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All sources NASA NTRS DOE OSTI

DOE OSTI2018

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer

Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between a nanoelectrospray ionization (nanoESI) emitter and an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot proteomic data with comparable depth to that of conventional two-dimensional LC approaches. This next generation FAIMS device incorporates improved ion sampling at the ESI–FAIMS interface, increased electric field strength, and a helium-free ion transport gas. With fast internal compensation voltage (CV) stepping (25 ms/transition), multiple unique gas-phase fractions may be analyzed simultaneously over the course of an MS analysis. We have comprehensively demonstrated how this device performs for bottom-up proteomics experiments as well as characterized the effects of peptide charge state, mass loading, analysis time, and additional variables. We also offer recommendations for the number of CVs and which CVs to use for different lengths of experiments. Internal CV stepping experiments increase protein identifications from a single-shot experiment to >8000, from over 100 000 peptide identifications in as little as 5 h. In single-shot 4 h label-free quantitation (LFQ) experiments of a human cell line, we quantified 7818 proteins with FAIMS using intra-analysis CV switching compared to 6809 without FAIMS. Single-shot FAIMS results also compare favorably with LC fractionation experiments. Furthermore, a 6 h single-shot FAIMS experiment generates 8007 protein identifications, while four fractions analyzed for 1.5 h each produce 7776 protein identifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

SERPENT 2 and TRIPOLI-4 neutronics benchmarking of the Jules Horowitz reactor

Jules Horowitz Reactor (JHR) is a future center for nuclear material testing in Europe, currently under construction at CEA Cadarache in southern France. It has been modelled extensively with CEA's HORUS3D/N neutron calculation package, that includes a Monte-Carlo neutron transport code TRIPOLI-4. In order to support the future computational analyses on the reactor core physics, VTT's Monte Carlo neutronics code SERPENT 2 has been used to create an alternative model of the JHR, taking advantage of the pre-existing Constructive Solid Geometry (CSG) structures on which the TRIPOLI-4 model was built. This work describes a benchmark, in which two JHR core configurations were analyzed using both of these models. The first configuration is a fresh fuel core at the beginning of life, in which aluminum based dummy-devices are installed in the reactor test positions. The second configuration represents the end-of-cycle equilibrium core with a heterogeneous burnup distribution, in which CALIPSO devices containing cladding material samples are installed at the in-core experimental positions, while the reflector positions are occupied by DEN-REP devices containing UO{sub 2} fuel. Neutron flux spectra and heat deposition are the parameters of interest in this study, due to their high importance in creating the desired experimental irradiation environment. The impact of delayed gamma energy deposition will be studied in detail, since the two models account for it with different methods. This work aims to establish a SERPENT 2 model of JHR, understanding its differences and agreements with TRIPOLI-4, and discussing its potential future applications. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

Co-flow injection for serial crystallography at X-ray free-electron lasers

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

3D printing↗

DOE OSTI2018

Detection of Delayed Neutrons from Fissionable Samples: Monte Carlo Modelling and Physical Assumptions for a Design of the DET-12 Device

An activation of fissionable materials with neutrons has been considered as a possible neutron diagnostic of D–D and D–T fusion plasma. Fission reaction caused by fusion neutrons leads up to emission of secondary neutrons: prompt and delayed. Physical assumptions have been outlined to design a new device (DET-12) for measurements of delayed neutrons emitted from samples of fissionable materials activated with neutrons at big fusion-plasma devices. The aim is to support a classic neutron activation method used as one of plasma diagnostics at tokamaks or stellarators. An interpretation of the time decay of delayed neutrons enables an assessment of the primary neutron flux which induced fission reaction. Monte Carlo calculations have been carried out in order to elaborate the method considered. Nuclides like: pure {sup 235}U, {sup 238}U and {sup 232}Th, have been selected as possible materials to be irradiated. Physical fundamentals of generation of the delayed neutrons are mentioned and a resulting concept of the DET-12 device, built in the Institute of Nuclear Physics, Poland, is presented. A general size and dimensions of particular constituent material layers, and a number and placement of neutron detectors are optimized by means of Monte Carlo modelling. Recommendations for a technical design of the measuring chamber were formulated. Detection efficiency of DET-12 has been also estimated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

MultiPEM Toolbox: User Manual [Rev. 2]

This document explains use of the Multi-Phenomenology Explosion Monitoring (Multi PEM) Toolbox, a collection of R scripts for estimating the unknown device parameters of a new event with uncertainty quantification. The methodology and application used for illustration in this user manual are fully documented in a Los Alamos National Laboratory technical report hereafter designated “WPA” for reference. Additional details on the application are found in a recent journal article. Two assessment types are available: rapid and complete. Rapid assessments are conducted in two stages, as described in Section 2. In the first stage, calibration data are used to estimate forward and error model parameters (WPA, §5.1) and (if relevant) errors-in-variables yield values for calibration sources (WPA, §3, Equation (3)). In the second stage, new event data are used to estimate the unknown new event device parameters (WPA, §5.2) with uncertainty quantification. Two options for treating the inferred first stage parameters in second stage Bayesian analysis are available: fixing them at their maximum likelihood estimate (default), or multiple imputation. Multiple imputation involves utilizing several posterior samples (imputations) of the first stage parameters as fixed values in the second stage posterior sampling of the new event device parameters. Second stage sampling is conducted across imputations in parallel to improve computational efficiency. This method produces improved uncertainty quantification of the new event device parameters compared with the default treatment of the first stage parameters, at the expense of additional computation. Complete assessments are conducted in a single stage, as described in Section 3. Calibration and (if relevant) new event data are used simultaneously to estimate all forward model, error model, and (if relevant) new event device parameters with uncertainty quantification on the latter. As the name suggests, rapid assessments generally run substantially faster than complete assessments (even with multiple imputation), because the results of first stage analysis can be stored and incorporated into estimating a relatively low-dimensional space of new event device parameters whenever relevant new event data becomes available. On the other hand, complete assessments must be run on the full set of model and device parameters with calibration and new event data every time the latter becomes available.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Composition and method for capture and degradation of PFAS

Materials for binding per- and polyfluoroalkyl substances (PFAS) are disclosed. A fluidic device comprising the materials for detection and quantification of PFAS in a sample is disclosed. The fluidic device may be configured for multiplexed analyses. Also disclosed are methods for sorbing and remediating PFAS in a sample. The sample may be groundwater containing, or suspected of containing, one or more PFAS.

Motkuri, Radha K.↗

DOE OSTI2024

Fluidic impedance platform for in-situ detection and quantification of PFAS in groundwater

Chatterjee, Sayandev↗

DOE OSTI2021

A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening

A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

SpinDX Case Study

SpinDX, often referred to as a "lab-on-a-disk" is a portable, medical diagnostic platform that uses a disposable, centrifugal disk with microfluidic flow paths to manipulate a biological sample. This allows multiple tests to be carried out on a single sample with no preparation required. The device operates by distributing drops of raw, unprocessed samples into different channels that function as dozens of tiny test tubes. When the disc spins, the samples interact with test reagents inside the channels. If there is a chemical interaction between the sample and the reagent, the tip of the channel will produce a fluorescent glow indicating that there is an infectious agent present. The data is then transferred to a software interface that displays the test results.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Site-specific plan-view (S)TEM sample preparation from thin films using a dual-beam FIB-SEM

To fully evaluate the atomic structure, and associated properties of materials using transmission electron microscopy, examination of samples from three non-collinear orientations is needed. This is particularly challenging for thin films and nanoscale devices built on substrates due to limitations with plan-view sample preparation. In this work, a new method for preparation of high-quality, site-specific, plan-view TEM samples from thin-films grown on substrates, is presented and discussed. Here, it is based on using a dual-beam focused ion beam scanning electron microscope (FIB-SEM) system. To demonstrate the method, the samples were prepared from thin films of perovskite oxide BaSnO 3 grown on a SrTiO 3 substrate and metal oxide IrO 2 on a TiO 2 substrate, ranging from 20–80 nm in thicknesses using molecular beam epitaxy. While the method is optimized for the thin films, it can be extended to other site-specific plan-view samples and devices build on wafers. Aberration-corrected STEM was used to evaluate the quality of the samples and their applicability for atomic-resolution imaging and analysis.

BaSnO3↗

DOE OSTI2015

Microtrap assembly for greenhouse gas and air pollution monitoring

A microtrap assembly includes a carbon nanotube sorbent. The microtrap assembly may be employed as a preconcentrator operable to deliver a sample to an analytical device to measure the concentrations of greenhouse gases. A system includes a microtrap having a carbon nanotube sorbent for measuring the concentrations of greenhouse gases in a sample.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Absence of evidence for chiral Majorana modes in quantum anomalous Hall-superconductor devices

A quantum anomalous Hall (QAH) insulator coupled to an s-wave superconductor is predicted to harbor chiral Majorana modes. A recent experiment interprets the half-quantized two-terminal conductance plateau as evidence for these modes in a millimeter-size QAH-niobium hybrid device. However, non-Majorana mechanisms can also generate similar signatures, especially in disordered samples. Here, we studied similar hybrid devices with a well-controlled and transparent interface between the superconductor and the QAH insulator. When the devices are in the QAH state with well-aligned magnetization, the two-terminal conductance is always half-quantized. Our experiment provides a comprehensive understanding of the superconducting proximity effect observed in QAH-superconductor hybrid devices and shows that the half-quantized conductance plateau is unlikely to be induced by chiral Majorana fermions in samples with a highly transparent interface.

Science & Technology - Other Topics↗

DOE OSTI2022

Thermal measurement apparatus and methods for anisotropic thermal materials

A system for characterizing thermal properties of thermally anisotropic heterogeneous samples includes a heating element, a first temperature sensing device, a second temperature sensing device, and a computing system. The heating element is positioned at a first location within a sample and heats the sample. The first temperature sensing device outputs data indicative of temperatures of the first location to the computing device. The second temperature sensing device outputs data indicative of temperatures of the second location to the computing device. The computing device computes a thermal conductivity of the sample based upon the temperatures of the first location. The computing device further outputs an indication of a portion of the sample to which the thermal conductivity pertains based upon the second temperatures.

Reyes, Karla Rosa↗

DOE OSTI2023

Thermal measurement apparatus and methods for anisotropic thermal materials

Reyes, Karla Rosa↗

DOE OSTI2022

Advances in Sampling and Situational Awareness Using Augmented and Virtual Reality Devices.

Abstract not provided.

Knowlton, Robert G.↗

DOE OSTI2015

Magnetic modification at sub-surface of FeRh bulk by energetic ion beam irradiation

Ferromagnetic layered structure has been made at sub-surface of the antiferromagnetic FeRh bulk samples by high energy He ion beam irradiation. In accordance with the Transport of Ions in Matter simulation, such ion beam can effectively deposit the elastic collision energy in several μm regions in the depth from the surface. Measurement with a superconducting quantum interference device reveals the irradiated samples to be ferromagnetic. Assuming that only the part the energy deposited can be modified to be ferromagnetic, the corresponding irradiation induced magnetization is consistent with the data that we previously reported. On the other hand, the X-ray magnetic circular dichroism (XMCD) spectra for the irradiated samples are totally unchanged as those for the unirradiated samples. Since XMCD signal in total emission yield method is considered to be surface sensitive with a typical probing depth of several nm, the surface magnetic state is maintained to be antiferromagnetic. By utilizing these phenomena, three-dimensional magnetic patterning of FeRh can be realized, which may potentially be used for future magnetic exchange device application such as nano-scale sensors and memories.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

A monolayer microfluidic device supporting mouse spermatogenesis with improved visibility

In our previous study, we produced a microfluidic device (MFD) which successfully maintained spermatogenesis for over 6 months in mouse testis tissues loaded in the device. In the present study, we developed a new MFD, a monolayer device (ML-D) with a barrier structure consisting of pillars and slits, which is simpler in design and easier to make. This ML-D was also effective for inducing mouse spermatogenesis and maintained it for a longer period than the conventional culture method. In addition, we devised a way of introducing sample tissue into the device during its production, just before bonding the upper layer of polydimethylsiloxane (PDMS) and bottom glass slide. The tissue can obtain nutrients horizontally from the medium running beside it and oxygen vertically from above through PDMS. In addition, the glass slide set at the bottom improved the visibility of the sample tissue with an inverted microscope. When we took photos of cultured tissue of the Acr-Gfp transgenic mouse testis in ML-D sequentially every day, morphological changes of the acrosome during spermiogenesis were successfully recorded. The ML-D is simple in design and useful for culturing testis tissue for inducing and maintaining spermatogenesis with clearer visibility. Due to the new method of sample loading, tissues other than testis should also be applicable.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

An Open Port Sampling Interface for Liquid Introduction Atmospheric Pressure Ionization Mass Spectrometry

RATIONALE: A simple method to introduce unprocessed samples into a solvent for rapid characterization by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The continuous flow, self-cleaning open port sampling interface introduced here fills this void. METHODS: The open port sampling interface used a vertically aligned, co-axial tube arrangement enabling solvent delivery to the sampling end of the device through the tubing annulus and solvent aspiration down the center tube and into the mass spectrometer ionization source via the commercial APCI emitter probe. The solvent delivery rate to the interface was set to exceed the aspiration rate creating a continuous sampling interface along with a constant, self-cleaning spillover of solvent from the top of the probe. RESULTS: Using the open port sampling interface with positive ion mode APCI and a hybrid quadrupole time of flight mass spectrometer, rapid, direct sampling and analysis possibilities are exemplified with plastics, ballpoint and felt tip ink pens, skin, and vegetable oils. These results demonstrated that the open port sampling interface could be used as a simple, versatile and self-cleaning system to rapidly introduce multiple types of unprocessed, sometimes highly concentrated and complex, samples into a solvent flow stream for subsequent ionization and analysis by mass spectrometry. The basic setup presented here could be incorporated with any self-aspirating liquid introduction ionization source (e.g., ESI, APCI, APPI, ICP, etc.) or any type of atmospheric pressure sampling ready mass spectrometer system. CONCLUSIONS: The open port sampling interface provides a means to introduce and quickly analyze unprocessed solid or liquid samples with liquid introduction atmospheric pressure ionization source without fear of sampling interface or ionization source contamination.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗