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At least 1,657 records · Page 92
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A large interlaboratory electron diffraction study of monolayer graphene

Standardisation of data collection and analysis is essential to enable commercialisation of 2D materials in a wide range of technologies. Selected area electron diffraction (SAED) in the transmission electron microscope (TEM) is one of the key methods for distinguishing monolayer from bilayer and few-layer graphene by comparing the 1st and 2nd order diffraction spot intensities. Yet there are many factors that can affect the reliability of data collection and interpretation, causing the measurement of monolayer samples to deviate from the literature boundary condition of $I_{\{\bar{2}110\}}$$/$$I_{\{1\bar{1}00\}}$ < 1 for monolayer graphene (1LG). Here we present the results of a large interlaboratory SAED comparison study, where 15 international laboratories measured and analysed nominally identical samples of chemical vapour deposited graphene. Large variations were observed in the measured ratios of diffraction spot intensities, with the largest variance associated with poor quality SAED data resulting from inadequate specimen handling and storage. To inform the reliable determination of monolayer thickness from SAED patterns we provide a description of best practice for specimen handling, TEM operation, data collection and analysis. This work was undertaken within VAMAS Technical Working Area 41: Graphene and related 2D materials—Project 9, the results of which have been directly incorporated into ISO/TS 21356–2 for the characterisation of graphene sheets. We find that when this methodology is followed, 1LG can be distinguished from bilayer or thicker material with high confidence where analysis of a single SAED pattern gives $I_{\{\bar{2}110\}}$$/$$I_{\{1\bar{1}00\}}$ < 1.2, even in the absence of precise specimen tilting.

2D materials↗
DOE OSTI2021

Large aperture and durable glass-engraved optical metasurfaces using nanoparticle etching masks: prospects and future directions

Abstract Metasurfaces (MSs), or surfaces consisting of engineered spatially oriented sub-wavelength elements—also known as meta-atoms—are quickly becoming a burgeoning field of interest due to their seemingly unparalleled control over the propagation of light. This article will discuss the emergence of a MS technology that is based on dewetting thin metal films to form dry etching masks for MS fabrication. The novelty this process presents is the ability to spatially vary mask features—which translates into spatially varying index of the finished surface—in a way that, rather than writing subwavelength elements one-by-one, writes entire areas at once to provide a route to easily scale the process up to meter-sized optics. Glass-engraved MSs have shown to be laser damage resistant, with damage thresholds close to the parent substrate damage thresholds. Furthermore, these surfaces have proven to be mechanically durable and capable of handling normal loads two orders of magnitude higher than that of an average fingerprint pressure. This indicates that accidental handling contact is not detrimental to the MS optical performance. Also discussed are the foreseeable technological challenges, potential solutions for those obstacles, and some currently unexplored directions for future efforts.

47 OTHER INSTRUMENTATION↗
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 OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

RF-Net 2: fast inference of virus reassortment and hybridization networks

Abstract Motivation A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. Results Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses. Availability and implementation RF-Net 2 is available at https://github.com/flu-crew/rf-net-2. Supplementary information Supplementary data are available at Bioinformatics online.

Markin, Alexey (ORCID:0000000332809050)↗
DOE OSTI2023

K-RET: knowledgeable biomedical relation extraction system

Abstract Motivation Relation extraction (RE) is a crucial process to deal with the amount of text published daily, e.g. to find missing associations in a database. RE is a text mining task for which the state-of-the-art approaches use bidirectional encoders, namely, BERT. However, state-of-the-art performance may be limited by the lack of efficient external knowledge injection approaches, with a larger impact in the biomedical area given the widespread usage and high quality of biomedical ontologies. This knowledge can propel these systems forward by aiding them in predicting more explainable biomedical associations. With this in mind, we developed K-RET, a novel, knowledgeable biomedical RE system that, for the first time, injects knowledge by handling different types of associations, multiple sources and where to apply it, and multi-token entities. Results We tested K-RET on three independent and open-access corpora (DDI, BC5CDR, and PGR) using four biomedical ontologies handling different entities. K-RET improved state-of-the-art results by 2.68% on average, with the DDI Corpus yielding the most significant boost in performance, from 79.30% to 87.19% in F-measure, representing a P-value of 2.91×10−12. Availability and implementation https://github.com/lasigeBioTM/K-RET.

Sousa, Diana F. (ORCID:0000000305979273)↗
DOE OSTI2014

Detecting differential protein expression in large-scale population proteomics

Mass spectrometry-based high-throughput quantitative proteomics shows great potential in clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, methods are needed to appropriately handle issues/challenges unique to mass spectrometry data in order to detect as many biomarker proteins as possible. One issue is that different mass spectrometry experiments generate quite different total numbers of quantified peptides, which can result in more missing peptide abundances in an experiment with a smaller total number of quantified peptides. Another issue is that the quantification of peptides is sometimes absent, especially for less abundant peptides and such missing values contain the information about the peptide abundance. Here, we propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

EMMA: an adaptive mesh refinement cosmological simulation code with radiative transfer

EMMA is a cosmological simulation code aimed at investigating the reionization epoch. It handles simultaneously collisionless and gas dynamics, as well as radiative transfer physics using a moment-based description with the M1 approximation. Field quantities are stored and computed on an adaptive three-dimensional mesh and the spatial resolution can be dynamically modified based on physically motivated criteria. Physical processes can be coupled at all spatial and temporal scales. We also introduce a new and optional approximation to handle radiation: the light is transported at the resolution of the non-refined grid and only once the dynamics has been fully updated, whereas thermo-chemical processes are still tracked on the refined elements. Such an approximation reduces the overheads induced by the treatment of radiation physics. A suite of standard tests are presented and passed by EMMA, providing a validation for its future use in studies of the reionization epoch. The code is parallel and is able to use graphics processing units (GPUs) to accelerate hydrodynamics and radiative transfer calculations. Depending on the optimizations and the compilers used to generate the CPU reference, global GPU acceleration factors between ×3.9 and ×16.9 can be obtained. As a result, vectorization and transfer operations currently prevent better GPU performance and we expect that future optimizations and hardware evolution will lead to greater accelerations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Standardized protocols and procedures can precisely and accurately quantify non-structural carbohydrates

Non-structural carbohydrates (NSCs), the stored products of photosynthesis, building blocks for growth, and fuel for respiration, are central to plant metabolism, but their measurement is challenging. Differences in methods and procedures among laboratories can cause results to vary widely, limiting our ability to integrate and generalize patterns in plant C balance among studies. A recent assessment found that NSC concentrations measured for a common set of samples can vary by an order of magnitude, but sources for this variability were unclear. We measured a common set of nine plant material types, and two synthetic samples with known NSC concentrations, using a common protocol for sugar extraction and starch digestion, and three different sugar quantification methods (ion chromatography, enzyme, acid) in six laboratories. We also tested how sample handling, extraction solvent, and centralizing parts of the procedure in one laboratory affected results. NSC concentrations measured for synthetic samples were within about 11.5% of known values for all three methods. However, differences among quantification methods were the largest source of variation in NSC measurements for natural plant samples because the three methods quantify different NSCs. The enzyme method quantified only glucose, fructose, and sucrose, with ion chromatography we additionally quantified galactose, while the acid method quantified a large range of mono- and oligosaccharides. For some natural samples, acid method quantification doubled sugar relative to the other methods, demonstrating that trees allocate C to a range of sugar molecules. Sample handling had little effect on measurements, while ethanol sugar extraction improved accuracy over water extraction. Our results demonstrate that reasonable accuracy of NSC measurements can be achieved when different methods are used, as long as protocols are robust and standardized. Thus, we provide detailed protocols for the extraction, digestion and quantification of NSCs in plant samples, which should improve the comparability of NSC measurements among laboratories.

Landhäusser, Simon M.↗
DOE OSTI2014

Joint US/Russian Studies of Population Exposures Resulting from Nuclear Production Activities in the Southern Urals

Beginning in 1948, the Soviet Union initiated a program for production of nuclear materials for a weapons program. The first facility for production of plutonium was constructed in the central portion of the country east of the southern Ural Mountains, about halfway between the major industrial cities of Ekaterinburg and Chelyabinsk. The facility now known as the Mayak Production Association and its associated town, now known as Ozersk, were built to irradiate uranium in reactors, separate the resulting plutonium in reprocessing plants, and prepare plutonium metal. The rush to production, coupled with inexperience in handling radioactive materials, lead to large radiation exposures, not only to the workers in the facilities, but also to the surrounding public. Fuel processing started with no controls on releases, and fuel dissolution and accidents in reactors resulted in release of about 37 PBq (1015 Bq) of 131I between 1948 and 1967. Designed disposals of low- and intermediate-level liquid radioactive wastes, and accidental releases via cooling water from tank farms of high-level liquid radioactive wastes, into the small Techa River caused significant contamination and exposures to residents of numerous small riverside villages downstream of the site. Discovery of the magnitude of the aquatic contamination in late 1951 caused revisions to the waste handling regimes, but not before over 200 PBq of radionuclides (with large contributions of 90Sr and 137Cs) were released. Liquid wastes were diverted to tiny Lake Karachay (which today holds over 4 EBq); cooling water was stopped in the tank farms. In 1957, one of the tanks in the tank farm overheated and exploded; over 70 PBq, disproportionately 90Sr, was blown over a large area to the northeast of the site; a large area was contaminated and many villages evacuated. This area today is known as the East Urals Radioactive Trace (EURT). Each of these releases was significant; together they have created a group of cohorts unrivaled in the world for their chronic, low-dose-rate radiation exposure. The 26,000 workers at Mayak were highly exposed to external gamma and inhaled plutonium. A cohort of individuals raised as children in Ozersk is under evaluation for their exposures to radioiodine. The Techa River Cohort consists of over 30,000 people who were born before the start of exposure in 1949 and lived along the Techa River. The Techa River Offspring Cohort consists of about 21,000 persons born to one or more exposed parents of this group - many of whom also lived along the contaminated river. The EURT Cohort consists of about 18,000 people who were evacuated from the EURT soon after the 1957 explosion and another 8000 who remained. These groups together are the focus of dose reconstruction and epidemiological studies funded by the US, Russia, and the European Union to address the question “Are doses delivered at low dose rates as effective in producing health effects as the same doses delivered at high dose rates?”

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2015

Radiation Safety of Sealed Radioactive Sources

Sealed radioactive sources are used in a wide variety of occupational settings and under differing regulatory/licensing structures. The definition of a sealed radioactive source varies between US regulatory authorities and standard-setting organizations. Potential problems with sealed sources cover a range of risks and impacts. The loss of control of high activity sealed sources can result in very high or even fatal doses to members of the public who come in contact with them. Sources that are not adequately sealed, and that fail, can cause spread of contamination and potential intake of radioactive material. There is also the possibility that sealed sources may be (or threatened to be) used for terrorist purposes and disruptive opportunities. Until fairly recently, generally-licensed sealed sources and devices received little, if any, regulatory oversight, and were often forgotten, lost or unaccounted for. Nonetheless, generally licensed devices can contain fairly significant quantities of radioactive material and there is some potential for exposure if a device is treated in a way that it was never designed. Industrial radiographers use and handle high activity and/or high-dose rate sealed sources in the field with a high degree of independence and minimal regulatory oversight. Failure to follow operational procedures and properly handle radiography sources can and has resulted in serious injuries and death. Industrial radiographers have experienced a disproportionately large fraction of incidents that result in unintended exposure to radiation. Sources do not have to contain significant quantities of radioactive material to cause problems in the event of their failure. A loss of integrity can cause the spread of contamination and potential exposure to workers and members of the public. The NCRP has previously provided recommendations on select aspects of sealed source programs. Future efforts to provide recommendations for sealed source programs are discussed.

radioactive material↗
DOE OSTI2026

Efficient atmospheric, solar, and supernova neutrino propagation through the Earth

Algorithms for computing neutrino oscillation probabilities in sharply varying matter potentials such as the Earth are becoming increasingly important. As the next generation of experiments, DUNE and HyperK as well as the IceCube upgrade and KM3NeT, come online, the computational cost for atmospheric and solar neutrinos will continue to increase. To address these issues, we expand upon our previous algorithm for long-baseline calculations to efficiently handle probabilities through the Earth for atmospheric, nighttime solar, and supernova neutrinos. The algorithm is fast, flexible, and accurate. It can handle arbitrary Earth models with two different schemes for varying density profiles. We also provide a c ++ implementation of the code called NUF ast- E arth along with a detailed user manual. The code intelligently keeps track of repeated calculations and only recalculates what is needed on each successive call which can also help provide significant speed-ups.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Comparison of momentum transport models for numerical relativity

The main problems of nonvacuum numerical relativity, compact binary mergers and stellar collapse, involve hydromagnetic instabilities and turbulent flows, so that kinetic energy at small scales leads to mean effects at large scale that drive the secular evolution. Notable among these effects is momentum transport. We investigate two models of this transport effect, a relativistic Navier-Stokes system and a turbulent mean stress model, that are similar to all of the prescriptions that have been attempted to date for treating subgrid effects on binary neutron star mergers and their aftermath. Our investigation involves both stability analysis and numerical experimentation on star and disk systems. We also begin the investigation of the effects of particle and heat transport on postmerger simulations. Here, we find that correct handling of turbulent heating is crucial for avoiding unphysical instabilities. Given such appropriate handling, the evolution of a differentially rotating star and the accretion rate of a disk are reassuringly insensitive to the choice of prescription. However, disk outflows can be sensitive to the choice of method, even for the same effective viscous strength. We also consider the effects of eddy diffusion in the evolution of an accretion disk and show that it can interestingly affect the composition of outflows.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Influence of humidity on performance and microscopic dynamics of an ionic liquid in supercapacitor

We investigated the influence of water molecules on the diffusion, dynamics, and electrosorption of a room temperature ionic liquid (RTIL), [BMIm + ][Tf 2 N - ], confined in carbide-derived carbon with a bimodal nanoporosity. Water molecules in pores improved the charge storage densities and rate handling abilities of these materials in supercapacitor electrode configurations. We measured the water-dependent microscopic dynamics of the RTIL cations using quasi-elastic neutron scatting (QENS). The ionic liquid demonstrated greater mobility with increasing water uptake, facilitated by the nanoporous carbon environment, up to a well-defined saturation point. We concluded that water molecules displaced RTIL ions attached to the pore surfaces and improved the diffusivity of the displaced cations. This effect consequently increased capacitance and rate handling of the electrolyte in water-containing pores. Our findings suggest the possible effect of immiscible co-solvents on energy and power densities of energy storage devices, as well as the operating viability of non-aqueous supercapacitor electrolytes in humid environments.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Model-independent particle accelerator tuning

We present a new model-independent dynamic feedback technique, rotation rate tuning, for automatically and simultaneously tuning coupled components of uncertain, complex systems. The main advantages of the method are: 1) It has the ability to handle unknown, time-varying systems, 2) It gives known bounds on parameter update rates, 3) We give an analytic proof of its convergence and its stability, and 4) It has a simple digital implementation through a control system such as the Experimental Physics and Industrial Control System (EPICS). Because this technique is model independent it may be useful as a real-time, in-hardware, feedback-based optimization scheme for uncertain and time-varying systems. In particular, it is robust enough to handle uncertainty due to coupling, thermal cycling, misalignments, and manufacturing imperfections. As a result, it may be used as a fine-tuning supplement for existing accelerator tuning/control schemes. We present multi-particle simulation results demonstrating the scheme’s ability to simultaneously adaptively adjust the set points of twenty two quadrupole magnets and two RF buncher cavities in the Los Alamos Neutron Science Center Linear Accelerator’s transport region, while the beam properties and RF phase shift are continuously varying. The tuning is based only on beam current readings, without knowledge of particle dynamics. We also present an outline of how to implement this general scheme in software for optimization, and in hardware for feedback-based control/tuning, for a wide range of systems.

42 ENGINEERING↗
DOE OSTI2013

Microcrystal manipulation with laser tweezers

Optical trapping has successfully been applied to select and mount microcrystals for subsequent X-ray diffraction experiments. X-ray crystallography is the method of choice to deduce atomic resolution structural information from macromolecules. In recent years, significant investments in structural genomics initiatives have been undertaken to automate all steps in X-ray crystallography from protein expression to structure solution. Robotic systems are widely used to prepare crystallization screens and change samples on synchrotron beamlines for macromolecular crystallography. The only remaining manual handling step is the transfer of the crystal from the mother liquor onto the crystal holder. Manual mounting is relatively straightforward for crystals with dimensions of >25 µm; however, this step is nontrivial for smaller crystals. The mounting of microcrystals is becoming increasingly important as advances in microfocus synchrotron beamlines now allow data collection from crystals with dimensions of only a few micrometres. To make optimal usage of these beamlines, new approaches have to be taken to facilitate and automate this last manual handling step. Optical tweezers, which are routinely used for the manipulation of micrometre-sized objects, have successfully been applied to sort and mount macromolecular crystals on newly designed crystal holders. Diffraction data from CPV type 1 polyhedrin microcrystals mounted with laser tweezers are presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Phaser.MRage: automated molecular replacement

The functionality of the molecular-replacement pipeline phaser.MRage is introduced and illustrated with examples. Phaser.MRage is a molecular-replacement automation framework that implements a full model-generation workflow and provides several layers of model exploration to the user. It is designed to handle a large number of models and can distribute calculations efficiently onto parallel hardware. In addition, phaser.MRage can identify correct solutions and use this information to accelerate the search. Firstly, it can quickly score all alternative models of a component once a correct solution has been found. Secondly, it can perform extensive analysis of identified solutions to find protein assemblies and can employ assembled models for subsequent searches. Thirdly, it is able to use a priori assembly information (derived from, for example, homologues) to speculatively place and score molecules, thereby customizing the search procedure to a certain class of protein molecule (for example, antibodies) and incorporating additional biological information into molecular replacement.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

A method is presented for screening fragment libraries using acoustic droplet ejection to co-crystallize proteins and chemicals directly on micromeshes with as little as 2.5 nl of each component. This method was used to identify previously unreported fragments that bind to lysozyme, thermolysin, and trypsin. Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗