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At least 1,567 records · Page 87

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DOE OSTI2024

Nr2f1 enhancers have distinct functions in controlling Nr2f1 expression during cortical development

There is evidence that transcription factor (TF) encoding genes, which temporally control development in multiple cell types, can have tens of enhancers that regulate their expression. The NR2F1 TF developmentally promotes caudal and ventral cortical regional fates. Here, we epigenomically compared the activity of Nr2f1’s enhancers during mouse cortical development with their activity in a transgenic assay. We identified at least six that are likely to be important in prenatal cortical development, with three harboring de novo mutants identified in ASD individuals. We chose to study the function of two of the most robust enhancers by deleting them singly or together. We found that they have distinct and overlapping functions in driving Nr2f1’s regional and laminar expression in the developing cortex. Thus, these two enhancers, probably in combination with the others that we defined epigenetically, precisely tune Nr2f1’s regional, cell type, and temporal expression during corticogenesis.

Liu, Zhidong↗

DOE OSTI2022

Alpert multi-wavelets for functional inverse problems: direct optimization and deep learning

Computational engineering models often contain unknown entities (e.g. parameters, initial and boundary conditions) that require estimation from other measured observable data. Estimating such unknown entities is challenging when they involve spatio-temporal fields because such functional variables often require an infinite-dimensional representation. Here, we address this problem by transforming an unknown functional field using Alpert wavelet bases and truncating the resulting spectrum. Hence the problem reduces to the estimation of few coefficients that can be performed using common optimization methods. We apply this method on a one-dimensional heat transfer problem where we estimate the heat source field varying in both time and space. The observable data is comprised of temperature measured at several thermocouples in the domain. This latter is composed of either copper or stainless steel. The optimization using our method based on wavelets is able to estimate the heat source with an error between 5% and 7%. We analyze the effect of the domain material and number of thermocouples as well as the sensitivity to the initial guess of the heat source. Finally, we estimate the unknown heat source using a different approach based on deep learning techniques where we consider the input and output of a multi-layer perceptron in wavelet form. We find that this deep learning approach is more accurate than the optimization approach with errors below 4%.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A Variable Eddington Factor Model for Thermal Radiative Transfer with Closure Based on Data-Driven Shape Function

Here, a new variable Eddington factor (VEF) model is presented for nonlinear problems of thermal radiative transfer (TRT). The VEF model is data-driven and acts on known (a-priori) radiation-diffusion solutions for material temperatures in the TRT problem. A linear auxiliary problem is constructed for the radiative transfer equation (RTE) whose emission source and opacities are evaluated at these known material temperatures. The solution to this RTE approximates the specific intensity distribution in phase-space and time. It is applied as a shape function to define the Eddington tensor for the presented VEF model. The shape function computed via the auxiliary RTE problem will capture some degree of transport effects within the TRT problem. The VEF moment equations closed with this approximate Eddington tensor will thus carry with them these captured transport effects. In this study, the temperature data comes from multigroup P 1 , P 1/3 , and flux-limited diffusion radiative transfer models. The proposed VEF model can be interpreted as a transport-corrected diffusion reduced-order model. Numerical results are presented on the Fleck-Cummings test problem which models a supersonic wavefront of radiation. The VEF model is shown to improve accuracy by 1–2 orders of magnitude compared to the considered radiation-diffusion model solutions to the TRT problem.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Lack of long-term effect of coarse woody debris dam restoration on ecosystem functioning and water quality in Coastal Plain streams

Coarse woody debris (CWD) addition is a restoration technique that has been used to reduce effects of landscape disturbance on instream habitat. However, efficacy of this technique for improving ecosystem condition is not well established, in part because monitoring designed to evaluate long-term efficacy is rare. We assessed the effectiveness of CWD additions in disturbed Coastal Plain streams at Fort Benning Military Installation, Georgia, USA, 14 y after initial restoration. In October 2003, 4 disturbed streams received CWD additions (restored streams), and 4 streams were left as unrestored controls. Pre-restoration (2001–2003) and post-restoration (2003–2006) monitoring of nutrient uptake, stream metabolism, and water-quality variables revealed 1) minimal change in water-quality variables, 2) increased stream metabolism and nutrient-uptake rates immediately following restoration, and 3) decreased metabolism and uptake over the remainder of the 3-y post-restoration period. We returned to these streams in 2017 and 2018, measured the same variables, and found minimal long-term effects of restoration on water quality, nutrient uptake, and whole-stream metabolism indicators; however, streamwater pH decreased in all streams 14 y after restoration, and there was a weak treatment × period interaction, indicating that CWD additions may decrease pH in the long term. Further, we found few relationships between watershed disturbance and water-quality variables and ecosystem function metrics, although some relationships were apparent during certain seasons and years. Furthermore, our study is one of the few that have assessed the long-term effects of CWD additions, or any other stream-restoration technique, on ecosystem function. These long-term assessments may be necessary to determine if restorations are a good use of limited resources.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Large area nanoscale patterning of functional materials using organosilicate ink based nanotransfer printing

Abstract This paper presents a versatile nanotransfer printing method for achieving large-area sub-micron patterns of functional materials. Organosilicate ink formulations combined with effective release layers have been shown to facilitate patterning of materials through the commonly used patterning approaches—lift off, physical etching and chemical etching. In this paper, we demonstrate that organosilicate ink formulations function as an effective resist owing to its superior physico-chemical stability whereas the release layers ensure clean removal of the resist post patterning. We successfully demonstrate patterning of sub-micron structures (800 nm feature sizes) of chromium metal through the lift off approach, silicon through reactive ion etching technique and silicon dioxide through wet chemical etching technique illustrating the versatility of the reported method. This patterning methodology represents a significant advancement in enabling nanostructure fabrication within resource-constrained laboratories. The approach requires nothing more than a master mold containing the desired structures, a spin coater, a low-temperature hotplate, and a desktop reactive ion etch tool.

Engineering↗

DOE OSTI2020

A Bayesian analysis of nuclear deformation properties with Skyrme energy functionals

In spite of numerous scientific and practical applications, there is still no comprehensive theoretical description of the nuclear fission process based solely on protons, neutrons and their interactions. Furthermore, the most advanced simulations of fission are currently carried out within nuclear density functional theory (DFT). In spite of being fully quantum-mechanical and rooted in the theory of nuclear forces, DFT still depends on a dozen or so parameters characterizing the energy functional. Calibrating these parameters on experimental data results in uncertainties that must be quantified for applications. This task is very challenging because of the high computational cost of DFT calculations for fission. In this paper, we use Gaussian processes to build emulators of DFT models in order to quantify and propagate statistical uncertainties of theoretical predictions for a range of nuclear deformations relevant to describing the fission process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Ab initio calculation of atomic solid hydrogen phases based on Gutzwiller many-body wave functions

We apply two ab initio many-body methods based on Gutzwiller wave functions, i.e., correlation matrix renormalization theory (CMRT) and Gutzwiller conjugate gradient minimization (GCGM), to the study of crystalline phases of atomic hydrogen. Both methods avoid empirical Hubbard U parameters and are free from double-counting issues. CMRT employs a Gutzwiller-type approximation that enables efficient calculations, while GCGM goes beyond this approximation to achieve higher accuracy at higher computational cost. By benchmarking against available quantum Monte Carlo (QMC) results, we demonstrate that while both methods are more accurate than the widely used density-functional theory, GCGM systematically captures additional correlation energy missing in CMRT, leading to significantly improved total energy predictions. We also show that by including the correlation energy Ec from local density approximation in the CMRT calculation, CMRT + E c produces energy in better agreement with the QMC results in these hydrogen lattice systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Transfer functions for Q A /Q B international regulatory limits for the safe transport of radioactive materials

This paper presents a proposed revision of the International Atomic Energy Agency transport regulations, related to the A 1 and A 2 limit values used to determine the radioactive transport classification. Based on the 'Q system', a novel methodology was introduced to derive Q A and Q B values related to scenarios involving external exposure from a distant source. These values are key parameters that respectively represent the total effective dose and total equivalent dose to the skin, from all primary and secondary particles contributing to radiation exposure. The International Working Group (WG A 1 /A 2 ) is established and associated with the TRANSSC Technical Expert Group on Radiation Protection. A review of the A 1 and A 2 values is performed in response to identified limitations within the existing Q system. The followed approach is based on Monte Carlo simulations that enabled the development of transfer functions aimed at reducing computational time and increasing the flexibility of dose evaluations for any radionuclide with known particle emission spectra. This method allows updating the Q A and Q B values to account for future data evolutions (decay data, fluence-to-dose conversion coefficients) and standardizing the calculation of regulation limits across all referenced radionuclides and scenarios related to external exposure. The transfer functions are established using three Monte Carlo simulation codes—FLUKA, Geant4, and MCNP—and address the previous limitations of the 'Q system', reflecting the latest International Commission for Radiation Protection recommendations and improvements in calculation techniques. The results of the WG show consistent agreement across the codes, with minor discrepancies observed at low primary energies due to statistical uncertainties and different handling of stopping power for electrons/positrons in the codes. This revised approach aligns with current standards and recommendations, ensuring that the radiological consequences of transport accidents are acceptable for the new A 1 and A 2 limits from a radiological protection perspective.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2019

Manipulating nanoscale structure to control functionality in printed organic photovoltaic, transistor and bioelectronic devices

Printed electronics is simultaneously one of the most intensely studied emerging research areas in science and technology and one of the fastest growing commercial markets in the world today. For the past decade the potential for organic electronic (OE) materials to revolutionize this printed electronics space has been widely promoted. Such conviction in the potential of these carbon-based semiconducting materials arises from their ability to be dissolved in solution, and thus the exciting possibility of simply printing a range of multifunctional devices onto flexible substrates at high speeds for very low cost using standard roll-to-roll printing techniques. However, the transition from promising laboratory innovations to large scale prototypes requires precise control of nanoscale material and device structure across large areas during printing fabrication. Maintaining this nanoscale material control during printing presents a significant new challenge that demands the coupling of OE materials and devices with clever nanoscience fabrication approaches that are adapted to the limited thermodynamic levers available. In this review we present an update on the strategies and capabilities that are required in order to manipulate the nanoscale structure of large area printed organic photovoltaic (OPV), transistor and bioelectronics devices in order to control their device functionality. This discussion covers a range of efforts to manipulate the electroactive ink materials and their nanostructured assembly into devices, and also device processing strategies to tune the nanoscale material properties and assembly routes through printing fabrication. The review finishes by highlighting progress in printed OE devices that provide a feedback loop between laboratory nanoscience innovations and their feasibility in adapting to large scale printing fabrication. The ability to control material properties on the nanoscale whilst simultaneously printing functional devices on the square metre scale is prompting innovative developments in the targeted nanoscience required for OPV, transistor and biofunctional devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Phase-space sensitivity (weight functions) of 3 MeV proton diagnostics

Abstract The weight function W ( X ) is a diagnostic sensitivity to phase-space variables X that relates the measured signal C to the distribution function F ( X ) through the equation C = ∫ W ( X ) F ( X ) d X . In the present work, an algorithm to calculate W for a diagnostic that measures 3 MeV protons produced in d(d,p)t fusion reactions between a fast ion and a thermal deuteron is developed. The emitted protons escape the tokamak on curved orbits and are detected. These curved orbits constitute effective diagnostic ‘sightlines’. The presented algorithm accounts for the complications associated with these curved sightlines. An initial calculation of time-reversed proton orbits computes effective solid angles and sightlines for the relevant range of incident proton velocity vectors. These precomputed orbits are then used within the framework of FIDASIM (2020 Plasma Phys. Cont. Fusion 62 105008) to calculate the reactivity averaged over the thermal distribution of the ‘target’ deuterons and the probability that a fast ion of specified energy and pitch has a gyroangle that is consistent with the kinematic equations along each of the sightlines. Comparisons with analytic formulas and with independent calculations for the Mega Amp Spherical Tokamak 3 MeV proton diagnostic verify the algorithm.

Physics↗

DOE OSTI2025

Large-scale tearing-mode hazard function analysis with standard matched equilibrium reconstructions

The association between features from standard tokamak equilibrium reconstructions and the onset of n = 1 tearing modes (TMs) is analyzed at scale. The TM onset rate is directly modeled with a ‘hazard’ function which gives the expected number of onsets (per unit time spent) in a given equilibrium parameter region. In particular the different statistical modeling performance achieved for magnetics-only reconstructions and motional Stark effect (MSE) enhanced reconstructions is studied. It is observed that a better hazard model for the TM onset rate can be built with the MSE-enhanced equilibria compared to the matched magnetics-only situation. This advantage disappears if internal profile details are withheld from the matched analysis. Plausibility of the hazard function is further demonstrated with visualizations of global trends in the operational space, and time-traces from specific tokamak discharges. As a result, TMs typically degrade tokamak plasma performance and may lead to plasma termination, motivating this statistical study.

equilibrium↗

DOE OSTI2022

Time-resolved ion energy distribution functions during a HiPIMS discharge with cathode voltage reversal

Abstract The effect on the ion energy distribution function (IEDF) of plasma produced during a high-power impulse magnetron sputtering (HiPIMS) discharge as the pulse conditions are varied is reported. Pressure was varied from 0.67–2.00 Pa (5–15 mTorr), positive kick pulses up to 200 V tested with a constant 4 μ s delay between negative and positive cycles. The results demonstrate that the resulting plasma during the positive cathode voltage reversal is the result of expansion through the largely neutral gas species between the end of the magnetic trap of the target and the workpiece. The plasma potential rises on similar time scale with the evolution of a narrow peak in the IEDF close to the applied bias. The peak of the distribution function remains narrow close to the applied bias irrespective of pulse length, and with only slight pressure dependence. One exception discovered is that the IEDF contains a broad high energy tail early in the kick pulse due to acceleration of ions present beyond the trap from the main pulse separate from the ionization front that follows.

Physics↗

DOE OSTI2024

Axion stars: mass functions and constraints

The QCD axion and axion-like particles, as leading dark matter candidates, can also have interesting implications for dark matter substructures if the Peccei-Quinn symmetry is broken after inflation. In such a scenario, axion perturbations on small scales will lead to the formation of axion miniclusters at matter-radiation equality, and subsequently the formation of axion stars. Such compact objects open new windows for indirect searches for axions. We compute the axion star mass function based on recent axion minicluster studies and Bose star simulations. Applying this mass function, we find post-inflation axion-like particles with masses 1.8 × 10$^{-21}$ eV

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Photometry, Centroid and Point-spread Function Measurements in the LSST Camera Focal Plane Using Artificial Stars

Abstract The Vera C. Rubin Observatory’s LSST Camera (LSSTCam) pixel response has been characterized using laboratory measurements with a grid of artificial stars. We quantify the contributions to photometry, centroid, point-spread function size, and shape measurement errors due to small anomalies in the LSSTCam CCDs. The main sources of those anomalies are quantum efficiency variations and pixel area variations induced by the amplifier segmentation boundaries and “tree-rings”—circular variations in silicon doping concentration. This laboratory study using artificial stars projected on the sensors shows overall small effects. The residual effects on point-spread function (PSF) size and shape are below 0.1%, meeting the ten-year LSST survey science requirements. However, the CCD mid-line presents distortions that can have a moderate impact on PSF measurements. This feature can be avoided by masking the affected regions. Effects of tree-rings are observed on centroids and PSFs of the artificial stars and the nature of the effect is confirmed by a study of the flat-field response. Nevertheless, further studies of the full-focal plane with stellar data should more completely probe variations and might reveal new features, e.g., wavelength-dependent effects. The results of this study can be used as a guide for the on-sky operation of LSSTCam.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Vectorization techniques for probability distribution functions using VecCore

Probability distribution functions (PDFs) are very used in modeling random processes and physics simulations. Improving the performance of algorithms that generate many random numbers under complex PDFs is often a very challenging task when methods as direct functions are not available. In this work we present general strategies on how to vectorize some PDFs using VecCore library. We show the results for the Exponential, Gaussian, discrete Poisson and Gamma probability distributions.

Chaparro Amaro, Oscar R.↗

DOE OSTI2020

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability and implementation All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary data are available at Bioinformatics online.

Hagemeijer, Marne C.↗

DOE OSTI2021

Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

ABSTRACT Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

MultiPhATE2: code for functional annotation and comparison of phage genomes

To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.

59 BASIC BIOLOGICAL SCIENCES↗