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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB

Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Gas Transport in the Insensitive High Explosive PBX 9502

Small-scale laboratory experiments were performed to analyze gas transport mechanics in PBX 9502, an insensitive high explosive (IHE) composition. Two independent investigations are reported here. First, gas permeametry and dynamic pycnometry techniques were used to measure the molecular flow (Knudsen) coefficient and the internally interconnected void fraction of pristine and thermally damaged samples in two uniaxial pressing orientations. The permeability of PBX 9502 was found to be unmeasurably low (of the same order of magnitude as PTFE) with gas transport being diffusion-dominated. Secondly, a pressure vessel experiment was developed to measure quasi-static and dynamic gas generation as the explosive was heated to self-ignition (cookoff). The gas generation results and the permeability/diffusivity findings provide evidence that PBX 9502 remains impermeable until seconds prior to self-ignition. At ignition, internal void-pressure drives macro-scale cracking and the sample becomes uniformly incorporated in the following deconsolidating deflagration. These results are discussed within the context of previous observations of pressure-dependent cookoff behavior of PBX 9502 and provide a more complete description of thermal damage evolution in this explosive composition.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2026

High-resolution Giant Metrewave Radio Telescope H I 21 cm Imaging of the Host Galaxy of FRB 20250316A

We report Giant Metrewave Radio Telescope (GMRT) H I 21 cm imaging of NGC 4141, the host galaxy of FRB 20250316A at z = 0.0063. Our GMRT H I 21 cm images have spatial resolutions, at z ≈ 0.0063, of ≈0.48–8.0 kpc, and provide evidence for (i) a companion galaxy, LEDA 2582852, to the southwest, (ii) a nearby (27 kpc distant) H i cloud to the southwest, (iii) disturbances in the H I distributions of both NGC 4141 and LEDA 2582852, and (iv) high H I column densities in the southwestern outskirts of NGC 4141. A Sloan Digital Sky Survey spectrum yields a low metallicity and a high star formation rate (SFR) surface density in the southwestern disk of NGC 4141, and an Hα-based SFR estimate that is significantly higher than that at the same location from the Galaxy Evolution Explorer near-ultraviolet image, indicating a recent burst of star formation. The total SFR of NGC 4141 is also found to be higher via the Hα line than from the 1.4 GHz radio continuum. The above evidence indicates that NGC 4141 has recently (within the last ≈3 Myr) acquired metal-poor gas, via either a merger or accretion, that resulted in the southwestern starburst and that may also have triggered large-scale star-formation activity in NGC 4141, resulting in the formation of the stellar progenitor of FRB 20250316A and the other transients. Our highest-resolution (480 pc) GMRT H I 21 cm image finds no H I 21 cm emission from the location of FRB 20250316A or the nearby star-forming region, suggesting that most of the H I here has been either ionized or converted into the molecular phase. Our nondetection of continuum emission at the location of FRB 20250316A yields the 3σ upper limit νL 1.38 GHz < 4.4 × 10 34 erg s −1 on the 1.38 GHz radio luminosity of a putative persistent radio source associated with FRB 20250316A, one of the strongest constraints on the radio luminosity of such an associated persistent radio source.

Kaur, Balpreet [Pune University (India)] (ORCID:00↗
DOE OSTI2021

Modeling Turbulence in Galactic Centers

Turbulence is a prevalent phenomenon in the interstellar medium, and in particular, the environment at the centers of galaxies. For example, detailed observations of the Milky Way’s Central Molecular Zone (CMZ) revealed that it has a complex and turbulent structure. Turbulence on galactic scales is often modeled using star formation and feedback. However, these effects do not appear to be sufficient for explaining the high-velocity dispersion observed in the CMZ, indicating that additional gas-stirring processes are likely to be operating. Here we introduce a proof-of-concept method to drive turbulence in gas that orbits under the influence of a galactic potential. Instead of relying on a particular physical mechanism, we have adopted a Fourier forcing module and have applied it using a smoothed particle hydrodynamics code. To test our method, we performed simulations of a simplistic model of the CMZ. Our turbulence injection method is capable of balancing the self-gravity of the gas, which allows us to run the simulations for long timescales and thereby follow the evolution of the CMZ. Our results show that turbulence induces a flocculent spiral pattern in our model, analogous to that found in galactic-scale simulations. Furthermore, we find that our turbulence injection method induces inward migration of gas, a result consistent with previous numerical simulations. We submit that this injection method is a promising new tool to simulate turbulence in galactic centers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Diffusion-to-Imbibition Transition in Water Sorption in Nanoporous Media: Theoretical Studies

The ability to predict multiphase fluid transport in nanoporous rocks such as shales is critical for many geoscience applications, for example unconventional hydrocarbon production, geologic carbon sequestration, and nuclear waste disposal. When the pore sizes approach nanoscales, the impact of the molecular interaction forces between fluids and solids becomes increasingly important. These forces can alter macroscopic fluid phase behavior and control transport. Recent experimental studies have shown that capillary condensation and subsequent imbibition of liquid water can occur in hydrophilic nanoporous media even if the vapor phase is at a critical relative humidity (rhcrit) well below vapor saturation. This study presents a theoretical investigation of the processes controlling adsorption, capillary condensation and imbibition in nanoporous media, using the square-gradient classical density functional theory. The proposed theoretical model explicitly includes the relevant interaction forces among fluids and solids in macroscopic porous media. Application of the model to a relative-humidity-controlled water adsorption experiment is presented to demonstrate the impact of water-pore wall attractive forces on multiphase water behavior in a hydrophilic silicon nanoporous medium. Here, the model represents well the measured time-dependent evolution of the water imbibition front inside the nanoporous medium and also explains the diffusion-like water transport regimes observed at rh < rh crit and the imbibition-like flow regimes observed at rh > rh crit . The study furthermore gives an insight on hysteresis phenomenon in adsorption and desorption isotherms.

58 GEOSCIENCES↗
DOE OSTI2020

Isotopic Evolution of the Inner Solar System Inferred from Molybdenum Isotopes in Meteorites

The fundamentally different isotopic compositions of non-carbonaceous (NC) and carbonaceous (CC) meteorites reveal the presence of two distinct reservoirs in the solar protoplanetary disk that were likely separated by Jupiter. However, the extent of material exchange between these reservoirs, and how this affected the composition of the inner disk, are not known. Here we show that NC meteorites display broadly correlated isotopic variations for Mo, Ti, Cr, and Ni, indicating the addition of isotopically distinct material to the inner disk. The added material resembles bulk CC meteorites and Ca–Al-rich inclusions in terms of its enrichment in neutron-rich isotopes, but unlike the latter materials is also enriched in s-process nuclides. The comparison of the isotopic composition of NC meteorites with the accretion ages of their parent bodies reveals that the isotopic variations within the inner disk do not reflect a continuous compositional change through the addition of CC dust, indicating an efficient separation of the NC and CC reservoirs and limited exchange of material between the inner and outer disk. Instead, the isotopic variations among NC meteorites more likely record a rapidly changing composition of the disk during infall from the Sun's parental molecular cloud, where each planetesimal locks the instant composition of the disk when it forms. Here, a corollary of this model is that late-formed planetesimals in the inner disk predominantly accreted from secondary dust that was produced by collisions among pre-existing NC planetesimals.

58 GEOSCIENCES↗
DOE OSTI2023

Locking water molecules via ternary O–H⋯O intramolecular hydrogen bonds in perhydroxylated closo -dodecaborate

A multitude of applications related to perhydroxylated closo-dodecaborate B 12 (OH) 12 2− in the condensed phase are inseparable from the fundamental mechanisms underlying the high water orientation selectivity based on the base B 12 (OH) 12 2− . Herein, we directly compare the structural evolution of water clusters, ranging from monomer to hexamer, oriented by functional groups in the bases B 12 H 12 2− , B 12 H 11 OH 2− and B 12 (OH) 12 2− using multiple theoretical methods. A significant revelation is made regarding B 12 (OH) 12 2− : each additional water molecule is locked into the intramolecular hydrogen bond B–O–H ternary ring in an embedded form. This new pattern of water cluster growth suggests that B–(H–O)⋯H–O interactions prevail over the competition from water–hydrogen bonds (O⋯H–O), distinguishing it from the behavior observed in B 12 H 12 2− and B 12 H 11 OH 2− bases, in which competition arises from a mixed competing model involving dihydrogen bonds (B–H⋯H–O), conventional hydrogen bonds (B–(H–O)⋯H–O) and water hydrogen bonds (O⋯H–O). Through aqueous solvation and ab initio molecular dynamics analysis, we further demonstrate the largest water clusters in the first hydrated shell with exceptional thermodynamic stability around B 12 (OH) 12 2− . These findings provide a solid scientific foundation for the design of boron cluster chemistry incorporating hydroxyl-group-modified borate salts with potential implications for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The complex polyploid genome architecture of sugarcane

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Evolution of PTCDA-derived seeds prior to graphene nanoribbon growth on Ge(001)

The synthesis of graphene nanoribbons (GNRs) can be realized via CH4 chemical vapor deposition (CVD) on substrates such as Ge(001) that promote highly anisotropic growth kinetics. Small polycyclic aromatic hydrocarbons (PAHs) are first sublimed onto Ge near room temperature to form graphene-like seeds that subsequently initiate GNR growth with CH4 exposure at 1173 K. The behaviors of PAHs in the time in between their sublimation onto Ge and GNR growth are unclear. Here, we study an archetypical PAH, perylene-3,4,9,10-tetracarboxyl acid dianhydride (PTCDA), on Ge(001) using both scanning tunneling microscopy (STM) and density functional theory (DFT) to characterize PAH conformation, surface diffusivity, and clustering, versus temperature. PTCDA becomes mobile above 673 K (consistent with a DFT calculated diffusion barrier of 2.01 eV). The mobile PTCDA molecules meet, cluster, and fuse at Ge step edges. These clusters have an apparent height of 0.4 nm, similar to small graphene islands, and grow laterally with increasing temperature – reaching 1.2 – 2.1 nm in width at 1173 K, consistent with the seed size extrapolated from CVD experiments. These results provide a plausible picture for how PTCDA forms seeds for anisotropic GNR CVD and show that PAHs with reduced surface diffusivity and inter-molecular reactivity are needed to enable more monodisperse PAH-seeded GNR synthesis.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Insights into the Structure and Energy of DNA Nanoassemblies

Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

First-Principles Simulation of Beam-Induced Processes Underlying Atomic Manipulation in Electron Microscopes

The development of experimental methods and apparatuses capable of promoting atomically precise material manipulations holds great promise for realizing the ultimate limit of feature miniaturization in materials and devices. The ability to modify materials atom by atom is anticipated to usher in new technologies in areas as diverse as separation science, medicine, and quantum information science. Historically, scanning probe-based techniques have been the most prominent approaches in this space. However, these methods are best suited for the manipulation of surface-exposed regions of materials, as the strong perturbations required for bond scission are delivered most effectively to atoms in the near-proximity to the scanning probe. In contrast, convergent electron beams with energies tuned slightly below the threshold for inducing irreversible knock-on damage have recently been employed (within scanning transmission electron microscopy) to promote atomic-scale bond rearrangements in various beam-stable solids. Currently, however, the efficiency and selectivity of beam-induced atomic manipulation processes with focused electron beams are such that long irradiation times are required to induce a desired atomic rearrangement. With a better understanding of the underlying physics dictating the outcome of a given irradiation event, methods can be devised to improve the efficiency of these techniques so that their promise can be fully realized through widespread adoption.To this end, this Account details our recent efforts to develop and apply tractable first-principles simulation approaches for studying the response of materials to electric beam-like external electric potentials applied in real space. We briefly review the concepts and capabilities in the area of atomically precise materials manipulation and review the early demonstrations of accomplishments in this area, focusing on studies using scanned convergent electron beam probes in particular. We expound upon the depth of the challenge and identify critical shortcomings of theoretical methods that have previously been employed in the simulation of beam-induced processes. We then describe the computational methods that we have generalized from the concepts and tools most commonly applied to the study of molecular photochemistry and how our adaptations of these methods can be employed to capture the relevant dynamical phenomena for beam-induced processes ranging from the initial electron scattering to the ensuing multistate reactions. Here, we contextualize these methods within the current state of the art in this area, which has historically focused primarily on the simulation of inelastic image formation in the electron microscope for the purpose of interpreting the results of quantitative electron microscopy experiments. We demonstrate that the spatial distribution of state-specific excitation rates due to the presence of an external (probe) electric charge is inhomogeneous, such that irradiation at particular locations in materials can favor specific electronic transitions (and disallow others). In addition to the potential for excited-state reaction pathways to be accessed through the initial inelastic scattering of the tightly focused electron beam from the targeted atoms, we also identify favorable conditions for the electronically nonadiabatic evolution of the highly vibrationally excited system to open complex multistate reaction pathways. Implications of the early results for understanding the mechanisms and potential routes to improved efficiency and selectivity in beam-induced reactions are discussed. We conclude with a summary of the current state of theory and modeling capabilities in this area and provide our perspective on future directions for theoretical and experimental developments that we view as crucial to advancing the use of convergent electron beams in mode-specific, atomically precise platforms for direct-write materials modifications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Modeling Dynamic Evolution of Oxygen Vacancies in Solid Oxide Materials

SOEC is a promising H 2 generation technology for mitigating climate change. Novel material design and optimization strategies, such as oxygen vacancy chemistries, can enhance SOEC efficiency. In this study, Monte Carlo-ReaxFF and eReaxFF simulations were used to study oxygen vacancies (O v ) and electron migration in BZY20 solid oxide material. Our results shows that O v migrate towards the surface, increasing surface O v concentration by 10%. Yttrium restricts electron mobility and functions as an electron trapping site, while Zr accelerates electron mobility and migration. These insights could improve solid-state electrolytes’ electrochemical performance in renewable energy applications.

13 HYDRO ENERGY↗
DOE OSTI2025

Impact of amorphous pockets on displacement damage evolution in silicon

Silicon has long been known to exhibit amorphization in response to heavy particle bombardment. For doses below the total amorphization threshold, partial amorphization is observed in the form of scattered amorphous pockets. While extensive research has gone into modeling the formation and evolution of amorphous pockets in response to irradiation, no studies yet investigate their impact on the evolution of other damage such as interstitial supersaturation and clustering. In this study, we survey the impact of amorphous pockets on defect evolution in silicon when treated as static sinks. MD is first used to show that amorphous pockets provide energetically favorable sites for point defects relative to the crystalline bulk, supporting the hypothesis that they act as sinks. A 0-D cluster dynamics model is then constructed, taking an interstitial clustering model from the literature and including amorphous pockets as a sink species. We conduct our survey for temperatures between 30 and 400 °C and sink strengths between 1 to 6 x 10 10 cm −2 . Both implantation- and radiation-induced damage states are investigated using interstitial and vacancy concentrations as initial condition variables. We find that, due to the differing migration rates of the interstitial and the vacancy, amorphous pockets have a non-monotonic impact on the final damage state depending on the effective sink strength of the amorphous pockets, resulting in increased damage formation in regimes of intermediate amorphization. In conclusion, this result emphasizes the important role of amorphous pockets in governing the evolution of damage in partially amorphized crystalline materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The ALMaQUEST Survey X: what powers merger induced star formation?

ABSTRACT Galaxy mergers are known to trigger both extended and central star formation. However, what remains to be understood is whether this triggered star formation is facilitated by enhanced star formation efficiencies (SFEs), or an abundance of molecular gas fuel. This work presents spatially resolved measurements of CO emission collected with the Atacama Large Millimetre Array (ALMA) for 20 merging galaxies (either pairs or post-mergers) selected from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey. Eleven additional merging galaxies are selected from the ALMA MaNGA QUEnching and STar formation (ALMaQUEST) survey, resulting in a set of 31 mergers at various stages of interaction and covering a broad range of star formation rates (SFRs). We investigate galaxy-to-galaxy variations in the resolved Kennicutt–Schmidt relation, (rKS: $\Sigma _{\textrm {H}_2}$ versus ΣSFR), the resolved molecular gas main sequence (rMGMS: Σ⋆ versus $\Sigma _{\textrm {H}_2}$), and the resolved star-forming main sequence (rSFMS: Σ⋆ versus ΣSFR). We quantify offsets from these resolved relations to determine if SFR, molecular gas fraction, or/and SFE is/are enhanced in different regions of an individual galaxy. By comparing offsets in all three parameters, we can discern whether gas fraction or SFE powers an enhanced ΣSFR. We find that merger-induced star formation can be driven by a variety of mechanisms, both within a galaxy and between different mergers, regardless of interaction stage.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2

Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic’s evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (M pro ), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. Here, this work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic “warhead” to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of M pro with micromolar affinities (K I of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quantum dynamics of cold atomic gas with SU(1,1) symmetry

Motivated by recent advances in quantum dynamics, we investigate the dynamics of the system with SU(1,1) symmetry. Instead of performing the time-ordered integral for the evolution operator of the time-dependent Hamiltonian, we show that the time evolution operator can be expressed as an SU(1,1) group element. Since the SU(1,1) group describes the “rotation” on a hyperbolic surface, the dynamics can be visualized on a Poincaré disk, a stereographic projection of the upper hyperboloid. As an example, we present the trajectory of the revival of Bose-Einstein condensation and that of the scale-invariant Fermi gas on the Poincaré disk. Further considering quantum gases in an oscillating lattice, we also study the dynamics of the system with time-dependent single-particle dispersion.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Nramp: Deprive and conquer?

Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.

59 BASIC BIOLOGICAL SCIENCES↗