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DOE OSTI2024

Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures

ABSTRACT The development of synthetic microbial consortia in recent years has revealed that complex interspecies interactions, notably the exchange of cytoplasmic material, exist even among organisms that originate from different ecological niches. Although morphogenetic characteristics, viable RNA and protein dyes, and fluorescent reporter proteins have played an essential role in exploring such interactions, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to further investigate interactions in synthetic or semisynthetic consortia. Despite its maturity, several challenges exist in using rRNA-FISH as a tool to quantify individual species population dynamics and interspecies interactions using high-throughput instrumentation such as flow cytometry. In this work, we resolve such challenges and apply rRNA-FISH to double and triple co-cultures of Clostridium acetobutylicum, Clostridium ljungdahlii, and Clostridium kluyveri . In pursuing our goal to capture each organism’s population dynamics, we demonstrate dynamic rRNA, and thus ribosome, exchange between the three species leading to the formation of hybrid cells. We also characterize the localization patterns of the translation machinery in the three species, identifying distinct, dynamic localization patterns among them. Our data also support the use of rRNA-FISH to assess the culture’s health and expansion potential, and, here again, our data find surprising differences among the three species examined. Taken together, our study argues for rRNA-FISH as a valuable and accessible tool for quantitative exploration of interspecies interactions, especially in organisms which cannot be genetically engineered or in consortia where selective pressures to maintain recombinant species cannot be used. IMPORTANCE Though dyes and fluorescent reporter proteins have played an essential role in identifying microbial species in co-cultures, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to quantitatively probe complex interactions between organisms in synthetic consortia. Despite its maturity, several challenges existed before rRNA-FISH could be used to study Clostridium co-cultures of interest. First, species-specific probes for Clostridium acetobutylicum and Clostridium ljungdahlii had not been developed. Second, “state-of-the-art” labeling protocols were tedious and often resulted in sample loss. Third, it was unclear if FISH was compatible with existing fluorescent reporter proteins. We resolved these key challenges and applied the technique to co-cultures of C. acetobutylicum , C. ljungdahlii , and Clostridium kluyveri . We demonstrate that rRNA-FISH is capable of identifying rRNA/ribosome exchange between the three organisms and characterized rRNA localization patterns in each. In combination with flow cytometry, rRNA-FISH can capture sub-population dynamics in co-cultures.

Hill, John D.↗

DOE OSTI2015

A taste of dark matter: Flavour constraints on pseudoscalar mediators

Dark matter interacting via the exchange of a light pseudoscalar can induce observable signals in indirect detection experiments and experience large self-interactions while evading the strong bounds from direct dark matter searches. The pseudoscalar mediator will however induce flavour-changing interactions in the Standard Model, providing a promising alternative way to test these models. We investigate in detail the constraints arising from rare meson decays and fixed target experiments for different coupling structures between the pseudoscalar and Standard Model fermions. The resulting bounds are highly complementary to the information inferred from the dark matter relic density and the constraints from primordial nucleosynthesis. We discuss the implications of our findings for the dark matter self-interaction cross section and the prospects of probing dark matter coupled to a light pseudoscalar with direct or indirect detection experiments. In particular, we find that a pseudoscalar mediator can only explain the Galactic Centre excess if its mass is above that of the B mesons, and that it is impossible to obtain a sufficiently large direct detection cross section to account for the DAMA modulation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Universal Jaynes-Cummings Control of an Oscillator

The Jaynes-Cummings (JC) interaction-the coherent exchange of excitations between a two-level system and a harmonic oscillator-is one of the fundamental interactions of quantum optics, realized across platforms such as cavity quantum electrodynamics, trapped ions, mechanical resonators, and superconducting circuits. Although JC interactions and qubit rotations form a universal gate set for oscillator control, practical implementations have not been demonstrated. Here we develop and experimentally demonstrate universal JC-based oscillator control by compiling arbitrary unitary gates into sequences of JC interactions and qubit rotations. In our experiment, the oscillator is realized using a mode of a high quality factor microwave cavity and the ancilla qubit using a superconducting transmon circuit, with the JC interaction implemented by a sideband interaction enabled by the Josephson nonlinearity. The native gates are constructed to be closed below a chosen cutoff photon number, encoding a qudit with suppressed leakage errors, while ancilla relaxation errors are detectable. We further find that the dispersive shift serves as a compilation resource that reduces circuit depths. We demonstrate universal qudit control and implement a single-qutrit gate set with a mean post-selected process fidelity of 96%, as well as ququart and ququint shift gates. These results establish Jaynes-Cummings control as a practical route to universal oscillator control, enabling programmable bosonic processors across a variety of quantum platforms.

Huang, Jordan [Rutgers U., Piscataway]↗

DOE OSTI2020

Mobile orbitons in Ca 2 CuO 3 : Crucial role of Hund's exchange

We investigate the Cu L 3 edge resonant inelastic x-ray scattering (RIXS) spectra of a quasi-1D antiferromagnet Ca 2 CuO 3 . In addition to the magnetic excitations, which are well-described by the two-spinon continuum, we observe two dispersive orbital excitations, the 3d xy and the 3d yz orbitons. We carry out a quantitative comparison of the RIXS spectra, obtained with two distinct incident polarizations, with a theoretical model. We show that any realistic spin-orbital model needs to include a finite, but realistic, Hund's exchange J H ≈ 0.5 eV . Its main effect is an increase in orbiton velocities, so that their theoretically calculated values match those observed experimentally. Even though Hund's exchange also mediates some interaction between spinon and orbiton, the picture of spin-orbit separation remains intact and describes orbiton motion in this compound.

1-dimensional spin chains↗

DOE OSTI2020

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Interactive effects of elevated CO 2 , warming, reduced rainfall, and nitrogen on leaf gas exchange in five perennial grassland species

Abstract Global changes can interact to affect photosynthesis and thus ecosystem carbon capture, yet few multi‐factor field studies exist to examine such interactions. Here, we evaluate leaf gas exchange responses of five perennial grassland species from four functional groups to individual and interactive global changes in an open‐air experiment in Minnesota, USA, including elevated CO 2 (eCO 2 ), warming, reduced rainfall and increased soil nitrogen supply. All four factors influenced leaf net photosynthesis and/or stomatal conductance, but almost all effects were context‐dependent, i.e. they differed among species, varied with levels of other treatments and/or depended on environmental conditions. Firstly, the response of photosynthesis to eCO 2 depended on species and nitrogen, became more positive as vapour pressure deficit increased and, for a C 4 grass and a legume, was more positive under reduced rainfall. Secondly, reduced rainfall increased photosynthesis in three functionally distinct species, potentially via acclimation to low soil moisture. Thirdly, warming had positive, neutral or negative effects on photosynthesis depending on species and rainfall. Overall, our results show that interactions among global changes and environmental conditions may complicate predictions based on simple theoretical expectations of main effects, and that the factors and interactions influencing photosynthesis vary among herbaceous species.

Pastore, Melissa A.↗

NASA NTRSDate not supplied

Immutable Secure Data Exchange and Storage for Urban Air Mobility Environments

Urban air mobility (UAM) is a concept that proposes to develop short-range aerial vehicles to overcome increasing surface congestion. Within the UAM environment, UAM operators work collaboratively to manage aerial vehicles in the urban environment. Providers of Services for UAM (PSU), UAM operators, and Supplemental Data Service Providers (SDSP) provide services to support flight operations within the UAM environment. The growth in the development of UAM systems, and the associated data exchange and service interactions will be at risk due to numerous types of cybersecurity attacks. To address these challenges, this research focuses on the secure data exchange and storage of this decentralized UAM environment. The intent of this research is to leverage a permissioned blockchain approach to address cybersecurity threats that may impact a UAM environment.

Urban Air Mobility↗

NASA NTRSDate not supplied

Immutable Secure Data Exchange and Storage for Urban Air Mobility Environments

Urban Air Mobility↗

NASA NTRS1982

A comparison of experimental and computer model results on the charge-exchange plasma flow from a 30 cm mercury ion thruster

Ion thrusters can be used in a variety of primary and auxiliary space-propulsion applications. A thruster produces a charge-exchange plasma which can interact with various systems on the spacecraft. The propagation of the charge-exchange plasma is crucial in determining the interaction of that plasma with the spacecraft. This paper compares experimental measurements with computer model predictions of the propagation of the charge-exchange plasma from a 30 cm mercury ion thruster. The plasma potentials, and ion densities, and directed energies are discussed. Good agreement is found in a region upstream of, and close to, the ion thruster optics. Outside of this region the agreement is reasonable in view of the modeling difficulties.

Gabriel, S. B.↗

NASA NTRS2023

A Blockchain Case Study for Urban Air Mobility Operational Intent

To realize the potential of Urban Air Mobility (UAM), an assurance of cybersecurity is critical for public acceptance. UAM is a concept that proposes to develop short-range, point-to-point transportation systems in metropolitan areas using vertical takeoff and landing (VTOL) aircraft to overcome increasing surface congestion. The growth in the development of UAM systems, and the associated data exchange and service interactions will be at risk due to numerous types of cybersecurity attacks. The intent of this work is to leverage a permissioned blockchain to simulate secure data exchange and storage for the UAM operational intent use case. In this case study, two vehicle operators are operating in the same airspace. Their intent is to fly vehicles that land at a shared vertiport, securely.

Urban Air Mobility↗

NASA NTRSDate not supplied

A Blockchain Case Study for Urban Air Mobility Operational Intent

UAM↗

NASA NTRS2023

A Blockchain Case Study for Urban Air Mobility Operational Intent

UAM↗

DOE OSTI2020

Turbulent exchanges between near-inertial waves and balanced flows

Wind generated near-inertial waves are ubiquitous in the upper ocean. An improved understanding of near-inertial wave dynamics following their excitation in the ocean and their subsequent interaction with mesoscale geostrophic balanced flows is key to decoding oceanic energy flow pathways. In this regard, multiple oceanic data sets accumulated over the past few decades reveal that the relative strength of near-inertial waves and geostrophic balanced eddy fields is highly variable, both geographically and seasonally. Inspired by these observations, we investigate turbulent interactions and energy exchanges between near-inertial waves and balanced flows using freely evolving numerical simulations of the non-hydrostatic Boussinesq equations. Here, we find accelerated vertical propagation and dissipation of the waves in regimes where balanced and wave fields have comparable strengths. In such regimes we also find that near-inertial waves directly extract energy from balanced flows, with O(10%) being the amount of balanced energy loss. In contrast, we find that near-inertial waves transfer energy to balanced flows in regimes where balance-to-wave energy ratio is small, with the gain in balanced energy being dependent on the relative strength of waves. Furthermore, these regimes are characterized by relatively weaker vertical propagation and dissipation of the near-inertial wave field. One of the key outcomes of this study is the demonstration of the lack of a unique direction for near-inertial wave-balanced flow energy transfers. Depending on the balance-to-wave energy ratio, near-inertial waves can act as an energy sink or energy source for the geostrophic balanced flow.

58 GEOSCIENCES↗

DOE OSTI2017

Better band gaps for wide-gap semiconductors from a locally corrected exchange-correlation potential that nearly eliminates self-interaction errors

Here, this work constitutes a comprehensive and improved account of electronic-structure and mechanical properties of silicon-nitride (${\rm Si}_{3}$ ${\rm N}_{4}$ ) polymorphs via van Leeuwen and Baerends (LB) exchange-corrected local density approximation (LDA) that enforces the exact exchange potential asymptotic behavior. The calculated lattice constant, bulk modulus, and electronic band structure of ${\rm Si}_{3}$ ${\rm N}_{4}$ polymorphs are in good agreement with experimental results. We also show that, for a single electron in a hydrogen atom, spherical well, or harmonic oscillator, the LB-corrected LDA reduces the (self-interaction) error to exact total energy to ~10%, a factor of three to four lower than standard LDA, due to a dramatically improved representation of the exchange-potential.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

dynamics of organic-mineral interactions at the metal oxide-solution interface as studied via binding energetics (Final report)

This project focused on addressing longstanding fundamental and experimental uncertainties on how dissolved organic substances (DOS) interact with metal oxide surface under environmentally relevant conditions. By leveraging a custom-built real-time, in-tandem flow adsorption microcalorimetry-UV-Vis/fluorescence spectroscopy platform, we characterized the binding energetics, kinetics and mechanistic pathways driving DOS-metal oxide interactions at temporal resolution on the order of 1-5 seconds. We studied a diverse suite of model organic compounds/substances – including monocarboxylates (e.g. acetate and benzoate), di-carboxylates (oxalate and succinate), amino acids, amino-based nanparticles and natural organic matter – interacting at the mineral-water interface of structurally- and/or chemically distinct metal oxides (including SiO2, boehmite, ferrihydrite, and γ-Al2O3). Our results indicated that DOS-metal oxide interactions are governed by multi-step reaction pathways, often switching between distinct, resolvable enthalpy- and entropy-driven non-electrostatic or electrostatic configurations. To quantify these interactions, we developed and implemented an analytical workflow that integrates peak deconvolution and Monte-Carlo based error propagation to determine site-specific thermodynamic and kinetic parameters for individual binding/debinding events. In addition to resolving apparent first-order rate constants of each event, we were able to quantify associated apparent equilibrium constants as well as free energy, enthalpy and entropy contribution to the activation and subsequent progression of the binding/debinding process across compounds, compound class and metal oxide surfaces. The kinetic-thermodynamic data produced in this study captured how the interplay between oxide surface reactivity and DOS molecular structure jointly drives binding-debinding dynamics. Notably, that at pH below PZC of the oxide surface, neutral species were heavily involved in monocarboxylate binding, while anionic species drove dicarboxylate binding. Also, that among amino acids 1) positional isomers show distinctive binding characteristics to each other while enantiomers show no significant differences in binding characteristics, 2) molecules that bind via outer-sphere complexation show a larger entropic shift between binding and debinding with no impact on oxide surface while 3) inner-sphere interactions increased anion exchange capacity of the oxide surface. The new insights and data from this work has great potential for improving predictive modeling of carbon dynamics and specifically organic-mineral interactions in environmental and industrial systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Calculating field emission current in nanodiodes—A multi-group formalism with space charge and exchange-correlation effects

Inclusion of electron-electron interaction is essential in nano-diodes to understand the underlying physical phenomenon and tailor devices accordingly. However, both space charge and exchange-correlation interaction involve electrons at different energies and hence a self-consistent multi-energy-group solution of the Schrödinger-Poisson system is required. It is shown here that the existence of a limiting density-dependent potential at low applied voltages allows calculation of the field emission current. Despite additional interactions, a Fowler-Nordheim behaviour is observed. It is also found that the exchange-correlation potential dominates at these voltages in nanogaps and possibly leads to a higher turn-on voltage.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

NASA NTRS1976

Effect of polarization on superfluidity in low density neutron matter

The singlet-state quasi-particle interaction in neutron matter is examined on the basis of results of a detailed evaluation of the Landau Fermi-liquid parameters for pure neutron effects, including polarization effects. This means that the interaction induced by exchange of density and spin-density excitations is taken into account. It is shown that polarization actually works to suppress the pairing matrix elements, owing to the spin dependence of the quasi-particle interaction and, ultimately, the balance of attraction, repulsion, and spin dependence in the fundamental two-neutron interaction. Since the isotropic energy gap and the condensation energy in low-density neutron-star matter are extremely sensitive functions of the pairing matrix elements, they will also be suppressed by the polarizability of the neutron medium.

Clark, J. W.↗

NASA NTRSDate not supplied

A Blockchain Case Study for Urban Air Mobility Operational Intent

The next generation of aerial passenger and cargo transportation may leverage the concept of Urban Air Mobility (UAM). UAM is a concept that proposes to develop short-range, point-to-point transportation systems in metropolitan areas using vertical takeoff and landing (VTOL) or short takeoff and landing (STOL) aircraft to overcome increasing surface congestion [1]. The UAM concept leverages a decentralized service-based architecture for airspace solutions. Within the environment, UAM operators work collaboratively to manage aerial vehicles in the urban environment. Providers of Services for UAM (PSU), UAM operators, and Supplemental Data Service Providers (SDSP) provide services to support flight operations within the UAM environment. Also, various views of UAM flight information are provided to the public and public safety entities [2]. The Federal Aviation Administration (FAA) can coordinate flight information between the FAA controlled National Airspace System (NAS) and the UAM environments through the FAA-Industry Data Exchange Protocol (FIDXP). To realize the potential of UAM, an assurance of cybersecurity is critical for public acceptance. Cybersecurity has come to the forefront highlighting the need to protect these networks and systems from cyberattacks. The growth in the development of UAM systems, and the associated data exchange and service interactions will be at risk due to numerous types of cybersecurity attacks. As these threats evolve, the UAM cybersecurity capabilities must adapt to these changes as well [3]. This research focuses on the secure data exchange and storage of this decentralized UAM environment to address these challenges. This research intends to leverage a permissioned blockchain approach to address cybersecurity threats that may impact a UAM environment. Blockchain technologies can be used for tracking transactions and verifying negotiated agreements between stakeholders in the NAS environment. For example, the record of the submitted flight plan and the approved flight plan could be verified using the Blockchain-based immutable ledger.

UAM↗