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DOE OSTI2021

In vitro functional analysis of gRNA sites regulating assembly of hepatitis B virus

The roles of RNA sequence/structure motifs, Packaging Signals (PSs), for regulating assembly of an HBV genome transcript have been investigated in an efficient in vitro assay containing only core protein (Cp) and RNA. Variants of three conserved PSs, within the genome of a strain not used previously, preventing correct presentation of a Cp-recognition loop motif are differentially deleterious for assembly of nucleocapsid-like particles (NCPs). Cryo-electron microscopy reconstruction of the T = 4 NCPs formed with the wild-type gRNA transcript, reveal that the interior of the Cp shell is in contact with lower resolution density, potentially encompassing the arginine-rich protein domains and gRNA. Symmetry relaxation followed by asymmetric reconstruction reveal that such contacts are made at every symmetry axis. We infer from their regulation of assembly that some of these contacts would involve gRNA PSs, and confirmed this by X-ray RNA footprinting. Mutation of the ε stem-loop in the gRNA, where polymerase binds in vivo, produces a poor RNA assembly substrate with Cp alone, largely due to alterations in its conformation. The results show that RNA PSs regulate assembly of HBV genomic transcripts in vitro, and therefore may play similar roles in vivo, in concert with other molecular factors.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Lithium oxidation and electrolyte decomposition at Li-metal/liquid electrolyte interfaces

In this work, we examine the evolution of events occurring when a Li metal surface is in contact with a 2 M solution of a Li salt in a solvent or mixture of solvents, via classical molecular dynamics simulations with a reactive force field allowing bond breaking and bond forming. The main events include Li oxidation and electrolyte reduction along with expansion of the Li surface layers forming a porous phase that is the basis for the formation of the solid-electrolyte interphase (SEI) components. Nucleation of the main SEI components (LiF, Li oxides, and some organics) is characterized. The analysis clearly reveals the details of these physical–chemical events as a function of time, during 20 nanoseconds. The effects of the chemistry of the electrolyte on Li oxidation and dissolution in the liquid electrolyte, and SEI nucleation and structure are identified by testing two salts: LiPF 6 and LiCF 3 SO 3 , and various solvents including ethers and carbonates and mixtures of them. The kinetics and thermodynamics of Li 6 F, the core nuclei in the LiF crystal, are studied by analysis of the MD trajectories, and via density functional theory calculations respectively. The SEI formed in this computational experiment is the “native” film that would form upon contact of the Li foil with the liquid electrolyte. As such, this work is the first in a series of computational experiments that will help elucidate the intricate interphase layer formed during battery cycling using metal anodes.

25 ENERGY STORAGE↗

DOE OSTI2022

Vapor detection and vapor pressure measurements of fentanyl and fentanyl hydrochloride salt at ambient temperatures

There is a need for non-contact, real-time vapor detection of drugs to combat illicit transportation and help curb the opioid epidemic. The low-volatility of drugs, like fentanyl, makes room temperature vapor detection of illicit drugs challenging, but feasible by atmospheric flow tube-mass spectrometry (AFT-MS). AFT-MS is a non-contact vapor detection approach capable of ultra-trace detection of drugs, including fentanyl and its analogs at low parts-per-quadrillion (ppqv) levels. The determination of vapor pressure values of fentanyl is necessary to understand potential vapor concentrations that may be available for detection. In this paper, vapor pressures of fentanyl free base and fentanyl hydrochloride salt (a common form of the illicit drug) were measured as a function of temperature at or near ambient conditions using the transpiration (gas saturation) method and AFT-MS. Based on our measurements, the vapor pressure of fentanyl at 25 °C is 9.0 × 10-14 atm (90 ppqv), and the vapor pressure of fentanyl hydrochloride at 25 °C is 1.8 x 10-17 atm (0.018 ppqv). We also demonstrate non-contact, real-time vapor detection of fentanyl. Preconcentration of vapors can further extend the detection capabilities. The collection, desorption, and detection of fentanyl vapors at ambient conditions was demonstrated for sampling times of seconds to an hour resulting in increased signal. AFT-MS is a viable detection method of fentanyl and other drugs for screening of packages and cargo.

atmospheric flow tube-mass spectrometry (AFT-MS), ↗

DOE OSTI2020

Three-Dimensional Evaluation of Sand Particle Fracture Using Discrete-Element Method and Synchrotron Microcomputed Tomography Images

Recent research showed that fracture of sand particles plays a significant role in determining the plastic bulk volumetric changes of granular materials under different loading conditions. One of the major tools used to better understand the influence of particle fracture on the behavior of granular materials is discrete-element modeling (DEM). This paper employed the bonded block model (BBM) to simulate the fracture behavior of sand. Each sand particle is modeled as an agglomerate of rigid blocks bonded at their contacts using the linear-parallel contact model, which can transmit both moment and force. DEM simulated particles closely matched the actual three-dimensional (3D) shape of sand particles acquired using high-resolution 3D synchrotron microcomputed tomography (SMT). Results from unconfined one-dimensional (1D) compression of a single synthetic silica cube were used to calibrate the model parameters. Particle fracture was investigated for specimens composed of three sand particles that were loaded under confined 1D compression. Breakage energy measured from DEM models matched well with that measured experimentally. The paper studied the effects of contact loading condition and particle interaction on the fracture mode of particles using BBM that can closely capture the 3D shape of real sand particles.

58 GEOSCIENCES↗

DOE OSTI2020

Identification and characterization of the dominant thermal resistance in lithium-ion batteries using operando 3-omega sensors

Poor thermal transport within lithium-ion batteries fundamentally limits their performance, safety, and lifetime, in spite of external thermal management systems. All prior efforts to understand the origin of batteries' mysteriously high thermal resistance have been confined to ex situ measurements without understanding the impact of battery operation. Here, we develop a frequency-domain technique that employs sensors capable of measuring spatially resolved intrinsic thermal transport properties within a live battery while it is undergoing cycling. Our results reveal that the poor battery thermal transport is due to high thermal contact resistance between the separator and both electrode layers and worsens as a result of formation cycling, degrading total battery thermal transport by up to 70%. We develop a thermal model of these contact resistances to explain their origin. These contacts account for up to 65% of the total thermal resistance inside the battery, leading to far-reaching consequences for the thermal design of batteries. Finally, our technique unlocks new thermal measurement capabilities for future battery research.

25 ENERGY STORAGE↗

DOE OSTI2020

Experimental and modeling study of 1/ f noise in multilayer MoS2 and MoSe2 field-effect transistors

In field-effect transistors (FETs) with two-dimensional (2D) transition metal dichalcogenide channels, the dependence of field-effect mobility on atomic layer thickness has been studied and interpreted in terms of interface scattering and interlayer coupling resistance (Rint). However, a model for 1/f noise, such as in MoS2 and in MoSe2 FETs, for various contact metals and layer number thicknesses has not been reported. In this work, we have experimentally studied current–voltage and 1/f noise on MoS2 and MoSe2 FETs with source and drain contacts of high and low work function metals to understand both the mobility and the noise behavior. We have developed a noise model incorporating layer number dependent Hooge parameters and Rint. The noise and mobility models utilize screening lengths for charge, mobility, and Hooge parameter to describe the variation of these quantities with a layer number. Using our single model topology with appropriate fitting parameters for each material and each contact metal, the model captures the experimentally observed layer thickness dependence of the Hooge parameter. Our noise analysis is fully comprehensive and, hence, could be applied to any 2D layered systems.

Kwon, Jiseok↗

DOE OSTI2021

Enhanced electro-osmosis in propylene carbonate salt solutions

Properties of solid–liquid interfaces and surface charge characteristics mediate ionic and molecular transport through porous systems, affecting many processes such as separations. Herein, we report experiments designed to probe the electrochemical properties of solid–liquid interfaces using a model system of a single polyethylene terephthalate (PET) pore in contact with aqueous and propylene carbonate solutions of LiClO 4 . First, the existence and polarity of surface charges were inferred from current–voltage curves recorded when a pore was placed in contact with a LiClO4 concentration gradient. Second, the electro-osmotic transport of uncharged polystyrene particles through the PET pore provided information on the polarity and the magnitude of the pore walls’ zeta potential. Our experiments show that the PET pores become effectively positively charged when in contact with LiClO 4 solutions in propylene carbonate, even though in aqueous LiClO 4 , the same pores are negatively charged. Additionally, the electro-osmotic velocity of the particles revealed a significantly higher magnitude of the positive zeta potential of the pores in propylene carbonate compared to the magnitude of the negative zeta potential in water. The presented methods of probing the properties of solid–liquid interfaces are expected to be applicable to a wide variety of solid and liquid systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Spherical and sessile droplet dynamics by fluctuating hydrodynamics

We simulate the mesoscopic dynamics of droplets formed by phase-separated fluids at nanometer scales where thermal fluctuations are significant. Both spherical droplets fully immersed in a second fluid and sessile droplets which are also in contact with a solid surface are studied. Our model combines a Cahn–Hilliard formulation with incompressible fluctuating hydrodynamics; for sessile droplets, the fluid–solid contact angle is specified as a boundary condition. Deterministic simulations with an applied body force are used to measure the droplets' mobility from which a diffusion coefficient is obtained using the Einstein relation. Stochastic simulations are independently used to obtain a diffusion coefficient from a linear fit of the variance of a droplet's position with time. In some scenarios, these two measurements give the same value but not in the case of a spherical droplet initialized near a slip wall or in the case of sessile droplets with large contact angles (≥90°) on both slip and no-slip surfaces.

Bell, John B↗

DOE OSTI2022

Spin dynamics in permalloy nano-ellipses for honeycomb and square lattices

We report experimental and theoretical studies of spin dynamics in lattice structures of permalloy (Ni 80 Fe 20 ) nano-ellipses, with four different types of networks including honeycomb and square lattices. The lattices are patterned at the center line of the co-planar wave guide and consist of non-contacting or contacting ellipses. Micromagnetic simulations show excellent agreement with the broadband ferromagnetic resonance (FMR) experimental results. We find the existence of a spin-wave mode localized in the vertex region of the contacting nano-ellipse network. Our finding has important implications when designing an artificial spin ice (ASI) network for functional magnonics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Hot carrier extraction from 2D semiconductor photoelectrodes

Hot carrier-based energy conversion systems could double the efficiency of conventional solar energy technology or drive photochemical reactions that would not be possible using fully thermalized, “cool” carriers, but current strategies require expensive multijunction architectures. Using an unprecedented combination of photoelectrochemical and in situ transient absorption spectroscopy measurements, we demonstrate ultrafast (<50 fs) hot exciton and free carrier extraction under applied bias in a proof-of-concept photoelectrochemical solar cell made from earth-abundant and potentially inexpensive monolayer (ML) MoS 2 . Our approach facilitates ultrathin 7 Å charge transport distances over 1 cm 2 areas by intimately coupling ML-MoS 2 to an electron-selective solid contact and a hole-selective electrolyte contact. Our theoretical investigations of the spatial distribution of exciton states suggest greater electronic coupling between hot exciton states located on peripheral S atoms and neighboring contacts likely facilitates ultrafast charge transfer. Our work delineates future two-dimensional (2D) semiconductor design strategies for practical implementation in ultrathin photovoltaic and solar fuel applications.

2D materials↗

DOE OSTI2023

Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention

The receptor tyrosine kinase KIT and its ligand stem cell factor (SCF) are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as acute myeloid leukemia, gastrointestinal stromal tumor, and mast cell leukemia, are driven by somatic gain-of-function KIT mutations. Here, we report cryo electron microscopy (cryo-EM) structural analyses of full-length wild-type and two oncogenic KIT mutants, which show that the overall symmetric arrangement of the extracellular domain of ligand-occupied KIT dimers contains asymmetric D5 homotypic contacts juxtaposing the plasma membrane. Mutational analysis of KIT reveals in D5 region an “Achilles heel” for therapeutic intervention. A ligand-sensitized oncogenic KIT mutant exhibits a more comprehensive and stable D5 asymmetric conformation. A constitutively active ligand-independent oncogenic KIT mutant adopts a V-shaped conformation solely held by D5-mediated contacts. Binding of SCF to this mutant fully restores the conformation of wild-type KIT dimers, including the formation of salt bridges responsible for D4 homotypic contacts and other hallmarks of SCF-induced KIT dimerization. These experiments reveal an unexpected structural plasticity of oncogenic KIT mutants and a therapeutic target in D5.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Thermal-Hydraulic-Mechanical Modeling and Simulation of Sodium-Potassium–Cooled MARVEL Microreactor Core

The U.S. Department of Energy's Microreactor Program, with Idaho National Laboratory's development of a nuclear microreactor applications test bed named MARVEL, aims to support R&D for the deployment of small, transportable reactors across civilian, industrial, and defense sectors. The MARVEL microreactor, an 85-kWth thermal fission reactor, incorporates TRIGA nuclear fuel and a sodium-potassium eutectic as its primary coolant, designed for safety and efficiency, with natural circulation eliminating the risk of critical heat flux conditions. The reliance on natural circulation for primary cooling means the reactor avoids using fuel spacers to minimize core pressure drop, which could disrupt the primary coolant's natural flow. However, the reactor core’s tight P/D ratio of 1.05, in the absence of fuel spacers, could pose a risk of fuel rod contact and increased peak cladding temperatures. To ensure the reactor safety, this study conducted computational modeling and simulations to investigate the reactor's thermal-hydraulic-mechanical characteristics, including the reactor core heat transfer coefficients, the potential for rod-to-rod contact, and assessed its impact on peak cladding temperature and overall reactor safety. The computational analyses of the MARVEL microreactor core revealed that the thermal deformation of fuel rods under worst-case scenario may lead to the fuel rod contact, but the peak cladding temperatures will remain significantly lower than the safety criteria, ensuring the safety operation reactor without fuel spacers under normal operating conditions.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

DOE OSTI2022

Impact of feed variability on cesium removal with multiple actual waste samples from the Hanford site

Here, the Tank Side Cesium Removal (TSCR) system, under development by Washington River Protection Solutions (WRPS), will send initial low-activity Hanford waste tank supernate feeds to the Hanford Waste Treatment and Immobilization Plant (WTP) Low-Activity Waste (LAW) Facility. In addition to entrained solids removal from the supernate, the primary goal of TSCR is to remove cesium-137 ( 137 Cs) by ion exchange, allowing contact handling of the liquid effluent product at WTP. Crystalline silicotitanate (CST) ion exchange media, manufactured by Honeywell UOP (product IONSIV™ R9140-B), was selected as the ion exchange media at TSCR. This lot of material was found to have superior performance in comparison to historic batches of CST. Ion exchange column and batch contact testing with supernate from Hanford tanks AP-105, AP-107 and AW-102 was performed to assess the impact of feed variability on system performance. These tests demonstrated that batch contact measurements provide a reasonable prediction of column capacities with some deviation in performance attributed to column dynamics. In addition, the variability in CST capacity for cesium in the various actual waste samples does not track with historical understanding of the competing cations, suggesting that tank waste samples contain other components that may significantly impact cesium loading.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

An alternative electrode design for accurate spectral induced polarization measurements in variably saturated porous media

SUMMARY Applications of spectral induced polarization (SIP) require electrodes that maintain hydrologic contact with surrounding soils to capture small electrical responses, often observed as phase shifts in milliradians. For unsaturated soils, electrodes must overcome increased electrical contact impedance due to reduced pore fluid. Traditional designs use a ceramic membrane electrode (CME) with a water reservoir and metal conductor, requiring periodic maintenance to retain electrolytic solution. For field applications where maintenance is impractical, alternative designs are needed. This study evaluated a new electrode design (silica flour electrode, SFE) alongside a CME. SFEs use packed silica flour to store water via capillary forces against a metal conductor. This study examined both designs in three variably saturated soils at soil suctions up to 700 mbar and soil water contents below 1 percent, with SIP measurements across 0.01 to 10 000 Hz frequencies. SFEs match CMEs at high frequencies and perform better at lower frequencies, without requiring ongoing maintenance, making them ideal for field use. In water-only experiments, CMEs produced errors and high noise below 1.5 Hz, whereas SFEs were more accurate. However, CMEs performed better above 300 Hz. In fine sand, SFEs performed better due to the relatively lower contact impedance as compared to CMEs. Both electrode types performed comparably in silty sand and silt loam soils, although CMEs required ongoing maintenance, suggesting potential for long-term reliability issues.

58 GEOSCIENCES↗

DOE OSTI2024

On alert for Ebola: public health risk assessment of travellers from Uganda to the USA during the 2022 outbreak

Abstract Background On 20 September 2022, the Ugandan Ministry of Health declared an outbreak of Ebola disease caused by Sudan ebolavirus. Methods From 6 October 2022 to 10 January 2023, Centers for Disease Control and Prevention (CDC) staff conducted public health assessments at five US ports of entry for travellers identified as having been in Uganda in the past 21 days. CDC also recommended that state, local and territorial health departments (‘health departments’) conduct post-arrival monitoring of these travellers. CDC provided traveller contact information, daily to 58 health departments, and collected health department data regarding monitoring outcomes. Results Among 11 583 travellers screened, 132 (1%) required additional assessment due to potential exposures or symptoms of concern. Fifty-three (91%) health departments reported receiving traveller data from CDC for 10 114 (87%) travellers, of whom 8499 (84%) were contacted for monitoring, 1547 (15%) could not be contacted and 68 (1%) had no reported outcomes. No travellers with high-risk exposures or Ebola disease were identified. Conclusion Entry risk assessment and post-arrival monitoring of travellers are resource-intensive activities that had low demonstrated yield during this and previous outbreaks. The efficiency of future responses could be improved by incorporating an assessment of risk of importation of disease, accounting for individual travellers’ potential for exposure, and expanded use of methods that reduce burden to federal agencies, health departments, and travellers.

General & Internal Medicine↗

DOE OSTI2023

Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Competition between roughness and strength for scale-dependent surfaces

Rocks famously have scale-dependent strength, yet the actual dependence is notoriously hard to measure or incorporate into any theoretical framework. Natural rough surfaces present an opportunity to solve the problem. Surfaces sliding in shear evolve as protrusions collide. These asperities can deform or break, thus creating a new surface shape. In particular, natural surfaces have roughness at all scales as well as scale-dependent strength. Based on a scaling analysis, we have previously suggested that the scale-dependent aspect ratio of steady-state surfaces should be proportional to the scale-dependent shear strain at yield. If true, scale-dependent strength could easily be inferred from natural surfaces. Thus, moving beyond the scaling argument to a rigorous treatment of scale-dependent strength for multiscale rough surfaces in shear is important. However, analytic frameworks for analyzing multiscale problems are challenging, as conventional continuum mechanics typically involves a single value for a material property across scales. Here, in this work, we build on the formalism of Persson (2001) that presents a method to compute contact area for rough surfaces with a prescribed topographic spectrum using a stochastic differential equation. The Persson formalism allows for plastic yield under normal loading of otherwise elastic materials and leaves open the possibility of scale-dependent yield stress. In this study, we pursue this route to develop a theory and numerical results for the yielding of a rough, elastoplastic surface with scale-dependent yield stress. Here, we examine surfaces for which the power spectrum of the topography 𝐶 and yield stress 𝑌 follow power laws as a function of scale 𝜆, such that 𝐶∼𝜆 −𝑚 and 𝑌∼𝜆 −𝑛 , respectively. In this formal treatment of the problem, we focus on surfaces in contact and the resulting yield and do not impose shear. Numerical solutions show that the deviation from the elastic scaling solution is bounded as expected by the prior 1D heuristic scaling argument that anticipates the Hurst exponent as 1−𝑛. We also show that the plasticity is expected to erode the contacts if 𝑚 is lower than 𝑛−3, which corresponds to a Hurst exponent lower than 1−𝑛/2. This result is rigorously sound for 2D, i.e., realistic surfaces, and quantitatively different than the prior scaling argument. The theory now permits a correspondingly quantitative approach to interpreting natural surfaces.

elasticity↗

DOE OSTI2022

Nanometer-Scale Measurement of Grid Finger Electrical Conduction Pathways to Detect Series Resistance Degradation of Utility-Scale Silicon Solar Cells

Here, we report on an electrical conduction mechanism for series resistance (Rs) degradation observed in a utility-scale photovoltaic power plant by imaging the local resistance at the Ag/Si interface of the c-Si front metallization. Scanning spreading resistance microscopy imaging with nanometer (nm) scale spatial resolution revealed that the number of point or small-area electrical contacts decreased substantially in a degraded cell compared to an unaffected cell, demonstrating the root cause of Rs degradation. The decrease in electrical contacts is likely caused by a structural change - the Ag particles in contact with the Si cell (or via a nm-thickness tunneling glass layer) aggregate into bulk Ag, and a highly resistive glass frit forms a belt shape at the Ag/Si interface. This resistive belt, with a thickness of ~1 um, blocks the current conduction from the cell emitter to the Ag grid. Our microscopy results help to unravel unambiguously the degradation mechanism and demonstrate an example of the multiscale characterization approach for understanding degradation in field-weathered PV module.

14 SOLAR ENERGY↗