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DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗

DOE OSTI2015

Response to Comment on "Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism"

Wang comments that the diffraction data for the structure of the A139T mutant of translocator protein TSPO from Rhodobacter sphaeroides should be used to 1.65 instead of 1.8 angstroms and that the density interpreted as porphyrin and monoolein is better fitted as polyethylene glycol. Although different practices of data processing exist, in this case they do not substantially influence the final map. Additional data are presented supporting the fit of a porphyrin and monooleins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

How initial conditions-, structural-, and parameter-based model uncertainty interact and influence predictions in permafrost ecosystems: Modeling Archive

This dataset contains model output and input data, as well as source code examples for the Terrestrial Ecosystem Model with the Dynamic Vegetation Model and Dynamic Organic Soil (DVM-DOS-TEM) for the field sites Imnavait creek and the Bonanza creek Long Term Ecological Research Network (LTER). The data covers simulations from the last glacial maximum (LGM) until 2100 for a selection of paleo scenarios, setting the mean temperature of the LGM up to 10°C lower than pre-industrial conditions. The model structure was modulated to represent various model versions, and this dataset contains the relevant changes in the source code. The raw output data, the processed statistical data, the setup and processing scripts as well as parameter value distribution files from a parameter sensitivity analysis are included as well. Model outputs include active layer depth, organic soil carbon, soil layer depths, gross primary productivity (GPP) with and without nitrogen limitation, net primary productivity (NPP), soil liquid water content, heterotrophic, maintenance, and growth respiration, soil temperature, and vegetation carbon (*.nc files). The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research.Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Raw/Translated data and metadata from sensor and leaf sample measurements at Manaus, Brazil, 24 May 2016 -16 March 2017

Raw and processed data from K34 tower site on a plateau near Manaus, Brazil including automated and manually collected time series data on leaf surface temperature (thermocouples, IR radiometer, thermocamera), leaf gas exchange fluxes of CO2, isoprene emissions, and H2O, sap flow, leaf water potential, soil moisture, and ambient concentrations of volatile organic compounds. IR radiometer data from the B34 tower in the nearby valley is also included.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Critical parameters in the faculty application process: A data-driven analysis

We report the process of applying for science and engineering faculty positions requires a significant time investment for both the applicant and hiring committees. Applicants face the daunting task of sifting through a seemingly endless amount of information related to crafting their application packages in preparation for a review process that is inherently highly subjective. Furthermore, while scientific supervisors are often the most valuable resource during this stage of career development, many years may have passed since they went through this process themselves, and they may not have experience with recent developments in the application process. Because expectations and job responsibilities of new faculty members are rapidly evolving, certain guidelines are often not clearly specified, and it is therefore becoming difficult for applicants to most effectively prepare their application documents. Without access to adequate information and assistance, early-career researchers in particular can be placed at a significant disadvantage in the hiring process. Several recent articles can help prospective applicants in materials science and engineering land a faculty position,1,2,3 but there is nevertheless a need for clarification on expectations for different aspects of the faculty application materials.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Development of Prognostic Models Using Plant Asset Data

The recent growth of machine learning and artificial intelligence technologies provides opportunities for leveraging data-driven algorithms to address the problems of diagnostics and prognostics in the nuclear power industry. The use of machine learning and other statistical methods as prognostic models is of particular interest in the nuclear industry to accurately predict future equipment or plant state given a set of measurements. Such predictive capability will enable predictive assessment of component condition and remaining life and allow for condition-based predictive maintenance. The resulting optimization of maintenance scheduling and reduction in unnecessary maintenance activities will lower overall maintenance costs and improve the economics of nuclear power. This report discusses the various aspects of data processing and model development that are likely to influence the performance of prognostic models. Data from a boiling-water reactor was used to evaluate several prognostic models to identify key considerations for developing such models to predict data-driven plant state and equipment degradation condition. Preliminary results indicate the need for data sets that are relevant to the problem at hand and contain signatures that may be correlated to the prediction problem. Assuming such data exist, development of prognostic models using data-driven methods requires an understanding of the various sources of influence on the prediction accuracy (such as the model architecture, data preprocessing approaches, and potentially external factors influencing the equipment or plant system under assessment). Ongoing research is evaluating these factors in greater detail and examining techniques for calculating prediction uncertainty bounds.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

Water Sorption Study of Various Polymers and Polymeric Composites

In the formulations of many composite materials, polymeric materials are often used as binder materials to enhance processability, functionality, and safety during manufacturing. For instance, poly(ester urethane), such as Estane® 5703, is used in the formulation of PBX 9501, and vinyl copolymer elastomer (VCE) is used in the formulation of VCE/filler compos ites. The stability of these binders directly impacts the overall stability and performance of their composites. Estane and VCE are prone to hydrolytic degradation, with water sorption behavior playing a significant role in their long-term stability and aging behavior. Hence, it is critical to study their water sorption behavior under various humidity and tempera ture conditions. To improve the accuracy and reduce labor-intensive work involved in water sorption experiments, an automated Dynamic Vapor Sorption (DVS) system was employed, which can generate large datasets. To efficiently process and analyze these datasets, Python scripts were developed. These scripts not only streamlined data processing, but also accu rately derived the Arrhenius parameters related to water diffusion and sorption properties for the tested materials. This approach offers a robust framework for evaluating water trans port and sorption processes in polymeric materials and adds valuable capabilities to future water sorption testing efforts.

36 MATERIALS SCIENCE↗

DOE OSTI2024

NDMAS Overview

Overview of the Nuclear Data Management and Analysis System detailed as: Overview of NDMAS System, NDMAS NQA-1 process, Data in NDMAS, and Future work and new additions.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

DUNE Software and Computing Challenges

The DUNE experiment will begin running in the late 2020's. The goals of the experiment include 1) studying neutrino oscillations using a beam of neutrinos from Fermilab in Illinois to the Sanford Underground Research Facility, 2) studying astrophysical neutrino sources and rare processes and 3) understanding the physics of neutrino interactions in matter. The DUNE Far Detector, consisting of four 17 kt LArTPC modules, will produce "events" rang-ing in size from 6 GBs to more than 100 TBs, posing unique challenges for DUNE software and computing. The data processing algorithms, particularly for raw data, drive the requirements for the future DUNE software framework documented here.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Data-driven simultaneous process optimization and adsorbent selection for vacuum pressure swing adsorption

Technologies for post-combustion carbon capture are essential for the reduction of greenhouse gas emissions to the atmosphere. However, they are still associated with high costs and energy consumption. Intensified processes for carbon capture have the potential to overcome these challenges due to their higher efficiency, lower capital cost, and increased operational flexibility. Here, this work investigates simultaneous optimization of process conditions and adsorbent selection for a modular Vacuum Pressure-Swing Adsorption system designed for CO 2 capture. Both surrogate-based Nonlinear Programming and Mixed-Integer Nonlinear Programming approaches are applied and compared in terms of computational efficiency and solution accuracy. Moreover, process performance results are examined by applying several data analytics techniques to gain insights into the material-process correlations. Data-driven classifiers and neural networks can accurately predict whether a material is likely to satisfy purity, recovery, and energy constraints when operated at optimal process conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

The integrated miniaturized electrostatic analyzer: A space plasma environment sensor

The integrated Miniaturized Electrostatic Analyzer (iMESA) was a satellite-based ionospheric sensor that operated on NASA’s Space Test Program Satellite (STPSat-3) from December 2013 to July 2019. The instrument’s scientific objective was to (1) measure the plasma density in low Earth orbit, (2) measure the plasma temperature in low Earth orbit, and (3) quantify the spacecraft potential with respect to the ambient plasma potential in the ionosphere. iMESA sampled the ionosphere every 10 s by measuring the ion current density through the ESA as a result of the motion of the spacecraft through the plasma. Current density spectra were transmitted to the ground where they were post-processed into ion density spectra and then analyzed numerically to determine the ion density, ion temperature, and spacecraft potential. This article discusses the instrument design and simulation, the determination of a geometric factor, and data processing procedures and evaluates the final data product with regard to the mission success criteria. Here, the ion density and ion temperature captured by the iMESA instrument are on the same order and range as the values predicted in the literature. The spacecraft potential was also quantified. The conclusion after the evaluation of the instrument’s data product is that the scientific mission is successful on all three points.

47 OTHER INSTRUMENTATION↗

DOE OSTI2016

IOTA : integration optimization, triage and analysis tool for the processing of XFEL diffraction images

Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA , which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.

Chemistry↗

DOE OSTI2017

Retrieving Historical Electrorefining Data

Pyrochemical Operations began at Los Alamos National Laboratory (LANL) during 1962 (1). Electrorefining (ER) has been implemented as a routine process since the 1980’s. The process data that went through the ER operation was recorded but had never been logged in an online database. Without a database new staff members are hindered in their work by the lack of information. To combat the issue a database in Access was created to collect the historical data. The years from 2000 onward were entered and queries were created to analyze trends. These trends will aid engineering and operations staff to reach optimal performance for the startup of the new lines.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2021

Geophysical and Environmental Monitoring Data, Lower Watershed, Teller Road Mile Marker 27, Seward Peninsula, Alaska, 2017-2019

This data set contains geophysical and environmental monitoring data acquired between September 2017 and 2019 at the lower Teller watershed, Seward Peninsula, Alaska. Geophysical data comprises processed resistivity data, acquired daily between Spring and Fall of 2018 and 2019, and a baseline measurement of Fall 2017. The environmental monitoring data comprises depth resolved, distributed soil moisture and soil temperature data. These measurements were obtained used Decagon 5TE sensors placed at 0.1 m, 0.2 m , 0.3 m, and 0.4 m depth. In addition, temperature data at 0.5 m, 1.0 m, and 1.5 m were acquired using Hobo temperature sensors. Data were collected to improve our understanding of the hydrological response of discontinuous permafrost systems, in particular focusing on multi-annual dynamics and short term disturbances, such as snowmelt or precipitation events. The electrical resistivity tomography (ERT) monitoring data are included as processed resistivity models, with model cells x dimension equal to the distance along the profile, and model z dimension being elevation. The start and end point of the transect are (UTM Zone 3N): E 454881.66 m, N 7178949.45 m, and E 454772.60, N 7178885.81. Locations of the soil moisture and temperature sensors are provided in the data package. This dataset is discussed in detail in the Uhlemann, S. et al 2021 paper listed in the references. This dataset includes one *.pdf user guide and 315 *.csv data files included within four zipped files.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

TEAMER: Twin Ocean Power Wave Energy Converter Comprehensive Overview

These files collectively provide a comprehensive overview of the testing process, data analysis, and validation for the Twin Ocean Power device tested at the O.H. Hinsdale Wave Research Laboratory, supported by TEAMER funding. This resource includes an overview of power results for a series of 7 trials. The files included in this comprehensive overview include a comprehensive log sheet for each trial, a summary of all trials, and processing scripts for the raw data. It includes all raw data in .tsv and MATLAB compatible formats, an average power chart, angular velocity charts for each trial, trial metrics, and power output files. This resource includes images of the Twin Ocean Power Wave Energy Converter device components and movement during testing and video recordings of each trial.

16 TIDAL AND WAVE POWER↗

DOE OSTI2019

ISRM Suggested Method: Determining Deformation and Failure Characteristics of Rocks Subjected to True Triaxial Compression

The purpose of this ISRM Suggested Method is to introduce a guideline on determining deformation and failure characteristics of rocks subjected to true triaxial compression on different stress path. Here, the true triaxial testing apparatus was reviewed by means of the function and engineering application. Some key techniques, such as stress and strain measurements, and reduction of end effect between specimen and metal platens, preventing metal platens interference, were stated and suggested in detail. Methodology of specimen processing, specimen shape, and testing procedure are characterized. There is an explanation of the experimental data processing on stress–strain curves, strength, and fracture mode.

42 ENGINEERING↗

DOE OSTI2021

Performance of Julia for High Energy Physics Analyses

We argue that the Julia programming language is a compelling alternative to currently more common implementations in Python and C++ for common data analysis workflows in high energy physics. We compare the speed of implementations of different workflows in Julia with those in Python and C++. Furthermore, our studies show that the Julia implementations are competitive for tasks that are dominated by computational load rather than data access. For work that is dominated by data access, we demonstrate an application with concurrent file reading and parallel data processing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Nanoscale Probing of Electrical Memory Effects in van der Waals Layered PdSe 2

Tunable electronic materials that can be switched between different impedance states are fundamental to the hardware elements for neuromorphic computing architectures. This “brain-like” computing paradigm uses highly paralleled and colocated data processing, leading to greatly improved energy efficiency and performance compared to traditional architectures in which data have to be frequently transferred between processor and memory. In this work, we use scanning microwave impedance microscopy for nanoscale electrical and electronic characterization of two-dimensional layered semiconductor PdSe 2 to probe neuromorphic properties. The local resolution of tens of nanometers reveals significant differences in electronic behavior between and within PdSe 2 nanosheets (NSs). In particular, we detected both n-type and p-type behaviors, although previous reports only point to ambipolar n-type dominating characteristics. Nanoscale capacitance–voltage curves and subsequent calculation of characteristic maps revealed a hysteretic behavior originating from the creation and erasure of Se vacancies as well as the switching of defect charge states. In addition, stacks consisting of two NSs show enhanced resistive and capacitive switching, which is attributed to trapped charge carriers at the interfaces between the stacked NSs. Stacking n- and p-type NSs results in a combined behavior that allows one to tune electrical characteristics. In conclusion, as local inhomogeneities of electrical and electronic behavior can have a significant impact on the overall device performance, the demonstrated nanoscale characterization and analysis will be applicable to a wide range of semiconducting materials.

2D material↗