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DOE OSTI2023

Active Thermochemical Tables: Enthalpies of Formation of Bromo- and Iodo-Methanes, Ethenes and Ethynes

Here, the thermochemistry of halocarbon species containing iodine and bromine is examined through an extensive interplay between new Feller–Peterson–Dixon (FPD) style composite methods and a detailed analysis of all available experimental and theoretical determinations using the thermochemical network that underlies the Active Thermochemical Tables (ATcT). From the computational viewpoint, a slower convergence of the components of composite thermochemistry methods is observed relative to species that solely contain first row elements, leading to a higher computational expense for achieving comparable levels of accuracy. Potential systematic sources of computational uncertainty are investigated, and, not surprisingly, spin-orbit coupling is found to be a critical component, particularly for iodine containing molecular species. The ATcT analysis of available experimental and theoretical determinations indicates that prior theoretical determinations have significantly larger uncertainties than originally reported, particularly in cases where molecular spin-orbit effects were ignored. Accurate and reliable heats of formation are reported for 38 halogen containing systems, based on combining the current computations with previous experimental and theoretical work via the ATcT approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Effect of Solvents on Lignin–Surface Interactions via Molecular Dynamics Simulations

Lignin, an essential building block of lignocellulosic biomass, is a potential abundant source of aromatic monomers for the polymer and chemical industry. Reductive catalytic fractionation (RCF) is one promising process that can produce high yields of phenolic monomers and oligomers from lignin under different catalytic conditions. An important choice in optimizing RCF is the selection of solvent; however, detailed insights into solvent effects on lignin behaviors and interactions remain limited. Here, in this work, we perform all-atom molecular dynamics simulations to study the solvation of lignin, solvent-mediated conformational changes, and the interaction of solvated lignin oligomers with model surfaces. We focus on the behavior of an oligomeric lignin model compound in methanol, ethanol, a binary mixture of ethanol and water, and water at both the RCF reaction temperature (473 K) and room temperature. Analysis of structural features of lignin suggests that these three organic solvent systems favorably solvate lignin, resulting in a more extended conformation suitable for catalytic conversion to valuable chemicals. We further introduce model palladium (Pd) and carbon (C) surfaces to understand how solvent choice impacts adsorption onto a representative catalytic surface and support, and to quantify the competition among the reactant and solvent molecules for the surface. Unbiased simulations suggest strong adsorption of lignin on both Pd and C surfaces at 473 K, with notable solvent-mediated differences in adsorption energies. Additionally, our findings indicate that lignin adsorption is promoted by the entropy change resulting from the displacement of solvent molecules from the surface. This study provides a molecular perspective of adsorption of lignin onto varying surfaces, which is a step towards understanding and optimizing the catalytic conversion of lignin into valuable chemicals.

adsorption↗

DOE OSTI2021

Observation of Single-Electron Transport and Charging on Individual Point Defects in Atomically Thin WSe 2

Defects significantly impact the properties of 2D semiconductors, providing in-gap quantum states that can serve as a natural platform for single-electron operations, localization sites for excitons to serve as single-photon sources, and potentially quantum spin memories. To date, however, a microscopic observation of such a single-electron transport (SET) behavior has been rarely reported on single defects of 2D semiconductors. In this study, we report a SET and charge-state transition on individual point-defect states buried in the bilayer WSe 2 using scanning tunneling microscopy. SET characteristics of their states is evidenced by both the Coulomb staircase and the saturation behavior of the transport current, consistent with the SET model. Furthermore, we demonstrate that, through the local field of a scanning tunneling microscope tip, it is possible to successively charge the defects by single electrons, suggested by both the ring structures and charging peaks in dI/dV measurements. Our results provide new insights into the quantum nature of these defect-bound states, as well as the possibility of using their single-electron behavior and response for applications in quantum information and local-field sensing.

2D semiconductor↗

DOE OSTI2023

Quantum Simulation of Polarized Light-Induced Electron Transfer with a Trapped-Ion Qutrit System

Electron transfer within and between molecules is crucial in chemistry, biochemistry, and energy science. Here this study describes a quantum simulation method that explores the influence of light polarization on electron transfer between two molecules. By implementing precise and coherent control among the quantum states of trapped atomic ions, we can induce quantum dynamics that mimic the electron-transfer dynamics in molecules. We use three-level systems (qutrits), rather than traditional two-level systems (qubits), to enhance the simulation efficiency and realize high-fidelity simulations of electron-transfer dynamics. We treat the quantum interference between the electron coupling pathways from a donor with two degenerate excited states to an acceptor and analyze the transfer efficiency. We also examine the potential error sources that enter the quantum simulations. The trapped-ion systems have favorable scalings with system size compared to those of classical computers, promising access to richer electron-transfer simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

MARLOWE: An Untargeted Proteomics, Statistical Approach to Taxonomic Classification for Forensics

General proteomics research for fundamental science typically addresses laboratory- or patient-derived samples of known origin and composition. However, in a few research areas, such as environmental proteomics, clinical identification of infectious organisms, archeology, art/cultural history, and forensics, attributing the origin of a protein-containing sample to the organisms that produced it is a central focus. A small number of groups have approached this problem and developed software tools for taxonomic characterization and/or identification using bottom-up proteomics. Most such tools identify peptides via database search, and many rely on organism-specific peptides as markers. Our group recently introduced MARLOWE, a software tool for taxonomic characterization of unknown samples based on de novo peptide identification and signal-erosion-resistant strong peptides, which are shared peptides distributed in a taxonomy-dependent manner. In the current work, we further characterize the utility of MARLOWE using publicly available proteomics data from forensically-relevant samples. MARLOWE characterizes samples based on their protein profile, and returns ranked organism lists of potential contributors and taxonomic scores based on shared strong peptides between organisms. Overall, the correct characterization rate ranges between 44 and 100%, depending on the sample type and data acquisition parameters (with lower numbers associated with lower-quality data sets). MARLOWE demonstrates successful characterization of true contributors and close relatives, and provides sufficient specificity to distinguish certain microbial species. MARLOWE demonstrates its ability to provide insight into potential taxonomic sources for a wide range of sample types without prior assumptions about sample contents. As a result, this approach can find utility in forensic science and also broadly in bioanalytical applications that utilize proteomics approaches for taxonomic characterization.

Bacteria↗

DOE OSTI2024

Adsorption of Neodymium, Dysprosium, and Ytterbium to Goethite under Varying Aqueous Chemistry Conditions

The adsorption of rare earth elements (REEs) to iron oxides can regulate the mobility of REEs in the environment and is heavily influenced by water chemistry. This study utilized batch experiments to examine the adsorption of Nd, Dy, and Yb to goethite under varying pH, electrolyte (type and concentration), and concentrations of dissolved inorganic carbon and citrate. REE adsorption was strongly influenced by pH, with an increase from essentially no adsorption at pH 3.0 to nearly complete adsorption at pH 6.5 and higher. Citrate enhanced the adsorption of REEs at low pH (<5.0), likely by forming goethite-REE-citrate ternary surface complexes. However, citrate inhibited the adsorption of REEs at higher pH (>5.0) by forming aqueous REE-citrate complexes. Ionic strength had a small influence on REE adsorption, and the presence of dissolved inorganic carbon had no discernible effect. Equilibrium adsorption was interpreted with a triple-layer surface complexation model (SCM). The selection of surface complexation reactions was guided by extended X-ray absorption fine structure spectra. An SCM with a single bidentate inner-sphere surface complexation reaction for Nd and two inner-sphere surface complexation reactions (one monodentate and one bidentate reaction) for Dy and Yb effectively simulated adsorption across a broad range of conditions in the absence of citrate. Accounting for the effects of citrate on REE adsorption required the addition of up to two ternary REE-citrate-goethite surface complexes. The SCM can enable predictions of REE transport in subsurface environments that have goethite as an important adsorbent mineral. Furthermore, this predictive capability could contribute to identifying potential REE sources and facilitating efficient extraction of REEs.

58 GEOSCIENCES↗

DOE OSTI2023

Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations

Abstract Sterane molecular fossils are broadly interpreted as eukaryotic biomarkers, although diverse bacteria also produce sterols. Steranes with side-chain methylations can act as more specific biomarkers if their sterol precursors are limited to particular eukaryotes and are absent in bacteria. One such sterane, 24-isopropylcholestane, has been attributed to demosponges and potentially represents the earliest evidence for animals on Earth, but enzymes that methylate sterols to give the 24-isopropyl side-chain remain undiscovered. Here, we show that sterol methyltransferases from both sponges and yet-uncultured bacteria function in vitro and identify three methyltransferases from symbiotic bacteria each capable of sequential methylations resulting in the 24-isopropyl sterol side-chain. We demonstrate that bacteria have the genomic capacity to synthesize side-chain alkylated sterols, and that bacterial symbionts may contribute to 24-isopropyl sterol biosynthesis in demosponges. Together, our results suggest bacteria should not be dismissed as potential contributing sources of side-chain alkylated sterane biomarkers in the rock record.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae

Carbohydrate rich substrates such as lignocellulosic hydrolysates remain one of the primary sources of potentially renewable fuel and bulk chemicals. The pentose sugar d-xylose is often present in significant amounts along with hexoses. Saccharomyces cerevisiae can acquire the ability to metabolize d-xylose through expression of heterologous d-xylose isomerase (XI). This enzyme is notoriously difficult to express in S. cerevisiae and only fourteen XIs have been reported to be active so far. We cloned a new d-xylose isomerase derived from microorganisms in the gut of the wood-feeding beetle Odontotaenius disjunctus. Although somewhat homologous to the XI from Piromyces sp. E2, the new gene was identified as bacterial in origin and the host as a Parabacteroides sp. Expression of the new XI in S. cerevisiae resulted in faster aerobic growth than the XI from Piromyces on d-xylose media. The d-xylose isomerization rate conferred by the new XI was also 72% higher, while absolute xylitol production was identical in both strains. Interestingly, increasing concentrations of xylitol (up to 8 g L –1 ) appeared not to inhibit d-xylose consumption. The newly described XI displayed 2.6 times higher specific activity, 37% lower KM for d-xylose, and exhibited higher activity over a broader temperature range, retaining 51% of maximal activity at 30 °C compared with only 29% activity for the Piromyces XI.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The effect of differential mineral shrinkage on crack formation and network geometry

Rock, concrete, and other engineered materials are often composed of several minerals that change volumetrically in response to variations in the moisture content of the local environment. Such differential shrinkage is caused by varying shrinkage rates between mineral compositions during dehydration. Using both 3D X-ray imaging of geo-architected samples and peridynamic (PD) numerical simulations, we show that the spatial distribution of the clay affects the crack network geometry with distributed clay particles yielding the most complex crack networks and percent damage (99.56%), along with a 60% reduction in material strength. We also demonstrate that crack formation, growth, coalescence, and distribution during dehydration, are controlled by the differential shrinkage rates between a highly shrinkable clay and a homogeneous mortar matrix. Sensitivity tests performed with the PD models show a clay shrinkage parameter of 0.4 yields considerable damage, and reductions in the parameter can result in a significant reduction in fracturing and an increase in material strength. Additionally, isolated clay inclusions induced localized fracturing predominantly due to debonding between the clay and matrix. These insights indicate differential shrinkage is a source of potential failure in natural and engineered barriers used to sequester anthropogenic waste.

58 GEOSCIENCES↗

DOE OSTI2025

Demonstration of active neutron interrogation of special nuclear materials using a high-intensity short-pulse-laser-driven neutron source

Detecting shielded special nuclear material, such as nuclear explosives, is a difficult challenge pursued by non-proliferation, anti-terrorism, and nuclear security programs worldwide. Interrogation with intense fast-neutron pulses is a promising method to characterize concealed nuclear material rapidly but is limited by suitable source availability and proven instrumentation. In this study we have pioneered a demonstration of such an interrogation method using a high-intensity, short-pulse, laser-driven neutron source that offers potential benefits compared to conventional neutron sources. The measurement results reported here represent the first experimental demonstration of this interrogation approach on enriched uranium items and demonstrate the feasibility of a precise measurement using realistic nuclear materials, representative of field scenarios, even with just a single laser-driven neutron pulse. Bright pulsed sources can overcome the nuisance background of items with strong internal neutron sources, improving analytical power, while single-shot assay is attractive in high-throughput situations where time is at a premium. The science and technology of this type of neutron production is developing rapidly, and we anticipate that practical mobile interrogation systems will become available based on the detection concepts demonstrated here to meet the growing measurement needs.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2025

Broadband coherent XUV light from e − / e + microbunching in an intense laser pulse

Attosecond pulses of coherent extreme ultraviolet (XUV) light are instrumental for investigating subatomic dynamics and can be produced using a free-electron laser (FEL). It has been suggested that an optical FEL, which employs a laser pulse in place of a conventional undulator, could enable a dramatically more compact implementation of such a light source. Yet, the high electron density and subsequent high emittance implied by an optical FEL makes this concept challenging to realize with an electron beam. There has been impressive progress in recent years producing collimated dense and relativistic beams of electrons and positrons in the laboratory. As we demonstrate here, the inherent stability of a quasi-neutral electron-positron beam mitigates Coulomb expansion, and renders it a promising alternative source of coherent light. Specifically, we show via computer simulations that broadband coherent light in the XUV domain, which takes the form of 8-as pulses at 92-as intervals, can be generated by microbunching of relativistic electrons and positrons in a laser pulse. This process occurs over a sub-millimeter length scale, enabling the development of light sources which are orders-of-magnitude more compact than existing sources, with potential applications in physics, chemistry, biology, and industry.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Use of machine learning to analyze chemistry card sort tasks

Education researchers are deeply interested in understanding the way students organize their knowledge. Card sort tasks, which require students to group concepts, are one mechanism to infer a student’s organizational strategy. However, the limited resolution of card sort tasks means they necessarily miss some of the nuance in a student’s strategy. Here in this work, we propose new machine learning strategies that leverage a potentially richer source of student thinking: free-form written language justifications associated with student sorts. Using data from a university chemistry card sort task, we use vectorized representations of language and unsupervised learning techniques to generate qualitatively interpretable clusters, which can provide unique insight in how students organize their knowledge. We compared these to machine learning analysis of the students’ sorts themselves. Machine learning-generated clusters revealed different organizational strategies than those built into the task; for example, sorts by difficulty or even discipline. There were also many more categories generated by machine learning for what we would identify as more novice-like sorts and justifications than originally built into the task, suggesting students’ organizational strategies converge when they become more expert-like. Finally, we learned that categories generated by machine learning for students’ justifications did not always match the categories for their sorts, and these cases highlight the need for future research on students’ organizational strategies, both manually and aided by machine learning. In sum, the use of machine learning to analyze results from a card sort task has helped us gain a more nuanced understanding of students’ expertise, and demonstrates a promising tool to add to existing analytic methods for card sorts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

An overview of the fusion landscape

Fusion is very attractive as a potential energy source, but it is taking a long time to develop into a commercial reality. Given the challenges of climate change and the need for dispatchable power as a complement to renewable energy sources that vary on daily and seasonal timescales, there is great enthusiasm internationally to accelerate the commercialization of fusion energy. Forty-five private companies around the globe, with total financing of $7.1 billion, are engaged in the development of fusion energy. In the United States, the White House has put forward a “Bold Decadal Vision for Commercial Fusion Energy,” with bipartisan support from Congress. To develop commercial fusion energy, certain goals must be met. In conclusion, a wide variety of approaches are being pursued to meet these goals.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Spurious solar-wind effects on acceleration noise in LISA Pathfinder

Spurious solar-wind effects are a potential noise source in future Laser Interferometer Space Antenna (LISA) measurements. One noise coupling mechanism is constrained by estimating solar-wind effects on acceleration noise in LISA Pathfinder (LPF). While LISA is designed for drag-free differential measurement, predicting the realistic impact both bounds the operational environment and assesses whether LISA could provide serendipitous space-weather observations. Data from NASA's Advanced Composition Explorer (ACE), situated at the L1 Lagrange point, serves as a reliable source of solar-wind data. The data sets are compared over the 114 d time period from 1 March 2016 to 23 June 2016. This period gives the longest readily-available open data set, without interference from other commissioning activities. To evaluate space weather effects, the data from both satellites are formatted, gap-filled/interpolated, and fast-Fourier transformed for amplitude spectral density and coherence comparisons. Solar wind effects are not seen in a coherence plot between LPF and ACE; modest coherence in the planned LISA observational frequency band can be attributed to chance. This result indicates that measurable correlation due to solar-wind acceleration noise over 3 month timescales will be a negligible noise source. LISA is unlikely to inform solar wind measurements routinely. Another source of noise from the Sun, solar radiation pressure, is estimated to impart greater acceleration noise, but has yet to be analyzed.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

The effect of curvature induced broken potential vorticity conservation on drift wave turbulences

Abstract The correlation theory of turbulence suppression (Zhang and Mahajan 1993 Phys. Fluids B5 2000) by velocity shear was constructed by invoking the ansatz of potential vorticity conservation (PVC) that holds for relatively simple (slab) models of drift wave turbulence. It is, therefore, surprising that a detailed modern simulation of the H mode pedestal, using the gyrokinetic code GENE (Hatch et al 2018 Plasma Phys. Control. Fusion 60 084003), found ‘striking agreement’ with the predictions of the analytic model. To understand the reasons for this remarkable agreement, an extended theory that contains finite (magnetic) curvature, and which does not conserve potential vorticity, is developed and ‘solved’ by calculating an inhomogeneous Green function reflecting the fact that the new system has a potential vorticity source. It is, then, demonstrated that the effect of the broken PVC is insignificant for the normal operation parameters in tokamaks; the correction due to curvature is at the order of 2 L 0 / R , where L 0 is the scale length of the local gradient and R is the major radius. The excellent agreement between simulation and slab model 1993 theory is therefore not accidental; the latter can be applied with confidence to the tokamak pedestal.

Physics↗

DOE OSTI2025

Next-generation tunnel FETs: exploring material perspectives and areal tunneling configurations

The end of Dennard scaling, which facilitated proportional increases in computing power without added energy costs until the mid-2000s, has underscored the urgent need for innovative semiconductor devices that can enhance energy efficiency. Tunnel field-effect transistors (TFETs) have emerged as promising candidates to surpass the energy efficiency of conventional metal oxide semiconductor field-effect transistors (MOSFETs). Unlike MOSFETs, which rely on thermionic emission to overcome the source-channel potential barrier, TFETs operate through quantum tunneling, potentially enabling sub-60 mV dec −1 subthreshold swing (SS) for low-voltage operation. However, lateral TFETs have faced challenges in achieving adequate on-state current (I ON ) and a broad SS operation window, limiting their practical utility. This review article advocates for areal TFETs, which utilize face-to-face tunnel junctions that ideally offer step-function current turn-on characteristics and allow I ON to scale with device area rather than width. We highlight recent advancements in integrating 2D materials into tunneling structures, which could facilitate efficient band-to-band tunneling through atomically thin layers, while addressing challenges of gate field screening. We then discuss the nearer-term prospects of epitaxial areal TFETs comprising III–V compound semiconductors and group-IV semiconductors based on recent experimental progress. The review examines both quantum mechanical and semiclassical modeling approaches for TFETs, including techniques to reduce the computational complexity. The article delves into ongoing challenges in material synthesis, interface engineering, device fabrication, and integration pathways, concluding with recommendations for future research directions to overcome the fundamental power density limitations of conventional transistor technology.

2D materials↗

DOE OSTI2022

Effects of Desiccation and Freezing on Microbial Ionizing Radiation Survivability: Considerations for Mars Sample Return

Increasingly, national space agencies are expanding their goals to include Mars exploration with sample return. To better protect Earth and its biosphere from potential extraterrestrial sources of contamination, as set forth in the Outer Space Treaty of 1967, international efforts to develop planetary protection measures strive to understand the danger of cross-contamination processes in Mars sample return missions. We aim to better understand the impact of the martian surface on microbial dormancy and survivability. Radiation resistance of microbes is a key parameter in considering survivability of microbes over geologic times on the frigid, arid surface of Mars that is bombarded by solar and galactic cosmic radiation. We tested the influence of desiccation and freezing on the ionizing radiation survival of six model microorganisms: vegetative cells of two bacteria (Deinococcus radiodurans, Escherichia coli) and a strain of budding yeast (Saccharomyces cerevisiae); and vegetative cells and endospores of three Bacillus bacteria (B. subtilis, B. megaterium, B. thuringiensis). Desiccation and freezing greatly increased radiation survival of vegetative polyploid microorganisms when applied separately, and when combined, desiccation and freezing increased radiation survival even more so. Thus, the radiation survival threshold of polyploid D. radiodurans cells can be extended from the already high value of 25 kGy in liquid culture to an astonishing 140 kGy when the cells are both desiccated and frozen. However, such synergistic radioprotective effects of desiccation and freezing were not observed in monogenomic or digenomic Bacillus cells and endospores, which are generally sterilized by 12 kGy. This difference is associated with a critical requirement for survivability under radiation, that is, repair of genome damage caused by radiation. Deinococcus radiodurans and S. cerevisiae accumulate similarly high levels of the Mn antioxidants that are required for extreme radiation resistance, as do endospores, though they greatly exceed spores in radioresistance because they contain multiple identical genome copies, which in D. radiodurans are joined by persistent Holliday junctions. We estimate ionizing radiation survival limits of polyploid DNA-based life-forms to be hundreds of millions of years of background radiation while buried in the martian subsurface. Our findings imply that forward contamination of Mars will essentially be permanent, and backward contamination is a possibility if life ever existed on Mars.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The primordial matter power spectrum on sub-galactic scales

The primordial matter power spectrum quantifies fluctuations in the distribution of dark matter immediately following inflation. Over cosmic time, overdense regions of the primordial density field grow and collapse into dark matter haloes, whose abundance and density profiles retain memory of the initial conditions. By analysing the image magnifications in 11 strongly lensed and quadruply imaged quasars, we infer the abundance and concentrations of low-mass haloes, and cast the measurement in terms of the amplitude of the primordial matter power spectrum. We anchor the power spectrum on large scales, isolating the effect of small-scale deviations from the Lambda cold dark matter (ΛCDM) prediction. Assuming an analytic model for the power spectrum and accounting for several sources of potential systematic uncertainty, including three different models for the halo mass function, we obtain correlated inferences of $\log _{10}\left(P / P_{\Lambda \rm {CDM}}\right)$, the power spectrum amplitude relative to the predictions of the concordance cosmological model, of $0.0_{-0.4}^{+0.5}$, $0.1_{-0.6}^{+0.7}$, and $0.2_{-0.9}^{+1.0}$ at k = 10, 25, and 50 $\rm {Mpc^{-1}}$ at $68 {{\ \rm per\ cent}}$ confidence, consistent with CDM and single-field slow-roll inflation.

79 ASTRONOMY AND ASTROPHYSICS↗