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DOE OSTI2022

Iraq/Afghanistan war lung injury reflects burn pits exposure

This descriptive case series retrospectively reviewed medical records from thirty-one previously healthy, war-fighting veterans who self-reported exposure to airborne hazards while serving in Iraq and Afghanistan between 2003 and the present. They all noted new-onset dyspnea, which began during deployment or as a military contractor. Twenty-one subjects underwent non-invasive pulmonary diagnostic testing, including maximum expiratory pressure (MEP) and impulse oscillometry (IOS). In addition, five soldiers received a lung biopsy; tissue results were compared to a previously published sample from a soldier in our Iraq Afghanistan War Lung Injury database and others in our database with similar exposures, including burn pits. We also reviewed civilian control samples (5) from the Stony Brook University database. Military personnel were referred to our International Center of Excellence in Deployment Health and Medical Geosciences, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell under the auspices of Northwell IRB: 17-0140-FIMR Feinstein Institution for Medical Research “Clinicopathologic characteristics of Iraq Afghanistan War Lung Injury.” We retrospectively examined medical records, including exposure data, radiologic imaging, and non-invasive pulmonary function testing (MGC Diagnostic Platinum Elite Plethysmograph) using the American Thoracic Society (ATS) standard interpretation based on Morgan et al., and for a limited cohort, biopsy data. Lung tissue, when available, was examined for carbonaceous particles, polycyclic aromatic hydrocarbons (Raman spectroscopy), metals, titanium connected to iron (Brookhaven National Laboratory, National Synchrotron Light Source II, Beamline 5-ID), oxidized metals, combustion temperature, inflammatory cell accumulation and fibrosis, neutrophil extracellular traps, Sirius red, Prussian Blue, as well as polarizable crystals/particulate matter/dust. Among twenty-one previously healthy, deployable soldiers with non-invasive pulmonary diagnostic tests, post-deployment, all had severely decreased MEP values, averaging 42% predicted. These same patients concurrently demonstrated abnormal airways reactance (X5Hz) and peripheral/distal airways resistance (D5–D20%) via IOS, averaging – 1369% and 23% predicted, respectively. These tests support the concept of airways hyperresponsiveness and distal airways narrowing, respectively. Among the five soldiers biopsied, all had constrictive bronchiolitis. We detected the presence of polycyclic aromatic hydrocarbons (PAH)—which are products of incomplete combustion—in the lung tissue of all five warfighters. All also had detectable titanium and iron in the lungs. Metals were all oxidized, supporting the concept of inhaling burned metals. Combustion temperature was consistent with that of burned petrol rather than higher temperatures noted with cigarettes. All were nonsmokers. Neutrophil extracellular traps were reported in two biopsies. Compared to our prior biopsies in our Middle East deployment database, these histopathologic results are similar, since all database biopsies have constrictive bronchiolitis, one has lung fibrosis with titanium bound to iron in fixed mathematical ratios of 1:7 and demonstrated polarizable crystals. These results, particularly constrictive bronchiolitis and polarizable crystals, support the prior data of King et al. (N. Engl. J. Med. 365:222–230, 2011) Soldiers in this cohort deployed to Iraq and Afghanistan since 2003, with exposure to airborne hazards, including sandstorms, burn pits, and improvised explosive devices, are at high risk for developing chronic clinical respiratory problems, including: (1) reduction in respiratory muscle strength; (2) airways hyperresponsiveness; and (3) distal airway narrowing, which may be associated with histopathologic evidence of lung damage, reflecting inhalation of burned particles from burn pits along with particulate matter/dust. Non-invasive pulmonary diagnostic tests are a predictor of burn pit-induced lung injury

36 MATERIALS SCIENCE↗

DOE OSTI2023

Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor

HMG-CoA reductase (HMGR), a rate-limiting enzyme of the mevalonate pathway in Gram-positive pathogenic bacteria, is an attractive target for development of novel antibiotics. In this study, we report the crystal structures of HMGR from Enterococcus faecalis (efHMGR) in the apo and liganded forms, highlighting several unique features of this enzyme. Statins, which inhibit the human enzyme with nanomolar affinity, perform poorly against the bacterial HMGR homologs. We also report a potent competitive inhibitor (Chembridge2 ID 7828315 or compound 315) of the efHMGR enzyme identified by a high-throughput, in-vitro screening. The X-ray crystal structure of efHMGR in complex with 315 was determined to 1.27 Å resolution revealing that the inhibitor occupies the mevalonate-binding site and interacts with several key active site residues conserved among bacterial homologs. Importantly, 315 does not inhibit the human HMGR. Our identification of a selective, non-statin inhibitor of bacterial HMG-CoA reductases will be instrumental in lead optimization and development of novel antibacterial drug candidates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Mass action model of solution activity via speciation by solvation and ion pairing equilibria

Abstract Solutes and their concentrations influence many natural and anthropogenic solution processes. Electrolyte and solution models are used to quantify and predict such behavior. Here we present a mechanistic solution model based on mass action equilibria. Solvation and ion pairing are used to model speciated solute and solvent concentrations such that they correlate to a solution’s vapor pressure (solvent activity) according to Raoult’s law from dilute conditions to saturation. This model introduces a hydration equilibrium constant ( K ha ) that is used with either an ion dissociation constant ( K id ) or a hydration modifier ( m ) with an experimentally determined ion dissociation constant, as adjustable parameters to fit vapor–liquid equilibrium data. The modeled solvation equilibria are accompanied by molecular dynamics (MD) studies that support a decline in the observed degree of solvation with increased concentration. MD calculations indicate this finding is a combination of a solvent that solvates multiple solutes, and changes in a solute’s solvation sphere, with the dominant factor changing with concentration. This speciation-based solution model is lateral to established electrostatics-based electrolyte theories. With its basis in mass action, the model can directly relate experimental data to the modeled solute and solvent speciated concentrations and structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Consequences of the failure of equipartition for the p – V behavior of liquid water and the hydration free energy components of a small protein

Earlier we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step δ t ≤ 0.5 fs to ensure equipartition between translational and rotational modes. Here we extend that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examine integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small δ t is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, and the dielectric constant, a measure of dipole moment fluctuations, are also seen to be sensitive to δ t . Using the mean volume estimated from the NpT simulation, we examine the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to δ t . In going from δ t = 2 fs to δ t = 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Secure Command Line Solution for Token-based Authentication

The WLCG is modernizing its security infrastructure, replacing X.509 client authentication with the newer industry standard of JSON Web Tokens (JWTs) obtained through the Open ID Connect (OIDC) protocol. There is a wide variety of software available using the standards, but most of it is for Web browser-based applications and doesn’t adapt well to the command line-based software used heavily in High Throughput Computing (HTC). OIDC command line client software did exist, but it did not meet our requirements for security and convenience. This paper discusses a command line solution we have made based on the popular existing secrets management software from Hashicorp called vault. We made a package called htvault-config to easily configure a vault service and another called htgettoken to be the vault client. In addition, we have integrated use of the tools into the HTCondor workload management system, although they also work well independent of HTCondor. All of the software is open source, under active development, and ready for use.

Dykstra, Dave↗

DOE OSTI2025

Label-based Virtual Directories In dCache

Traditional filesystems organize data in directories. These directories are typically a collection of files whose grouping is based on a single criterion, e.g., the starting date of an experiment, experiment name, beamline ID, measurement device, or instrument. However, each file in a directory can belong to several logical groups, such as a special event type, experiment condition, or a part of a selected dataset. dCache is a storage system developed to store large amounts of scientific data, used by many HEP and Photon Science experiments. With recent developments in dCache, we have introduced a concept of file tagging, which dynamically groups files with the same label into virtual directories. The file labels can be added, removed, renamed, and deleted through the admin interface or via REST API. The files in virtual directories are exposed through all protocols supported by dCache. This contribution will describe the details of the implementation for file tagging in dCache and present our future development plans on automatic metadata extractions, a feature that will significantly simplify data management. Additionally, we are exploring the future use of virtual directories as a way to translate scientific data catalogs into filesystem views for direct data analysis.

Sahakyan, Marina [DESY]↗

DOE OSTI2023

Equation of state for 304L stainless steel

Here, a new equation of state for 304L stainless steel has been constructed and entered in the Los Alamos National Laboratory SESAME database with material ID 4273. The equation of state is based on a multiphase approach. The solid and liquid phases were fitted to available experimental data for thermal expansion, heat capacity, and shock Hugoniot, as well as to data from density functional theory calculations of the cold curve and quantum molecular dynamics of the liquid regime. The electronic thermal contribution over the entire equation of state range is based on Tartarus (Green’s functions) average atom calculations. For this low-carbon stainless steel both the density functional and electronic thermal calculations are comprised of 19 wt% Cr, 10 wt% Ni, and the remainder Fe.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry

Visualizing 3D molecular structures is crucial to understanding and predicting their chemical behavior. However, static 2D hand-drawn skeletal structures remain the preferred method of chemical communication. Here, we combine cutting-edge technologies in augmented reality (AR), machine learning, and computational chemistry to develop MolAR, an open-source mobile application for visualizing molecules in AR directly from their hand-drawn chemical structures. Users can also visualize any molecule or protein directly from its name or protein data bank ID and compute chemical properties in real time via quantum chemistry cloud computing. MolAR provides an easily accessible platform for the scientific community to visualize and interact with 3D molecular structures in an immersive and engaging way.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Coded-mask-based wavefront sensing technique for APS nanofocusing beamline diagnostics

Here, we extend our recently developed coded-mask wavefront sensing technique to enable single-shot measurements of nanofocused x-ray beams. This method accurately reconstructs the focal beam profile by backpropagating the wavefront measured downstream of the beam focus. To validate its performance, we benchmarked it against the conventional fluorescence wire scan method, successfully measuring ∼120 nm focal spots at the 28-ID-B beamline of the Advanced Photon Source using a polymeric compound refractive lens. The results highlight the effectiveness of coded-mask wavefront sensing for high-precision beam profiling and its application as a real-time wavefront monitoring tool.

Shi, Xianbo [Argonne National Laboratory (ANL), Ar↗

DOE OSTI2025

A quantitative imaging framework for lithium morphology: Linking deposition uniformity to cycle stability in lithium metal batteries

Characterizing the morphology of lithium (Li) is crucial for developing long-lasting lithium metal batteries. It is well established that more uniform Li deposition correlates with better cell performance. Li morphology is often characterized through qualitative analysis of scanning electron microscopy (SEM) images; however, there are no widely accepted metrics to quantitatively describe deposition uniformity. Here, we propose a framework to quantify uniformity through SEM image analysis via the index of dispersion (ID) metric, which is defined and presented in the context of Li metal batteries. We also explore experimental impacts of sampling protocols onIDmeasurements. Our results demonstrate that theIDmetric is highly sensitive to variations in deposition uniformity, including the coexistence and uniformity of multiple morphologies, uniformity within a single morphology, and particle size distribution uniformity. Furthermore, it is demonstrated that uniformity, as measured by theID, can be related to the average potential of Li||Li symmetric cells over cycling. Higher capacity cycling leads to more pronounced changes in bothIDand average cell potential. Local minima/maxima are found consistently in bothIDand average cell potential immediately before cells short-circuit, which we suggest may indicate a collapse of the microstructure prior to failure. We put forward this framework as a more robust approach to quantify Li deposition uniformity, advancing the development of Li metal batteries that are safer and longer lasting.

Science & Technology - Other Topics↗

DOE OSTI2021

Specific absorbed fractions for a revised series of the UF/NCI pediatric reference phantoms: internal photon sources

Assessment of radiation absorbed dose to internal organs of the body from the intake of radionuclides, or in the medical setting through the injection of radiopharmaceuticals, is generally performed based upon reference biokinetic models or patient imaging data, respectively. Biokinetic models estimate the time course of activity localized to source organs. The time-integration of these organ activity profiles are then scaled by the radionuclide S-value, which defines the absorbed dose to a target tissue per nuclear transformation in various source tissues. S-values are computed using established nuclear decay information (particle energies and yields), and a parameter termed the specific absorbed fraction (SAF). The SAF is the ratio of the absorbed fraction—fraction of particle energy emitted in the source tissue that is deposited in the target tissue—and the target organ mass. While values of the SAF may be computed using patient-specific or individual-specific anatomic models, they have been more widely available through the use of computational reference phantoms. In this study, we report on an extensive series of photon SAFs computed in a revised series of the University of Florida and the National Cancer Institute pediatric reference phantoms which have been modified to conform to the specifications embodied in the ICRP reference adult phantoms of Publication 110 (e.g. organs modeled, organ ID numbers, blood contribution to elemental compositions). Following phantom anatomical revisions, photon radiation transport simulations were performed using MCNPX v2.7 in each of the ten phantoms of the series—male and female newborn, 1 year old, 5 year old, 10 year old, and 15 year old—for 60 different tissues serving as source and/or target regions. A total of 25 photon energies were considered from 10 keV to 10 MeV along a logarithm energy grid. Detailed analyses were conducted of the relative statistical errors in the Monte Carlo target tissue energy deposition tallies at low photon energies and over all energies for source–target combinations at large intra-organ separation distances. Based on these analyses, various data smoothing algorithms were employed, including multi-point weighted data smoothing, and log–log interpolation at low energies (1 keV and 5 keV) using limiting SAF values based upon target organ mass to bound the interpolation interval. The final dataset is provided in a series of ten electronic supplemental files in MS Excel format. Finally, the results of this study were further used as the basis for assessing the radiative component of internal electron source SAFs as described in our companion paper (Schwarz et al 2021) for this same pediatric phantom series.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2021

Specific absorbed fractions for a revised series of the UF/NCI pediatric reference phantoms: internal electron sources

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Effect of detachment on Magnum-PSI ELM-like pulses: direct observations and qualitative results

Abstract Conditions similar to those at the end of the divertor leg in a tokamak were replicated in the linear plasma machine Magnum-PSI. The neutral pressure in the target chamber is then increased to cause the target to transition from an attached to a detached state. Superimposed to this steady state regime, edge localised mode (ELM)-like pulses are reproduced, resulting in a sudden increase in plasma temperature and density, such that the heat flux increases transiently by half an order of magnitude. Visible light emission, target thermography, and Thomson scattering are used to demonstrate that the higher the neutral pressure the more energy is removed from the ELM-like pulse in the volume. If the neutral pressure is sufficiently high, the ELM-like pulse can be prevented from affecting the target and the plasma energy is fully dissipated in the volume instead (ID 4 in table 1). The visible light images allow the division of the ELM-plasma interaction process of ELM energy dissipation into 3 ‘stages’ ranging from no dissipation to full dissipation (the target plasma is detached). In the second publication related to this study, spectroscopic data is analysed with a Bayesian approach, to acquire insights into the significance of molecular processes in dissipating the plasma energy and particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

First data from the CUPID-Mo neutrinoless double beta decay experiment

The CUPID-Mo experiment is searching for neutrinoless double beta decay in $^{100}$Mo, evaluating the technology of cryogenic scintillating Li$_{2}^{100}$MoO$_4$ detectors for CUPID (CUORE Upgrade with Particle ID). CUPID-Mo detectors feature background suppression using a dual-readout scheme with Li$_{2}$MoO$_4$ crystals complemented by Ge bolometers for light detection. The detection of both heat and scintillation light signals allows the efficient discrimination of $\alpha$ from $\gamma$&$\beta$ events. In this proceedings, we discuss results from the first 2 months of data taking in spring 2019. In addition to an excellent bolometric performance of 6.7$\,$keV (FWHM) at 2615$\,$keV and an $\alpha$ separation of better than 99.9% for all detectors, we report on bulk radiopurity for Th and U. Finally, we interpret the accumulated physics data in terms of a limit of $T_{1/2}^{0\nu}\,> 3\times10^{23}\,$yr for $^{100}$Mo and discuss the sensitivity of CUPID-Mo until the expected end of physics data taking in early 2020.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Development of a Superconducting Adaptive Gap Undulator Prototype for NSLS-II

The photon flux and brightness of synchrotron radiation, crucial parameters for any light source, vary significantly depending on the type of source employed. Among the 23 Insertion Device (ID) sources at the National Synchrotron Light Source II (NSLS-II) at Brookhaven National Lab (BNL), the 12-year-old 3m-long In-Vacuum Undulator (IVU20) stands out for its superior performance, although it no longer represents the cutting edge of technology. Recently, there has been a shift in focus towards developing next-generation sources, particularly Superconducting Undulators (SCUs), characterized by smaller gaps, shorter periods, and maximum lengths. However, despite ongoing research and development efforts, SCUs have yet to surpass their predecessors, the Cryogenic Permanent Magnet Undulators (CPMUs), in terms of performance. This is largely attributed to the limitations posed by traditional superconducting wire, as well as challenges in the design of the magnetic structure and vacuum chamber. In this paper, we aim to overcome such limitations through the development of a unique prototype Superconducting Adaptive Gap Undulator (SC-AGU) magnet core and vacuum chamber design. This paper will outline a novel technical approach aimed at constructing a compact prototype magnet array utilizing state-of-the-art superconducting wire technology. This approach provides a more efficient magnetic structure, allowing for enhanced magnetic field strength and stability.

36 MATERIALS SCIENCE↗

DOE OSTI2020

First Calorimetric Energy Reconstruction of Beam Events with ARAPUCA Light Detector in ProtoDUNE-SP

ProtoDUNE Single Phase at CERN is the large scale prototype for the far detector of the future DUNE experiment. ProtoDUNE is in stable operation since Oct. 2018 at the CERN Neutrino Platform. Test beam data in the energy range of sub-GeV to a few GeV were collected in fall 2018 providing a set of key measurements. Particles (electrons, protons, pions, muons and kaons) are identified combining information from a set of beam-line detectors (Time of Flight, Cherenkov) and TPC reconstruction. Three different technologies are implemented in the protoDUNE photon detector system (PDS). Results from the ARAPUCA response, one of the PDS components, are presented providing first calorimetric energy measurements and particle ID of beam events from LAr scintillation light signals.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Signal processing to reduce dark noise impact in precision timing

We introduce a technique to mitigate the effects of low frequency noise on precision timing. The example of Dark Count Noise Rate (DCR) in Silicon Photomultipliers (SiPMs) is emphasized. This technique exploits the correlation between time shifts on the leading edge of a signal and the residual slope of the baseline (due to noise) which remains after baseline subtraction. In fast timing applications (such as for Time-of-flight particle ID) the signal arrival time is typically captured on the signal leading edge. The signal risetime is often fixed by the physics of the sensor and input circuit. Then accurate pulse timing can be achieved by correcting a leading edge threshold time (depending on a slope proportional to both the Amplitude and the risetime) to a “constant fraction” time. This compensation for time walk due to amplitude fluctuations breaks down once we introduce interference from low frequency noise on the leading edge. In this paper we demonstrate that an additional measurement of the slope at threshold can be used to correct for this noise jitter.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗