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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions

The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50,000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire dataset. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property—the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good tradeoff between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.

Nielson, Felicity F.↗
DOE OSTI2020

Probing the electrical double layer by operando X‐ray photoelectron spectroscopy through a graphene‐carbon nanotube composite window

Abstract The electrical double layer is known to spontaneously form at the electrode‐electrolyte interface, impacting many important chemical and physical processes as well as applications including electrocatalysis, electroorganic synthesis, nanomaterial preparation, energy storage, and even emulsion stabilization. However, it has been challenging to study this fundamental phenomenon at the molecular level because the electrical double layer is deeply “buried” by the bulk electrolyte solution. Here, we report a quantitative probing of the electrical double layer of ionic liquids from the solid side of a photoelectron‐transparent graphene‐carbon nanotube hybrid membrane electrode using X‐ray photoelectron spectroscopy. The membrane window is ultrathin (1‐1.5 nm), large (~1 cm 2 ), and robust, enabling a tight seal of the electrolyte and quantitative measurement with excellent photoelectron signals. By operando monitoring the population changes of cations and anions in response to the applied electrical potentials, we experimentally resolve the chemical structure and dynamics of the electrical double layer, which corroborate results from molecular dynamics simulations. image

Wang, Peng↗
DOE OSTI2021

Enabling Magnesium Anodes by Tuning the Electrode/Electrolyte Interfacial Structure

Here, a new deposition mechanism is presented in this study to achieve highly reversible plating and stripping of magnesium (Mg) anodes for Mg-ion batteries. It is known that the reduction of electrolyte anions such as bi s (trifluoromethanesulfonyl) imide (TFSI - ) causes Mg surface passivation, resulting in poor electrochemical performance for Mg-ion batteries. We reveal that the addition of sodium cations (Na + ) in Mg-ion electrolytes can fundamentally alter the interfacial chemistry and structure at the Mg anode surface. The molecular dynamics simulation suggests that Na + cations contribute to a significant population in the interfacial double layer so that TFSI - anions are excluded from the immediate interface adjacent to the Mg anode. As a result, the TFSI - decomposition is largely suppressed so does the formation of passivation layers at the Mg surface. This mechanism is supported by our electrochemical, microscopic, and spectroscopic analyses. The resultant Mg deposition demonstrates smooth surface morphology and lowered overpotential compared to the pure Mg(TFSI) 2 electrolyte.

25 ENERGY STORAGE↗
DOE OSTI2021

Probabilistic Evaluation of Geoscientific Hypotheses with Geophysical Data: Application to Electrical Resistivity Imaging of a Fractured Bedrock Zone

As climate changes and populations grow, groundwater sustainability is becoming increasingly important. Groundwater models, based on a conceptual understanding of the subsurface structure, are crucial tools for making sustainable management decisions. Conceptual models of the subsurface are based on knowledge of geological processes, and, frequently, observations from geophysical data. A frequent problem in groundwater model development occurs when multiple geological phenomena could explain a single subsurface observation. Uncertainty in geophysical data makes it even more difficult to discern which explanations are consistent with the geophysics. Here, we present a framework for testing geological when a geological feature is observed in geophysical data, but its physical characteristics are uncertain. The framework builds on Popper-Bayes methods developed in previous work, and is applied to study a fractured bedrock zone in a mountainous watershed in southwest Colorado. First, we outline six hypotheses based on the geological history of the watershed. Then, using the proposed Popper-Bayes approach, we demonstrate that three of the six hypotheses are inconsistent with measured electrical resistivity data, even after accounting for uncertainty. Finally, we discuss the importance of the prior model, and how this framework for handling geophysical uncertainty can be applied in other settings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Learning to concentrate: multi-tracer forecasts on local primordial non-Gaussianity with machine-learned bias

Local primordial non-Gaussianity (LPNG) is predicted by many non-minimal models of inflation, and creates a scale-dependent contribution to the power spectrum of large-scale structure (LSS) tracers, whose amplitude is characterized by b Φ . Knowledge of b Φ for the observed tracer population is therefore crucial for learning about inflation from LSS. Recently, it has been shown that the relationship between linear bias b 1 and b Φ for simulated halos exhibits significant secondary dependence on halo concentration. We leverage this fact to forecast multi-tracer constraints on ${f}^{loc}_{NL}$. We train a machine learning model on observable properties of simulated IllustrisTNG galaxies to predict b Φ for samples constructed to approximate DESI emission line galaxies (ELGs) and luminous red galaxies (LRGs). We find σ(${f}^{loc}_{NL}$) = 2.3, and σ(${f}^{loc}_{NL}$) = 3.7, respectively. These forecasted errors are roughly factors of 3, and 35% improvements over the single-tracer case for each sample, respectively. When considering both ELGs and LRGs in their overlap region, we forecast σ(${f}^{loc}_{NL}$) = 1.5 is attainable with our learned model, more than a factor of 3 improvement over the single-tracer case, while the ideal split by b Φ could reach σ(${f}^{loc}_{NL}$) < 1. In conclusion, we also perform multi-tracer forecasts for upcoming spectroscopic surveys targeting LPNG (MegaMapper, SPHEREx) and show that splitting tracer samples by b Φ can lead to an order-of-magnitude reduction in projected σ(${f}^{loc}_{NL}$) for these surveys.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Level structure of light neutron-rich La isotopes beyond the 𝑁 = 82 shell closure

Here, the high spin excited states of Lanthanum isotopes 140–143 La, above the 𝑁 = 82 closed shell, were populated in fission reactions. The prompt 𝛾-ray transitions were measured using two complementary methods: (a) in coincidence with the isotopically identified fragments produced in the fission of the 238 U + 9 Be system using the Variable Mode Spectrometer (VAMOS++) and the Advanced Gamma Tracking Array (AGATA) spectrometer, and (b) high statistics threefold 𝛾−𝛾−𝛾 and fourfold 𝛾−𝛾−𝛾−𝛾 coincidence data from the spontaneous fission of 252 Cf using the Gammasphere. This work reports the first identification of a pair of parity doublet structures in 143 La and the new high spin level structure in 140–142 La from prompt 𝛾-ray spectroscopy. The level structures are interpreted in terms of the systematics of neighboring odd-𝑍 nuclei above the 𝑍 = 50 shell closure and large-scale shell model calculations. The present results indicate the presence of stable octupole deformation in 143 La. The excitation energy pattern and their comparison with neighboring isotones, moving away from the 𝑁 = 82 closed shell, point towards a transition from single-particle structures to an alternating parity rotational band structure in the La isotopic chain.

Navin, A. [Centre National de la Recherche Scienti↗
DOE OSTI2026

Elucidating Norrish type I reactive pathways by ultrafast X-ray absorption spectroscopy

Norrish type I reactions selectively cleave carbon–carbon bonds directly adjacent to carbonyl groups. Despite their broad use in combination with aromatic carbonyls for additive manufacturing and dental UV curing applications, the nature of the photochemically active state and its population mechanism remain insufficiently understood. Detailed mechanistic insight requires mapping of the photoexcited population flow involving internal conversion and intersystem crossing. We present a time-domain study of gas phase acetophenone as a prototypical aromatic carbonyl combining soft X-ray time-resolved near-edge X-ray absorption fine structure (TR-NEXAFS) spectroscopy at the oxygen K-edge with ab initio multiple spawning (AIMS) simulations. Exploiting the specific sensitivity of TR-NEXAFS spectroscopy to states with nπ* character, we observe population transfer from the initially excited 1 ππ* state to the 1 nπ* state with a time constant of (0.13 ± 0.02) ps after an initial induction period of (0.12 ± 0.02) ps without population transfer, in quantitative agreement with the AIMS simulations. The population in the 1 nπ* state subsequently decays via intersystem crossing, likely mediated by a 3 ππ* state, within (3.17 ± 0.66) ps to a long-lived 3 nπ* state, which is presumed to be active towards Norrish type I chemistry.

Graßl, Martin [SLAC National Accelerator Laborator↗
DOE OSTI2022

Synthesis, Crystal and Electronic Structures, Nonlinear Optical Properties, and Magnetic Properties of Two Thiophosphates: KInP 2 S 7 and KCrP 2 S 7

Two thiophosphates, KInP 2 S 7 and KCrP 2 S 7 , were structurally characterized without investigating any optical properties. Herein in this work, KInP 2 S 7 and KCrP 2 S 7 were revisited to investigate their optical and magnetic properties, respectively. Pure polycrystalline samples and crystals of KInP 2 S 7 and KCrP 2 S 7 were grown by high temperature solid state reactions, where mm-sized crystals of KCrP 2 S 7 were collected. KCrP 2 S 7 is isostructural to KInP 2 S 7 , which features a layered structure. KInP 2 S 7 and KCrP 2 S 7 possess close relationship to the layered thiophosphate M 2 P 2 S 6 (M = Fe, Co, Zn, etc.). The bonding pictures of KInP 2 S 7 were studied using the electron localization function (ELF) coupled with crystal orbital Hamilton population (COHP) calculations. The intrinsically distorted [PS 4 ] tetrahedra and [InS 6 ] octahedra are made by strong covalent P-S interactions and ionic In-S interactions, respectively. Electronic structure analysis confirmed that the optical properties of KInP 2 S 7 are mainly contributed to by [PS 4 ] tetrahedra together with small amounts of the contributions coming from [InS 6 ] octahedra. Magnetic measurement on mm-sized crystals of KCrP 2 S 7 verified that there is an antiferromagnetic transition around 21 K, and the Cr atoms are trivalent. KInP 2 S 7 is predicated to be an indirect bandgap semiconductor of 2.38 eV, which is confirmed by the UV-Vis measurement of 2.4(1) eV. KInP 2 S 7 is not a type-I phase-matching material and exhibits moderate second harmonic generation (SHG) response (0.51 × AgGaS 2 , sample of particle size of 100 µm). The laser damage threshold (LDT) of KInP 2 S 7 is very high of 5.2 × AgGaS 2 . Bandgap engineering were undergone to enhance the SHG response of KInP 2 S 7 .

36 MATERIALS SCIENCE↗
DOE OSTI2026

Structural Aspects of Neutron Survival Probabilities

The neutron survival probability (and related quantities including probabilities of extinction and initiation) is a central element of the broader stochastic theory of neutron populations and finds application in fields including reactor start-up, analysis of reactor power bursts and criticality accidents, and safeguards. In a full neutron transport formulation, the equation governing the single-neutron survival probability is a backward or adjoint-like integro-partial differential equation with the added complexity of being highly nonlinear. Analogous formulations of this equation exist in the context of many approximate theories of neutron transport, with the point kinetics formulation having received significant theoretical attention since the 1940s. This work continues this tradition by providing a novel analysis of the single-neutron survival probability equation using the tools of boundary layer theory. The analysis reveals that the “fully dynamic” solution of the single-neutron survival probability equation—and some key probability distributions derived from it—may be cast as a singular perturbation around the underlying quasi-static single-neutron probability of initiation. In this perturbation solution, the expansion parameter is the ratio of the neutron generation time to a macroscopic time scale characterizing the overall system evolution; this interpretation illuminates some of the fundamental structural aspects of neutron survival phenomena.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Assessing the cumulative effects of nearshore habitat restoration actions for multiple populations of juvenile salmon in Whidbey Basin, Washington: foundation and approach for synthesis and evaluation

Ecosystem restoration is a common tool for re-establishing ecosystem processes, structures, and functions to improve biodiversity and services in coastal and estuarine ecosystems. In the Salish Sea, salmon habitats have been fragmented, reduced in size, and diminished in quality, and the ecosystem processes that form and sustain these habitats have been degraded and disrupted as well. This loss is especially prevalent in estuaries, where up to 90% of former salmon habitat has been lost or compromised. Salmon species are integral to the identities and cultures of people in the Pacific Northwest, yet salmon abundances remain at historic lows, especially in urbanized areas. Recent investments in restoration are creating rearing habitat and repairing lost ecosystem function. However, restoration efforts in this region have largely proceeded at the site scale, with less attention to big-picture thinking regarding how restoration will effectively recover degraded or lost habitats for target species. As a result, no landscape-scale evaluation program exists, and the cumulative benefits of multiple interventions are unknown. We describe innovative methods for science synthesis related to the evaluation of cumulative effects of ecosystem restoration for Pacific salmon, using years of existing, but disparate data. Building from previous work on cumulative effects evaluation and incorporating a hierarchy of hypotheses approach, we propose using causal inference across numerous hypotheses in a framework to assess the cumulative benefits to Pacific salmon from multiple estuarine restoration projects. We present the framework as a method that can be used to address many complex questions and provide examples from the Salish Sea where the approach is being implemented. The framework draws on science synthesis from numerous fields and uses a hierarchy of hypotheses, causal analysis at multiple scales, and a new hierarchy of synthesis for assessing multiple lines of evidence documenting restoration effects on Pacific salmon. We propose causal inference to synthesize dissimilar data streams, in our case, to identify various manifestations of cumulative effects of restoration and benefits to salmon, and to further inform restoration and recovery planning. A unifying framework would allow for the detection of thresholds at which restoration provides measurable improvement and would greatly advance understanding of the effects of restoration on ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Stochastic parametric skeletal dosimetry model for humans: Pediatric and adult computational skeleton phantoms for internal bone marrow dosimetry

Currently, computational phantoms that simulate skeletal tissues are used in active red bone marrow (AM) internal dosimetry. Up-to-date reference computational phantoms recommended by the ICRP are based on the analysis of CT-images of cadavers. Such phantoms have significant disadvantages. One disadvantage is that the assessment of uncertainty due to the population variability of skeleton dimensions and microstructure results from the limited availability of autopsy material. Another disadvantage is the simplified modelling of cortical layer and bone microarchitecture. A method of stochastic parametric skeletal dosimetry modelling of the bone structures – SPSD modelling – has been developed as an alternative to the ICRP reference phantoms. In the framework of this approach, skeletal phantom parameters are evaluated based on extensively reviewed results of published measurements of real bones. The SPSD approach allows for the assessment of both population-average values and their variability. SPSD-phantoms of the skeleton are modelled in voxel representation. They consist of smaller phantoms of the bone sites – segments – described by simple geometric shapes with uniform microarchitecture parameters. Such segmentation makes it possible to account for non-homogeneous skeletal microarchitecture and to model the bone structure with the required voxel resolution to elaborate suitable skeletal phantoms. The current study presents the parameters of the SPSD skeletal phantoms for the following age-groups: newborn, 1-year-old, 5-year-old, 10-year-old, 15-year-old (male and female), and adult (male and female). This skeletal phantom can be used for dosimetry as an alternative to available reference phantoms for bone-seeking radionuclides. The above-mentioned age- and sex-specific skeletal phantoms are comprised of 289 unique segments. The characteristics of the SPSD phantoms do not contradict published data and are in good agreement with the measurement results of real bones.

Science & Technology - Other Topics↗
DOE OSTI2020

The last Black man with HIV in San Francisco: the potential role of gentrification on HIV getting to zero achievements

San Francisco was the first city in the USA to develop a Getting to Zero HIV elimination strategy. The cause of decreased HIV incidence has been attributed to the use of biomedical prevention methods, such as pre-exposure prophylaxis (PrEP) and treatment as prevention (TasP). These strategies have benefitted White men who have sex with men (MSM), whose population has increased over the past decade. However, Black MSM in San Francisco continue to have higher HIV incidence and outmigration rates. We posit that the declining overall HIV incidence, including among White MSM, is not only explained by the use of TaSP and PrEP, but is also due to the declining Black population and rising HIV incidence among Black MSM, who have historically been more likely to acquire HIV due to structural, racial, and criminal justice-related factors than have White MSM.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural studies of the IFNλ4 receptor complex using cryoEM enabled by protein engineering

Abstract IFNλ4 has posed a conundrum in human immunology since its discovery in 2013, with its expression linked to complications with viral clearance. While genetic and cellular studies revealed the detrimental effects of IFNλ4 expression, extensive structural and functional characterization has been limited by the inability to express and purify the protein, complicating explanations of its paradoxical behavior. In this work, we report a method for robust production of IFNλ4. We then use yeast surface display to affinity-mature IL10Rβ and solve the 72 kilodalton structures of IFNλ4 (3.26 Å) and IFNλ3 (3.00 Å) in complex with their receptors IFNλR1 and IL10Rβ using cryogenic electron microscopy. Comparison of the structures highlights differences in receptor engagement and reveals a distinct 12-degree rotation in overall receptor geometry, providing a potential mechanistic explanation for differences in cell signaling, downstream gene induction, and antiviral activities. Further, we perform a structural analysis using molecular modeling and simulation to identify a unique region of IFNλ4 that, when replaced, enables secretion of the protein from cells. These findings provide a structural and functional understanding of the IFNλ4 protein and enable future comprehensive studies towards correcting IFNλ4 dysfunction in large populations of affected patients.

Science & Technology - Other Topics↗
DOE OSTI2021

The White Dwarfs of the Old, Solar-metallicity Open Star Cluster Messier 67: Properties and Progenitors

The old, solar-metallicity open cluster Messier 67 has long been considered a lynchpin in the study and understanding of the structure and evolution of solar-type stars. The same is arguably true for stellar remnants; the white dwarf population of M67 provides crucial observational data for understanding and interpreting white dwarf populations and evolution. In this work, we determine the white dwarf masses and derive their progenitor star masses using high signal-to-noise spectroscopy of warm (≳10,000 K) DA white dwarfs in the cluster. From this, we are able to derive each white dwarf’s position on the initial–final mass relation (IFMR), with an average M {sub WD} = 0.60 ± 0.01 M {sub ⊙} and progenitor mass M {sub i} = 1.52 ± 0.04 M {sub ⊙}. These values are fully consistent with recently published linear and piecewise linear fits to the semiempirical IFMR and provide a crucial, precise anchor point for the IFMR for solar-metallicity, low-mass stars. The mean mass of M67 white dwarfs is also consistent with the sharp narrow peak in the local field white dwarf mass distribution, indicating that a majority of recently formed field white dwarfs come from stars with progenitor masses of ≈1.5 M {sub ⊙}. Our results enable more precise modeling of the Galactic star formation rate encoded in the field white dwarf mass distribution.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

HIV drug resistance during antiretroviral therapy scale-up in Uganda, 2012–19: a population-based, longitudinal study

Background With scale-up of antiretroviral therapy (ART) in sub-Saharan Africa, increasing pretreatment HIV drug resistance has been reported; however, the broader effect of ART expansion on population-level resistance patterns remains insufficiently quantified. We aimed to estimate the longitudinal prevalence of drug resistance and resistance-conferring mutations. Methods This study used data collected as part of the Rakai Community Cohort Study (RCCS), an open population-based census and cohort study conducted in southern Uganda. At each survey round, residents aged 15–49 years are invited to participate and receive a structured questionnaire that obtains sociodemographic, behavioural, and health information, including self-reported past and current ART use. Voluntary HIV testing is conducted using a rapid test algorithm and a venous blood sample. People with HIV provide samples for viral load quantification and deep sequencing. We analysed RCCS survey, HIV viral load, and deep sequencing (which was used to predict resistance) data from five survey rounds. The key outcomes were the population prevalence of viraemic people with HIV with non-nucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), protease inhibitor, or multiclass resistance among all participants (regardless of HIV serostatus) in the 2015 and 2017 surveys. Prevalence of class-specific resistance and resistance-conferring substitutions were estimated using robust log-Poisson regression. Findings Between Aug 10, 2011, and Nov 4, 2020, there were 43 361 participants in the RCCS and 7923 (18·27%) people with HIV. Over five survey rounds, 93 622 participant visits occurred, among which 17 460 (18·65%) were from people with HIV. Over the analysis period, the median age of study participants remained similar (28 years [22–35] in 2012 and 29 years [21–38] in 2019). Sufficient data were available to reliably genotype 4072 (90·03%) of 4523 participant visits from 3407 people with HIV for at least one drug. Overall population prevalence of resistance contributed by viraemic pretreatment people with HIV decreased between 2012 and 2017 from 0·56% (95% CI 0·42–0·75) to 0·25% (0·18–0·33) for NNRTI and from 0·24% (0·15–0·37) to 0·05% (0·02–0·10) for NRTI (prevalence ratio 0·44 [0·29–0·68] for NNRTI and 0·21 [0·09–0·47] for NRTI). Between 2012 and 2017, NNRTI resistance among viraemic pretreatment people with HIV increased from 4·86% (3·69–6·42) to 9·61% (7·27–12·7; prevalence ratio 1·98 [1·34–2·91]). The prevalence of NNRTI and NRTI resistance was substantially higher among viraemic treatment-experienced people with HIV (51·49% [46·24–57·34] for NNRTI and 36·46% [30·06–44·22] for NRTI in 2017) than among pretreatment people with HIV. NNRTI and NRTI resistance was predominantly attributable to rtK103N and rtM184V. inT97A was observed at a similar prevalence among viraemic treatment-experienced (9·96% [6·41–15·48]) and viraemic pretreatment (10·56% [8·01–13·93]) people with HIV; no major dolutegravir resistance mutations were observed. Interpretation Despite rising NNRTI resistance among pretreatment people with HIV, overall population prevalence of pretreatment HIV drug-resistant viraemia decreased due to increasing ART uptake and viral suppression. This finding underscores the crucial role of achieving and maintaining high ART coverage in reducing transmission of drug-resistant HIV. The high prevalence of mutations conferring resistance to components of first-line ART regimens among viraemic people with HIV is potentially concerning. Funding National Institutes of Health, Johns Hopkins University Center for AIDS Research, Bill & Melinda Gates Foundation, and the US Centers for Disease Control and Prevention.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Model Package Report: Geoframework Model of the Hanford Site 100 Area

The purpose of the 100 Area Geoframework Model (GFM) is to provide a reasonable, consistent, and defensible three dimensional representation of the hydrostratigraphic units below the River Corridor at the Hanford Site to support contaminant fate and transport models. The GFM is a three dimensional representation of the subsurface geologic structure. From this, three dimensional geologic model-exported results, in the form of points or surfaces, are used as inputs to populate and assemble the various numerical model architectures. The objective of this report is to define the process used to produce a hydrostratigraphic model for the hydrostratigraphic units beneath the Hanford Site 100 Area. The GFM may support several other CH2M HILL Plateau Remediation Company project needs and objectives, including providing geologic information to support remedial investigations and actions and as a tool to present River Corridor geology and contaminant extents. The GFM was constructed based on information through 2019 available in the Integrated Data Management System, Hanford Environmental Information System, and the Hanford Site geologic contacts (GeoContacts) datasets. Revisions to the 100 Area GFM may occur to incorporate new data and information. Each version will be maintained in configuration control using date stamps for identifying supporting databases, figures, and interpretations. Supporting data include the final three dimensional geoframework surfaces, two dimensional structure and isopach maps, and all the geologic contact inputs and interpreted geologic log data. These final products provide a supporting set of geologic information that together allow the creation of the GFM. This information is managed, updated, and maintained via CH2M HILL Plateau Remediation Company under the Environmental Model Management Archive.

58 GEOSCIENCES↗
DOE OSTI2025

AI-Assisted Conceptual Development of a Pre-Geometric Cosmological Model - An Exercise in AI-Assisted Conceptual Framework Generation, Paper III: Cosmological Structure and Predictions

This paper develops the cosmological consequences of the replication-driven cosmogenesis framework introduced in Paper I and the emergent geometric structure established in Paper II. After the replication epoch freezes out, the coherent sector occupies a finite spectral band and contains a population of excited states. The relaxation of these excited coherent configurations does not produce coherent radiation; instead, all released energy flows into the incoherent substrate, where the randomizer acts as a rapid phase-scrambling mechanism. This process generates an effectively thermal radiation bath, providing a natural reheating mechanism that requires neither inflaton oscillations nor scalar-field potentials, and can be contrasted with standard scenarios of nonperturbative reheating dynamics. Subsequent symmetry-breaking transitions in the coherent vacuum inject additional radiation, yielding a multi-stage thermal history with well-defined energy transfers. We derive the effective equations of state for each component—the cosmological vacuum, the coherent vacuum, and the radiation bath—and show how their interplay produces an FRW-like expansion. The discrete sequence of coherent-state relaxations imprints a distinctive multi-peaked stochastic gravitational-wave background, whose spectral structure reflects the underlying hierarchy of coherent frequencies. Potential observational signatures in the LISA and mid-band frequency ranges are highlighted, providing concrete avenues to test this replication-based cosmological framework in the context of standard cosmological gravitational-wave backgrounds and LISA-oriented forecasts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Structural and Proteomic Studies of the Aureococcus anophagefferens Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing

Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual virus particles themselves are rare. We used shotgun proteomics to quantitatively identify 43 virus-encoded proteins packaged within purified Aureococcus anophagefferens Virus (AaV) particles, normalizing data to the per-virion level using a 9.5-Å-resolution molecular reconstruction of the 1900-Å (AaV) particle that we generated with cryogenic electron microscopy. This packaged proteome was used to determine similarities and differences between members of different giant virus families. We noted that proteins involved in sugar degradation and binding (e.g., carbohydrate lyases) were unique to AaV among characterized giant viruses. To determine the extent to which this virally encoded metabolic capability was ecologically relevant, we examined the TARA Oceans dataset and identified genes and transcripts of viral origin. Our analyses demonstrated that putative giant virus carbohydrate lyases represented up to 17% of the marine pool for this function. In total, our observations suggest that the AaV particle has potential prepackaged metabolic capabilities and that these may be found in other giant viruses that are widespread and abundant in global oceans.

59 BASIC BIOLOGICAL SCIENCES↗