undergone extensive geological and geomechanical characterization through the acquisition of 3D seismic data, geophysical well logs, and core. This workflow constrains a numerical hydromechanical model by applying a penalty function formed between "modeled" versus "observed" time-lapse compressional and shear seismic velocity changes. Analyses of geophysical logs and ultra-sonic measurements on core exhibit measurable sensitivities to changes in both fluid saturation and mean effective stress. These data are used to develop a site-specific rock physics model and stress-velocity relationship, which inform the numerical models used to generate the "modeled" portion of the penalty function. The "observed" portion of the penalty function is provided by a novel elastic full-waveform inversion of the available 3D baseline and three monitor surveys to produce high-quality estimates of time-lapse compressional and shear seismic velocity changes. The modeling workflow accounts sequentially for fluid substitution and stress impacts. Hydrodynamic and geomechanical properties of the 3D coupled numerical model are estimated through geostatistical integration of well log and core data with 3D seismic inversion products. Changes in seismic velocities due to fluid substitution are computed using the Biot-Gassmann workflow and site-specific rock physics. Stress impacts on time-lapse seismic velocity changes are modeled from the effective stress output of the hydromechanical model and are initially based on the velocity versus effective stress relationship extracted from core mechanical testing. Based on the principle of superposition of seismic wavefields, seismic velocity changes attributed to fluid substitution and that due to changes in mean effective stress are treated as linearly additive. The modeled results are upscaled using Backus averaging to reconcile scale discrepancies between the modeled and measured datasets to formulate the penalty function. This manuscript presents the forward modeling process and concludes that for the base case, the seismic velocity changes due to mean effective stress dominates over the seismic velocity changes attributed to fluid substitution because of the extensive range of the pressure perturbations. Successful minimization of this penalty function calibrates the coupled hydrodynamic geomechanical numerical model and affirms the suitability of acoustic time-lapse measurements such as 4D-VSP for geomechanical calibration.

02 PETROLEUM↗

DOE OSTI2023

Evaluation of Potential DAS Array Geometries for the Source Physics Experiment, Phase III

Distributed Acoustic Sensing (DAS) is a rapidly developing technology that can record acoustic wavefields at high sampling rates and with dense spatial spacing difficult to achieve with seismometers. However, the geophysical community has not fully explored DAS survey parameters to characterize the ideal array design. A better quantitative understanding of DAS array behavior prior to SPE Phase III acquisition can help improve the quality of the data recorded by guiding the DAS array design. Here we use array response functions as well as beamforming and backprojection results from forward modelling calculations to assess the performance of varying DAS array geometries to record regional and local sources. A seven-sided polygon DAS array demonstrated improved capabilities for recording regional sources over segmented linear arrays, with potential improvements in recording and locating local sources. These results help reveal DAS array performance as a function of geometry.

58 GEOSCIENCES↗

DOE OSTI2023

Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex

The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

In-Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway

The low-density lipoprotein receptor (LDLR) is a major apolipoprotein receptor that regulates cholesterol homeostasis. LDLR deficiency is associated with cognitive impairment by the induction of synaptopathy in the hippocampus. Despite the close relationship between LDLR and neurodegenerative disorders, proteomics research for protein profiling in the LDLR knockout (KO) model remains insufficient. Therefore, understanding LDLR KO-mediated differential protein expression within the hippocampus is crucial for elucidating a role of LDLR in neurodegenerative disorders. In this study, we conducted first-time proteomic profiling of hippocampus tissue from LDLR KO mice using tandem mass tag (TMT)-based MS analysis. LDLR deficiency induces changes in proteins associated with the transport of diverse molecules, and activity of kinase and catalyst within the hippocampus. Additionally, significant alterations in the expression of components in the major synaptic pathways were found. Furthermore, these synaptic effects were verified using a data-independent acquisition (DIA)-based proteomic method. In conclusion, our data will serve as a valuable resource for further studies to discover the molecular function of LDLR in neurodegenerative disorders.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Kubernetes for the Deep Underground Neutrino Experiment Data Acquisition

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long-baseline neutrino experiment based in the USA which is expected to start taking data in 2029. DUNE aims to precisely measure neutrino oscillation parameters by detecting neutrinos from the LBNF beamline (Fermilab) at the Far Detector, 1,300 kilometres away, in South Dakota at the Sanford Underground Research Facility. The Far Detector will consist of four cryogenic Liquid Argon Time Projection Chamber detectors of 17 kT, each producing more than 1 TB/sec of data. The main requirements for the data acquisition system are the ability to run continuously for extended periods of time, with a 99% up-time requirement, and the functionality to record both beam neutrinos and low energy neutrinos from the explosion of a neighbouring supernova, should one occur during the lifetime of the experiment. The key challenges are the high data rates that the detectors generate and the deep underground environment, which places constraints on power and space. To overcome these challenges, DUNE plans to use a highly optimised C++ software suite and a server farm of about 110 nodes continuously running about two hundred multicore processes located close to the detector, 1.5 kilometres underground. Thirty nodes will be at the surface and will run around two hundred processes simultaneously. DUNE is studying the use of the Kubernetes framework to manage containerised workloads and take advantage of its resource definitions and high up-time services to run the DAQ system. Progress in deploying these systems at the CERN neutrino platform on the prototype DUNE experiments is reported.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea

Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, “Candidatus Methanovorans” (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

A Hybrid System for High-Accuracy Timekeeping Using Millisecond Pulsars

Millisecond pulsars exhibit extremely stable rotational periods with negligible long-term variation, comparable to atomic clocks. Leveraging pulsar signal stability, this paper presents a hybrid Pulse Per Second (PPS) generation system for high-accuracy and GPS-independent timing. The system combines pulsar and GPS signals through a high-speed data acquisition platform featuring FPGA-driven processing and techniques. This design provides a reliable and precise timekeeping solution for energy systems, ensuring functionality when GPS signals are unavailable.

Wu, Ori [ORNL] (ORCID:0000000326723410)↗

DOE OSTI2021

Trade-Offs Between Growth Rate and Other Fungal Traits

If we better understand how fungal responses to global change are governed by their traits, we can improve predictions of fungal community composition and ecosystem function. Specifically, we can examine trade-offs among traits, in which the allocation of finite resources toward one trait reduces the investment in others. We hypothesized that trade-offs among fungal traits relating to rapid growth, resource capture, and stress tolerance sort fungal species into discrete life history strategies. We used the Biolog Filamentous Fungi database to calculate maximum growth rates of 37 fungal species and then compared them to their functional traits from the fun fun database. In partial support of our hypothesis, maximum growth rate displayed a negative relationship with traits related to resource capture. Moreover, maximum growth rate displayed a positive relationship with amino acid permease, forming a putative Fast Growth life history strategy. A second putative life history strategy is characterized by a positive relationship between extracellular enzymes, including cellobiohydrolase 6, cellobiohydrolase 7, crystalline cellulase AA9, and lignin peroxidase. These extracellular enzymes were negatively related to chitosanase 8, an enzyme that can break down a derivative of chitin. Chitosanase 8 displayed a positive relationship with many traits that were hypothesized to cluster separately, forming a putative Blended life history strategy characterized by certain resource capture, fast growth, and stress tolerance traits. These trait relationships complement previously explored microbial trait frameworks, such as the Competitor-Stress Tolerator-Ruderal and the Yield-Resource Acquisition-Stress Tolerance schemes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Evaluation of Station Performance of the Idaho National Laboratory Seismic Monitoring Network Using Network Detection Thresholds

The Idaho National Laboratory (INL) Seismic Monitoring Network is located in eastern Idaho and monitors a portion of the intermountain seismic belt. It has been in place for 50 yr and has undergone several major changes, the most recent of which has been the transition to the Antelope real‐time acquisition system and the implementation of automatic phase picking algorithms to aid in analysis. This study discusses the efforts to evaluate the performance of the INL seismic monitoring network (and other surrounding stations) using the new real‐time acquisition system. The method outlined by Wilson et al. (2021) is used to develop an empirical relationship between the observability of local earthquakes as a function of magnitude and distance. This relationship is used to produce detection thresholds for Pwaves for all stations of interest. The INL seismic network has two main goals: monitor tectonic‐and volcanic‐related events and measure ground motions for input into seismic hazard analysis. Because of these two overall objectives, several seismic stations have been installed near critical facilities and, therefore, are not as quiet as stations that are used primarily for earthquake detection. This is reflected in their detection thresholds, which are much smaller for stations away from facilities. This study shows that the INL Seismic Monitoring Network is able to detect earthquakes near INL facilities with M L > 1.2, with redundancies built in to ensure this sensitivity even if data became unavailable from some stations. This study also shows “holes” in the monitoring network where the detection of smaller earthquakes is highly dependent on sparsely placed seismic stations. In conclusion, the results of this study will be used to govern plans for expansion of earthquake monitoring in Idaho and the surrounding region and to fine‐tune the detection thresholds for individual stations.

58 - GEOSCIENCES↗

DOE OSTI2022

Carbon acquisition ecological strategies to connect soil microbial biodiversity and carbon cycling

Soil carbon feedbacks to global change are uncertain, and the biological processes that govern soil organic matter decomposition are not resolved in current ecosystem models. Though it is recognized that microbial biodiversity influences decomposition rates, incorporating this relationship into ecosystem models is challenging because microbial communities are prohibitively diverse. It is likely necessary to distill microbial biodiversity by focusing on functional groups or ecological strategies. The ecological strategies that currently dominate the microbial ecology literature derive from macroecological theory, have clear weaknesses, and have had limited success when applied to predict soil carbon dynamics. Here, we present a new framework for soil microorganisms: Carbon Acquisition Ecological Strategies (CAES), and we outline a path toward incorporating microbial biodiversity into ecosystem models using this framework to enhance predictions of soil carbon feedbacks to global change. Because a microorganism's diet is central to its ecological niche and likely to covary with other ecologically significant traits, we posit that carbon acquisition may serve as a tractable foundation for developing ecological strategies. Further, we describe four candidate ecological strategies for soil microorganisms: 1° decomposers that assimilate complex plant polymers, 2° decomposers that assimilate microbial necromass, passive consumers that assimilate dissolved organic carbon, and predatory microbes that assimilate live microbial biomass. These strategies are directly linked to soil carbon pools currently represented in ecosystem models and may provide a foundation for greater integration of microbial community dynamics into ecosystem models.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Towards scanning nanostructure X-ray microscopy

This article demonstrates spatial mapping of the local and nanoscale structure of thin film objects using spatially resolved pair distribution function (PDF) analysis of synchrotron X-ray diffraction data. This is exemplified in a lab-on-chip combinatorial array of sample spots containing catalytically interesting nanoparticles deposited from liquid precursors using an ink-jet liquid-handling system. A software implementation is presented of the whole protocol, including an approach for automated data acquisition and analysis using the atomic PDF method. The protocol software can handle semi-automated data reduction, normalization and modeling, with user-defined recipes generating a comprehensive collection of metadata and analysis results. By slicing the collection using included functions, it is possible to build images of different contrast features chosen by the user, giving insights into different aspects of the local structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Finally, our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Single-cell proteomics of Arabidopsis leaf mesophyll reveals dynamic protein responses to water-deficit stress

Background The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far, most single-cell studies in plant systems have been limited to RNA-sequencing approaches, which only provide indirect readouts of cellular functions. Results Here, we present a single-cell proteomics workflow for plant cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, and ion mobility-based MS data acquisition method for label-free single-cell proteomics analysis of Arabidopsis leaf mesophyll cells. From a single leaf protoplast, over 3,000 proteins were quantified with high precision. The workflow is demonstrated to identify stress associated changes in protein abundance by analyzing 117 protoplasts from well-watered and water-deficit stressed plants. Additionally, we describe a new approach for constructing covarying protein networks at the single-cell level and demonstrate how single-cell protein covariation analysis can reveal previously unrecognized protein functions while also capturing stress-induced changes in protein–protein dynamics. Conclusions The label-free scProteomic approach presented here represents a significant advance through the demonstration of a facile protoplast isolation method combined with deep and precise proteomic coverage of Arabidopsis leaf mesophyll cell types. We believe this study will serve as an informative reference to future plant scProteomic investigations.

Arabidopsis↗

DOE OSTI2021

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1—Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Deep transfer operator learning for partial differential equations under conditional shift

Transfer learning enables the transfer of knowledge gained while learning to perform one task (source) to a related but different task (target), hence addressing the expense of data acquisition and labelling, potential computational power limitations and dataset distribution mismatches. Here, we propose a new transfer learning framework for task-specific learning (functional regression in partial differential equations) under conditional shift based on the deep operator network (DeepONet). Task-specific operator learning is accomplished by fine-tuning task-specific layers of the target DeepONet using a hybrid loss function that allows for the matching of individual target samples while also preserving the global properties of the conditional distribution of the target data. Inspired by conditional embedding operator theory, we minimize the statistical distance between labelled target data and the surrogate prediction on unlabelled target data by embedding conditional distributions onto a reproducing kernel Hilbert space. We demonstrate the advantages of our approach for various transfer learning scenarios involving nonlinear partial differential equations under diverse conditions due to shifts in the geometric domain and model dynamics. Our transfer learning framework enables fast and efficient learning of heterogeneous tasks despite considerable differences between the source and target domains.

42 ENGINEERING↗

DOE OSTI2025

Real-time evaluation of cybersecurity threats to DER inverter grid-support functions

In this project we aim to contribute to the understanding of the type and severity of potential cybersecurity attacks to the grid-support functionalities of DER systems interconnected to the AC distribution grid via inverters. Our preliminary work focused on developing a small-scale testbed allowing to study cybersecurity threats to an isolated photovoltaic-battery system using a real-time simulator (Typhoon HIL602+) with a real DNP3 communication connection over TCP/IP, allowing for safe and efficient monitoring and manipulation of data traffic between the simulated hardware and supervisory control and data acquisition (SCADA) system. In this project we propose to expand upon this development by utilizing a) a recently acquired NovaCor RTDS (Real Rime digital Simulator) to emulate the DER-inverter-grid topology including main grid-support functions as defined by IEEE Std. 1547-2018, and b) an industrial control and automation device to enable realistic evaluation of control functions and utilization of communication protocols for real-time data transmission.

24 POWER TRANSMISSION AND DISTRIBUTION↗