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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 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

‘ Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. Here, we describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160 ± 3 μmol L -1 d -1 . The DCM degrader attained 5.25 × 10 7 ± 1.0 × 10 7 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4 ± 0.8 μm long and 0.4 ± 0.1 μm wide. Furthermore, based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, ‘Candidatus Dichloromethanomonas elyunquensis’.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2018

Atomic Orbital Implementation of Extended Symmetry-Adapted Perturbation Theory (XSAPT) and Benchmark Calculations for Large Supramolecular Complexes

We report an implementation of extended symmetry-adapted perturbation theory (XSAPT) in the atomic orbital basis, extending this method to systems where the monomers are large. In our “XSAPT(KS)” approach, monomers are described using range-separated Kohn–Sham (KS) density functional theory (DFT), with correct asymptotic behavior set by tuning the range-separation parameter ω in a monomer-specific way. This is accomplished either by conventional ionization potential (IP)-based tuning, in which ω is adjusted to satisfy the condition ε HOMO (ω) = -IP(ω), or else using a “global density-dependent” (GDD) condition, in which ω is fixed based on the size of the exchange hole. The latter procedure affords better results for both total interaction energies and energy components, when used in conjunction with our third-generation pairwise atom–atom dispersion potential (+aiD 3 ). Three-body (triatomic) dispersion terms are found to be important when the monomers are large, and we incorporate these by means of an Axilrod–Teller–Muto term, E disp,3B ATM , which reduces errors in supramolecular interaction energies by about a factor of 2. The XSAPT(KS) + aiD 3 + E disp,3B ATM (ωGDD) approach affords mean absolute errors as low as 1.2 and 4.2 kcal/mol, respectively, for the L7 and S12L benchmark test sets of large dimers. Such errors are comparable to those afforded by far more expensive methods, such as DFT-SAPT, and the closely related second-order perturbation theory with coupled dispersion (MP2C). We also survey the performance of various other quantum-chemical methods for these data sets and identify several semiempirical and DFT-based approaches whose accuracy approaches that of MP2C, at dramatically reduced cost.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Simple Model for the Benzene Hexafluorobenzene Interaction

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions, and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2017

Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase

Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. In this work, we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also highlights why tRNAPyl recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme. Furthermore, using standard microbiological culture equipment, we established a new method for laboratory evolution—a noncontinuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. Finally, we employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a noncanonical amino acid.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization’s goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2015

Three-dimensional imaging of the ultracold plasma formed in a supersonic molecular beam

Double-resonant excitation of nitric oxide in a seeded supersonic molecular beam forms a state-selected Rydberg gas that evolves to form an ultracold plasma. This plasma travels with the propagation of the molecular beam in z over a variable distance as great as 600 mm to strike an imaging detector, which records the charge distribution in the dimensions, x and y. The ω{sub 1} + ω{sub 2} laser crossed molecular beam excitation geometry convolutes the axial Gaussian distribution of NO in the molecular beam with the Gaussian intensity distribution of the perpendicularly aligned laser beam to create an ellipsoidal volume of Rydberg gas. Detected images describe the evolution of this initial density as a function of selected Rydberg gas initial principal quantum number, n{sub 0}, ω{sub 1} laser pulse energy (linearly related to Rydberg gas density, ρ{sub 0}) and flight time. Low-density Rydberg gases of lower principal quantum number produce uniformly expanding, ellipsoidal charge-density distributions. Increase either of n{sub 0} or ρ{sub 0} breaks the ellipsoidal symmetry of plasma expansion. The volume bifurcates to form repelling plasma volumes. The velocity of separation depends on n{sub 0} and ρ{sub 0} in a way that scales uniformly with ρ{sub e}, the density of electrons formed in the core of the Rydberg gas by prompt Penning ionization. Conditions under which this electron gas drives expansion in the long axis dimension of the ellipsoid favours the formation of counter-propagating shock waves.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Non-linear non-local molecular electrodynamics with nano-optical fields

The interaction of optical fields sculpted on the nano-scale with matter may not be described by the dipole approximation since the fields may vary appreciably across the molecular length scale. Rather than incrementally adding higher multipoles, it is advantageous and more physically transparent to describe the optical process using non-local response functions that intrinsically include all multi-poles. In this work, we present a semi-classical approach for calculating non-local response functions based on the minimal coupling Hamiltonian. The first, second, and third order response functions are expressed in terms of correlation functions of the charge and the current densities. Finally, this approach is based on the gauge invariant current rather than the polarization, and on the vector potential rather than the electric and magnetic fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2015

Contact interaction in an unitary ultracold Fermi gas

An ultracold Fermi atomic gas at unitarity presents universal properties that in the dilute limit can be well described by a contact interaction. By employing a guiding function with correct boundary conditions and making simple modifications to the sampling procedure we are able to calculate the properties of a true contact interaction with the diffusion Monte Carlo method. The results are obtained with small variances. Our calculations for the Bertsch and contact parameters are in excellent agreement with published experiments. The possibility of using a more faithful description of ultracold atomic gases can help uncover additional features of ultracold atomic gases. In addition, this work paves the way to perform quantum Monte Carlo calculations for other systems interacting with contact interactions, where the description using potentials with finite effective range might not be accurate.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
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↗