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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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At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. Here, the spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review,we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.

42 ENGINEERING↗
DOE OSTI2022

Instanton Effects in Euclidean vacuum, Real Time Production, and in the Light-front Wave Functions

Nontrivial topological structures of non-Abelian gauge fields were discovered in the 1970s. Instanton solutions, describing vacuum tunneling through topological barriers, have fermionic zero modes which are at the origin of ‘t Hooft effective Lagrangian. In the 1980s, instanton ensembles have been used to explain chiral symmetry breaking. In the 1990s, a large set of numerical simulations were performed deriving Euclidean correlation functions. The special role of scalar diquarks in nucleons and color superconductivity in dense quark matter has been elucidated. In these lectures, we discuss further developments of physics related to gauge topology. We show that the instanton–anti-instanton “streamline” configurations describe “sphaleron transitions” in high-energy collisions, which result in production of hadronic clusters with nontrivial topological/chiral charges. (They are not yet observed, but discussions of dedicated experiments at the LHC and RHIC are ongoing.) Another new direction is instanton effects in hadronic spectroscopy, both in the rest frame and on the light front. We will discuss their role in central and spin-dependent potentials, form factors and antiquark nuclear “sea”. Finally, we summarize the advances in the semiclassical theory of deconfinement, and chiral phase transitions at finite temperature, in QCD, and in some of its “deformed” versions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Monolayer Vanadium‐Doped Tungsten Disulfide: A Room‐Temperature Dilute Magnetic Semiconductor

Abstract Dilute magnetic semiconductors (DMS), achieved through substitutional doping of spin‐polarized transition metals into semiconducting systems, enable experimental modulation of spin dynamics in ways that hold great promise for novel magneto–electric or magneto–optical devices, especially for two‐dimensional (2D) systems such as transition metal dichalcogenides that accentuate interactions and activate valley degrees of freedom. Practical applications of 2D magnetism will likely require room‐temperature operation, air stability, and (for magnetic semiconductors) the ability to achieve optimal doping levels without dopant aggregation. Here, room‐temperature ferromagnetic order obtained in semiconducting vanadium‐doped tungsten disulfide monolayers produced by a reliable single‐step film sulfidation method across an exceptionally wide range of vanadium concentrations, up to 12 at% with minimal dopant aggregation, is described. These monolayers develop p‐type transport as a function of vanadium incorporation and rapidly reach ambipolarity. Ferromagnetism peaks at an intermediate vanadium concentration of ~2 at% and decreases for higher concentrations, which is consistent with quenching due to orbital hybridization at closer vanadium–vanadium spacings, as supported by transmission electron microscopy, magnetometry, and first‐principles calculations. Room‐temperature 2D‐DMS provide a new component to expand the functional scope of van der Waals heterostructures and bring semiconducting magnetic 2D heterostructures into the realm of practical application.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Methanobactin: A Novel Copper-Binding Compound Produced by Methanotrophs

Aerobic methanotrophs are a novel group of microorganisms that play a critical role in the global carbon cycle. Expression and activity of a key enzyme in the metabolism in these microbes, the methane monooxygenase, is controlled by the availability of copper. To sequester copper, some methanotrophs produce a ribosomally synthesized post-translationally modified polypeptide called methanobactin. Here, this peptide, or chalkophore, has unique features, with all known forms being small (< 1300 Da) with two heterocyclic rings with associated thioamide groups that bind copper quite strongly. Here we provide an overview of the known diversity of methanobactins, describe the genetics underlying methanobactin biosynthesis, the variety of functions methanobactin has been observed to have, as well as various environmental, industrial and medical applications of methanobactin.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Modeling rarefied gas chemistry with QuiPS, a novel quasi-particle method

The goal of this work is to build up the capability of quasi-particle simulation (QuiPS), a novel flow solver, such that it can adequately model the rarefied portion of an atmospheric reentry trajectory. Direct simulation Monte Carlo (DSMC) is the conventional solver for such conditions, but struggles to resolve transient flows, trace species, and high-level internal energy states due to stochastic noise. Quasi-particle simulation (QuiPS) is a novel Boltzmann solver that describes a system with a discretized, truncated velocity distribution function. The resulting fixed-velocity, variable weight quasi-particles enable smooth variation of macroscopic properties. The distribution function description enables the use of a variance-reduced collision model, greatly minimizing expense near equilibrium. This work presents the addition of a neutral air chemistry model to QuiPS and some demonstrative 0D simulations. The explicit representation of internal distributions in QuiPS reveals some of the flaws in existing physics models. Overall, variance reduction, a key feature of QuiPS, can greatly reduce expense of multi-dimensional calculations, but is only cheaper when the gas composition is near chemical equilibrium.

42 ENGINEERING↗
DOE OSTI2026

Isospin symmetry holds beyond the proton drip line: First observation of excited states in 55Cu

Isospin symmetry, combined with shell-model description, has long been successful in reproducing nuclear structure and predicting mirror energy differences. However, these descriptions have been primarily limited to mirror nuclei with well-bound ground states. As one approaches the proton drip line, coupling to the continuum becomes important. Despite this, little is known about medium-mass nuclei at the drip line. Here we report the measurement of the excitation energies of several unbound states in a nucleus beyond the proton drip line, 55Cu, performed via γ-ray spectroscopy at the Radioactive Isotope Beam Factory (RIKEN). Several low-lying yrast states are observed to decay predominantly by γ-ray emission. In contrast, the state–predicted to be strongly populated in the one-proton knockout reaction–is notably absent, suggesting that it decays primarily via prompt proton emission. We show that even for such an unbound system, shell-model calculations based on a harmonic oscillator potential reproduce the observed mirror energy differences remarkably well in all the observed states. Based on this result, we propose that a general pattern might emerge where, in medium-mass systems at the proton drip line, the stronger Coulomb barrier together with the centrifugal barrier effectively confines the wave functions, so that the shell model is able to describe low-lying states, enabling accurate predictions of mirror energy differences between isobaric analogue states.

Pigliapoco, S [Dipartimento di Fisica e Astronomia↗
DOE OSTI2024

NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials

Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Idea2Data: Toward a New Paradigm for Drug Discovery

Increasing the success rate and throughput of drug discovery will require efficiency improvements throughout the process that is currently used in the pharmaceutical community, including the crucial step of identifying hit compounds to act as drivers for subsequent optimization. Hit identification can be carried out through large compound collection screening and frequently involves the generation and testing of many hypotheses based on available knowledge. In practice, hypothesis generation can involve the selection of promising chemical structures from compound collections using predictive models built from previous screening/ assay results. Available physical collections, typically used during hit identification, are of the order of 10 6 compounds but represent only a small fraction of the small molecule drug-like chemical space. In an effort to survey a larger portion of chemical space and eliminate inefficiencies during hit identification, we introduce a new process, termed Idea2Data (I2D) that tightly integrates computational and experimental components of the drug discovery process. I2D provides the ability to connect a vast virtual collection of compounds readily synthesizable on automated synthesis systems with computational predictive models for the identification of promising structures. This new paradigm enables researchers to process billions of virtual molecules and select structures that can be prepared on automated systems and made available for biological testing, allowing for timely hypothesis testing and follow-up. Since its introduction, I2D has positively impacted several portfolio efforts through identification of new chemical scaffolds and functionalization of existing scaffolds. In this Innovations paper, we describe the I2D process and present an application for the discovery of new ULK inhibitors.

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

Magnetoelectric Coupling in a Mn 4 Na–Organic Complex under Pulsed Magnetic Fields up to 73 T

Research on the magnetoelectric (ME) effect (or spin-electric coupling) in molecule-based magnetic materials is a relatively nascent but promising topic. Molecule-based magnetic materials have diverse magnetic functionalities that can be coupled to electrical properties. Here, in this study, we investigate a realization of ME coupling that is fundamental but not heavily studied─the coupling of magnetic spin level crossings to changes in electric polarization. A mixed-valence Mn 4 Na complex with a total ground-state spin S = 5/2 under zero magnetic field and S = 17/2 under high magnetic field undergoes a cascade of ground-state level crossings of the S z states with increasing magnetic field. Magnetization and electrical polarization measurements under pulsed magnetic fields up to 73 T show that each spin level crossing is accompanied by a significant change in electric polarization that is an even function of the applied magnetic field. A molecular Hamiltonian describing antiferromagnetic exchange in a distorted tetrahedron of three Mn III and one Mn II ions matches the data well. We conclude that the ME coupling is caused by magnetostriction within the polar molecule as it distorts to lower its magnetic exchange energy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

The 2021 update of the EPA’s adverse outcome pathway database

The EPA developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Here we present the most recent version of the EPA Adverse Outcome Pathway Database (AOP-DB), version 2. AOP-DB v.2 introduces several substantial updates, which include automated data pulls from the AOP-Wiki 2.0, the integration of tissue-gene network data, and human AOP-gene data by population, semantic mapping and SPARQL endpoint creation, in addition to the presentation of the first publicly available AOP-DB web user interface. Potential users of the data may investigate specific molecular targets of an AOP, the relation of those gene/protein targets to other AOPs, cross-species, pathway, or disease-AOP relationships, or frequencies of AOP-related functional variants in particular populations, for example. Version updates described herein help inform new testable hypotheses about the etiology and mechanisms underlying adverse outcomes of environmental and toxicological concern.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phyla

Abstract Pyrosomes are tunicates in the phylum Chordata, which also contains vertebrates. Their gigantic blooms play important ecological and biogeochemical roles in oceans. Pyrosoma , meaning “fire-body”, derives from their brilliant bioluminescence. The biochemistry of this light production is unknown, but has been hypothesized to be bacterial in origin. We found that mixing coelenterazine—a eukaryote-specific luciferin—with Pyrosoma atlanticum homogenate produced light. To identify the bioluminescent machinery, we sequenced P. atlanticum transcriptomes and found a sequence match to a cnidarian luciferase (RLuc). We expressed this novel luciferase (PyroLuc) and, combined with coelenterazine, it produced light. A similar gene was recently predicted from a bioluminescent brittle star, indicating that RLuc-like luciferases may have evolved convergently from homologous dehalogenases across phyla (Cnidaria, Echinodermata, and Chordata). This report indicates that a widespread gene may be able to functionally converge, resulting in bioluminescence across animal phyla, and describes and characterizes the first putative chordate luciferase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Quantifying local and global mass balance errors in physics-informed neural networks

Physics-informed neural networks (PINN) have recently become attractive for solving partial differential equations (PDEs) that describe physics laws. By including PDE-based loss functions, physics laws such as mass balance are enforced softly in PINN. This paper investigates how mass balance constraints are satisfied when PINN is used to solve the resulting PDEs. We investigate PINN’s ability to solve the 1D saturated groundwater flow equations (diffusion equations) for homogeneous and heterogeneous media and evaluate the local and global mass balance errors. We compare the obtained PINN’s solution and associated mass balance errors against a two-point finite volume numerical method and the corresponding analytical solution. We also evaluate the accuracy of PINN in solving the 1D saturated groundwater flow equation with and without incorporating hydraulic heads as training data. We demonstrate that PINN’s local and global mass balance errors are significant compared to the finite volume approach. Tuning the PINN’s hyperparameters, such as the number of collocation points, training data, hidden layers, nodes, epochs, and learning rate, did not improve the solution accuracy or the mass balance errors compared to the finite volume solution. Mass balance errors could considerably challenge the utility of PINN in applications where ensuring compliance with physical and mathematical properties is crucial.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A methodology to compute the critical current limit in Nb3Sn magnets

Numerous experiments have shown that the loads applied to Nb3Sn strands and cables can reduce their critical current. Experiments, performed on uniaxially loaded strands, allowed to define clear laws to describe the evolution of the critical surface as a function of the applied current, field, temperature and strain. It is, however, still unclear how these laws can be applied to superconducting magnets. The present paper proposes a methodology to estimate the critical current and temperature margin reduction on superconducting magnets due to stress on the superconducting material. The methodology is tested on the MQXF magnets, a quadrupole developed for the High Luminosity LHC project, and successfully validated by comparing computed strain with data from strain gauge measurements. Overall, results suggested that, because of the stresses arising in winding during assembly, cool-down and powering, the current limit of the magnet is lower than the expected short sample limit, and that the most critical region does not coincide with the peak field location.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Gibbs mixing of partially distinguishable photons with a polarising beamsplitter membrane

For a thought experiment concerning the mixing of two classical gases, Gibbs concluded that the work that can be extracted from mixing is determined by whether or not the gases can be distinguished by a semi-permeable membrane; that is, the mixing work is a discontinuous function of how similar the gases are. Here we describe an optomechanical setup that generalises Gibbs’ thought experiment to partially distinguishable quantum gases. Specifically, we model the interaction between a polarisation dependent beamsplitter, that plays the role of a semi-permeable membrane, and two photon gases of non-orthogonal polarisation. We find that the work arising from the mixing of the gases is related to the potential energy associated with the displacement of the microscopic membrane, and we derive a general quantum mixing work expression, valid for any two photon gases with the same number distribution. The quantum mixing work is found to change continuously with the distinguishability of the two polarised gases. In addition, fluctuations of the work on the microscopic membrane become important, which we calculate for Fock and thermal states of the photon gases. Our findings generalise Gibbs’ mixing to the quantum regime and open the door for new quantum thermodynamic (thought) experiments with quantum gases with non-orthogonal polarisations and microscopic pistons that can distinguish orthogonal polarisations.

distinguishability↗
DOE OSTI2020

High-throughput mapping of the phage resistance landscape in E. coli

Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Vibronic States and Their Effect on the Temperature and Strain Dependence of Silicon-Vacancy Qubits in 4$\textit{H}$-SiC

Silicon-vacancy qubits in silicon carbide ( Si C ) are emerging tools in quantum-technology applications due to their excellent optical and spin properties. In this paper, we explore the effect of temperature and strain on these properties by focusing on the two silicon-vacancy qubits, V1 and V2, in 4$\textit{H}$-SiC. We apply density-functional theory beyond the Born-Oppenheimer approximation to describe the temperature-dependent mixing of electronic excited states assisted by phonons. We obtain a polaronic gap of around 5 and 22 meV for the V1 and V2 centers, respectively, which results in a significant difference in the temperature-dependent dephasing and zero-field splitting of the excited states, which explains recent experimental findings. Finally, we also compute how crystal deformations affect the zero-phonon line of these emitters. Our predictions are important ingredients in any quantum applications of these qubits sensitive to these effects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗