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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Vorticity screening by dense layers

We investigate variable density layers in the presence of vortices, by analogy to line charges in the presence of a dielectric slab. We adapt solutions for dielectric layers from the literature to the variable density fluid case, obtaining exact hypergeometric expressions for flow velocities induced everywhere by a vortex in the vicinity of a finite-thickness slab of different densities. The dimensionless Atwood number, which appears naturally in other variable density phenomena, such as the Rayleigh–Taylor instability, reappears here as the natural ordering parameter for the influence of the slab, which acts primarily to screen the influence of vorticity across the slab to a lower effective circulation. The solution takes the form of scaling correction factors that might be applied to computational models or evaluated directly. Extensions, where vorticity is localized within the dense layer itself and amplified outside of it, are considered, as well as some speculative applications such as inertial confinement fusion capsule designs.

42 ENGINEERING↗
DOE OSTI2015

Long-range electrostatic screening in ionic liquids

Significance Liquid solutions with high concentrations of electrically charged ions are key elements of many energy storage technologies and are prevalent in biology. Nevertheless, they remain poorly understood. We study ionic liquids—liquids composed solely of ions—with the goal of providing a general picture of concentrated ionic solutions. Using molecular-scale experiments, we show that, surprisingly, less than 0.1% of the ions in ionic liquids are “free” to contribute to electrostatic screening, with the remainder “stuck” as neutral aggregates. Our temperature-dependent results provide fundamental guidance for designing high-performance ionic liquids for numerous applications. More broadly, we provide a novel way of envisioning concentrated ionic solutions with wide-ranging implications, such as elucidating the nanoscale properties of underwater bioadhesives and other self-assembled biomolecules.

Gebbie, Matthew A.↗
DOE OSTI2018

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen

The rapid emergence of antibiotic-resistant pathogenic bacteria has accelerated the search for new antibiotics. Many clinically used antibacterials were discovered through culturing a single microbial species under nutrient-rich conditions, but in the environment, bacteria constantly encounter poor nutrient conditions and interact with neighboring microbial species. In an effort to recapitulate this environment, we generated a nine-strain actinomycete community and used 16S rDNA sequencing to deconvolute the stochastic production of antimicrobial activity that was not observed from any of the axenic cultures. We subsequently simplified the community to just two strains and identified Amycolatopsis sp. AA4 as the producing strain and Streptomyces coelicolor M145 as an inducing strain. Bioassay-guided isolation identified amycomicin (AMY), a highly modified fatty acid containing an epoxide isonitrile warhead as a potent and specific inhibitor of Staphylococcus aureus . Amycomicin targets an essential enzyme (FabH) in fatty acid biosynthesis and reduces S. aureus infection in a mouse skin-infection model. The discovery of AMY demonstrates the utility of screening complex communities against specific targets to discover small-molecule antibiotics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

M06-SX screened-exchange density functional for chemistry and solid-state physics

Significance Density functionals with Hartree–Fock exchange have been widely used for a wide range of chemical applications, but the nonlocal character of exchange makes long-range exchange computationally expensive for solid-state calculations with periodic boundary conditions, and full exchange is nonphysical for condensed-phase systems. Here, we present a screened-exchange (SX) density functional, M06-SX, that is especially designed to have good accuracy for both solid-state physics and chemical applications with less computational cost than full Hartree–Fock exchange. The M06-SX functional gives accuracy comparable to functionals with full Hartree–Fock exchange for predicting chemical properties of molecules, while also being practical with good accuracy for plane wave calculations on band gaps and lattice constants of solids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Screened Hybrid and DFT + U Studies of the Structural, Electronic, and Optical Properties of U3O8

A systematic comparison of the structures and electronic and optical properties of U3O8 in the c2mm, P¯62m, and P21/m structures (the α, β, and γ phases, respectively) is performed using density functional theory + U (PBE + U) and the Heyd–Scuseria–Ernzerhof screened hybrid functional (HSE). The relationship between the semiconducting C2mm phase of U3O8 and the high temperature, metallic P¯62m phase is explored in more detail. Our calculated results show that the HSE functional gives a better description of the electronic and optical properties when compared with available experimental data for the α and β phases, but neither approach does particularly well for the high pressure γ phase.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2013

Screening the fifth force in the Horndeski's most general scalar-tensor theories

We study how the Vainshtein mechanism operates in the most general scalar-tensor theories with second-order equations of motion. The field equations of motion, which can be also applicable to most of other screening scenarios proposed in literature, are generally derived in a spherically symmetric space-time with a matter source. In the presence of a field coupling to the Ricci scalar, we clarify conditions under which the Vainshtein mechanism is at work in a weak gravitational background. We also obtain the solutions of the field equation inside a spherically symmetric body and show how they can be connected to exterior solutions that accommodate the Vainshtein mechanism. We apply our general results to a number of concrete models such as the covariant/extended Galileons and the DBI Galileons with Gauss-Bonnet and other terms. In these models the fifth force can be suppressed to be compatible with solar-system constraints, provided that non-linear field kinetic terms coupled to the Einstein tensor do not dominate over other non-linear field self-interactions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Astrophysical black holes in screened modified gravity

Chameleon, environmentally dependent dilaton, and symmetron gravity are three models of modified gravity in which the effects of the additional scalar degree of freedom are screened in dense environments. They have been extensively studied in laboratory, cosmological, and astrophysical contexts. In this paper, we present a preliminary investigation into whether additional constraints can be provided by studying these scalar fields around black holes. By looking at the properties of a static, spherically symmetric black hole, we find that the presence of a non-uniform matter distribution induces a non-constant scalar profile in chameleon and dilaton, but not necessarily symmetron gravity. An order of magnitude estimate shows that the effects of these profiles on in-falling test particles will be sub-leading compared to gravitational waves and hence observationally challenging to detect.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Weak lensing of large scale structure in the presence of screening

A number of alternatives to general relativity exhibit gravitational screening in the non-linear regime of structure formation. We describe a set of algorithms that can produce weak lensing maps of large scale structure in such theories and can be used to generate mock surveys for cosmological analysis. By analysing a few basic statistics we indicate how these alternatives can be distinguished from general relativity with future weak lensing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Conical singularities and the Vainshtein screening in full GLPV theories

In Gleyzes-Langlois-Piazza-Vernizzi (GLPV) theories, it is known that the conical singularity arises at the center of a spherically symmetric body (r = 0) in the case where the parameter α{sub H}4 characterizing the deviation from the Horndeski Lagrangian L{sub 4} approaches a non-zero constant as r → 0. We derive spherically symmetric solutions around the center in full GLPV theories and show that the GLPV Lagrangian L{sub 5} does not modify the divergent property of the Ricci scalar R induced by the non-zero α{sub H}4. Provided that α{sub H}4 = 0, curvature scalar quantities can remain finite at r = 0 even in the presence of L{sub 5} beyond the Horndeski domain. For the theories in which the scalar field φ is directly coupled to R, we also obtain spherically symmetric solutions inside/outside the body to study whether the fifth force mediated by φ can be screened by non-linear field self-interactions. We find that there is one specific model of GLPV theories in which the effect of L{sub 5} vanishes in the equations of motion. We also show that, depending on the sign of a L{sub 5}-dependent term in the field equation, the model can be compatible with solar-system constraints under the Vainshtein mechanism or it is plagued by the problem of a divergence of the field derivative in high-density regions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

The screening Horndeski cosmologies

We present a systematic analysis of homogeneous and isotropic cosmologies in a particular Horndeski model with Galileon shift symmetry, containing also a Λ-term and a matter. The model, sometimes called Fab Five, admits a rich spectrum of solutions. Some of them describe the standard late time cosmological dynamic dominated by the Λ-term and matter, while at the early times the universe expands with a constant Hubble rate determined by the value of the scalar kinetic coupling. For other solutions the Λ-term and matter are screened at all times but there are nevertheless the early and late accelerating phases. The model also admits bounces, as well as peculiar solutions describing “the emergence of time”. Most of these solutions contain ghosts in the scalar and tensor sectors. However, a careful analysis reveals three different branches of ghost-free solutions, all showing a late time acceleration phase. We analyse the dynamical stability of these solutions and find that all of them are stable in the future, since all their perturbations stay bounded at late times. However, they all turn out to be unstable in the past, as their perturbations grow violently when one approaches the initial spacetime singularity. We therefore conclude that the model has no viable solutions describing the whole of the cosmological history, although it may describe the current acceleration phase. We also check that the flat space solution is ghost-free in the model, but it may acquire ghost in more general versions of the Horndeski theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

BREAKING THE OBSCURING SCREEN: A RESOLVED MOLECULAR OUTFLOW IN A BURIED QSO

We present Keck laser guide star adaptive optics observations of the nearby buried quasi-stellar object (QSO) F08572+3915:NW. We use near-infrared integral field data taken with the OH-Suppressing Infra-Red Imaging Spectrograph to reveal a compact disk and molecular outflow using Paα and H{sub 2} rotational-vibrational transitions at a spatial resolution of 100 pc. The outflow emerges perpendicular to the disk into a bicone of one-sided opening angle 100° up to distances of 400 pc from the nucleus. The integrated outflow velocities, which reach at least –1300 km s{sup –1}, correspond exactly to those observed in (unresolved) OH absorption, but are smaller (larger) than those observed on larger scales in the ionized (neutral atomic) outflow. These data represent a factor of >10 improvement in the spatial resolution of molecular outflows from mergers/QSOs, and plausibly represent the early stages of the excavation of the dust screen from a buried QSO.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Evaluation of PCR Systems for Field Screening of Bacillus anthracis

There is little published data on the performance of hand-portable polymerase chain reaction (PCR) instruments that could be used by first responders to determine if a suspicious powder contains a potential biothreat agent. We evaluated five commercially available hand-portable PCR instruments for detection of Bacillus anthracis (Ba). We designed a cost-effective, statistically-based test plan that allows instruments to be evaluated at performance levels ranging from 0.85-0.95 lower confidence bound (LCB) on the probability of detection (POD) at confidence levels of 80-95%. We assessed specificity using purified genomic DNA from 13 Ba strains and 18 Bacillus near neighbors, interference with 22 common hoax powders encountered in the field, and PCR inhibition when Ba spores were spiked into these powders. Our results indicated that three of the five instruments achieved >0.95 LCB on the POD with 95% confidence at test concentrations of 2,000 genome equivalents/mL (comparable to 2,000 spores/mL), displaying more than sufficient sensitivity for screening suspicious powders. These instruments exhibited no false positive results or PCR inhibition with common hoax powders, and reliably detected Ba spores spiked into common hoax powders, though some issues with instrument controls were observed. Our testing approach enables efficient instrument performance testing to a statistically rigorous and cost-effective test plan to generate performance data that will allow users to make informed decisions regarding the purchase and use of biodetection equipment in the field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Actinomycetota isolated from the sponge Hymeniacidon perlevis as a source of novel compounds with pharmacological applications: diversity, bioactivity screening, and metabolomic analysis

Abstract Aims To combat health conditions, such as multi-resistant bacterial infections, cancer, and metabolic diseases, new drugs need to be urgently found and, in this respect, marine Actinomycetota have a high potential to produce secondary metabolites with pharmacological importance. We aimed to study the cultivable Actinomycetota community associated with a marine sponge from the Portuguese coast, Hymeniacidon perlevis, and investigate the potential of the retrieved isolates to produce compounds with antimicrobial, anticancer and anti-obesity properties. Methods and results The analysis of the 16S rRNA gene revealed 79 Actinomycetota isolates affiliated with 12 genera—Brachybacterium, Dietzia, Glutamicibacter, Gordonia, Micrococcus, Micromonospora, Nocardia, Nocardiopsis, Paenoartrhobacter, Rhodococcus, Streptomyces, and Tsukamurella, most of which affiliated with the genus Streptomyces. The screening of antimicrobial activity revealed 13 strains, all belonging to the Streptomyces genus, capable of inhibiting the growth of Candida albicans, Bacillus subtilis, or Staphylococcus aureus. Forty-three extracts exhibited cytotoxic activity against at least one tested cell line (HepG2, HCT-116, and hCMEC-D3). Three extracts that were active against the two cancer cell lines tested, did not reduce the viability of the non-cancer endothelial cell line, hCMEC-D3. One Gordonia strain exhibited anti-obesity activity, revealed by its ability to reduce the neutral lipids in zebrafish larvae. Mass spectrometry-based dereplication analysis of active extracts identified several compounds associated with known Actinomycetota natural products. Nonetheless, five clusters contained metabolites that did not match any annotated natural products, suggesting they may represent new bioactive molecules. Conclusions This work contributed to increase the knowledge on the diversity and bioactive potential of Actinomycetota associated with H. perlevis.

Fonseca, Ana C.↗
DOE OSTI2019

A screening platform to monitor RNA processing and protein-RNA interactions in ribonuclease P uncovers a small molecule inhibitor

Ribonucleoprotein (RNP) complexes and RNA-processing enzymes are attractive targets for antibiotic development owing to their central roles in microbial physiology. For many of these complexes, comprehensive strategies to identify inhibitors are either lacking or suffer from substantial technical limitations. Here, we describe an activity-binding-structure platform for bacterial ribonuclease P (RNase P), an essential RNP ribozyme involved in 5' tRNA processing. A novel, real-time fluorescence-based assay was used to monitor RNase P activity and rapidly identify inhibitors using a mini-helix and a pre-tRNA-like bipartite substrate. Using the mini-helix substrate, we screened a library comprising 2560 compounds. Initial hits were then validated using pre-tRNA and the pre-tRNA-like substrate, which ultimately verified four compounds as inhibitors. Biolayer interferometry-based binding assays and molecular dynamics simulations were then used to characterize the interactions between each validated inhibitor and the P protein, P RNA and pre-tRNA. X-ray crystallographic studies subsequently elucidated the structure of the P protein bound to the most promising hit, purpurin, and revealed how this inhibitor adversely affects tRNA 5' leader binding. This integrated platform affords improved structure-function studies of RNA processing enzymes and facilitates the discovery of novel regulators or inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening

Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3' end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.

Lountos, George T.↗
DOE OSTI2024

Signature analysis of high-throughput transcriptomics screening data for mechanistic inference and chemical grouping

Abstract High-throughput transcriptomics (HTTr) uses gene expression profiling to characterize the biological activity of chemicals in in vitro cell-based test systems. As an extension of a previous study testing 44 chemicals, HTTr was used to screen an additional 1,751 unique chemicals from the EPA’s ToxCast collection in MCF7 cells using 8 concentrations and an exposure duration of 6 h. We hypothesized that concentration-response modeling of signature scores could be used to identify putative molecular targets and cluster chemicals with similar bioactivity. Clustering and enrichment analyses were conducted based on signature catalog annotations and ToxPrint chemotypes to facilitate molecular target prediction and grouping of chemicals with similar bioactivity profiles. Enrichment analysis based on signature catalog annotation identified known mechanisms of action (MeOAs) associated with well-studied chemicals and generated putative MeOAs for other active chemicals. Chemicals with predicted MeOAs included those targeting estrogen receptor (ER), glucocorticoid receptor (GR), retinoic acid receptor (RAR), the NRF2/KEAP/ARE pathway, AP-1 activation, and others. Using reference chemicals for ER modulation, the study demonstrated that HTTr in MCF7 cells was able to stratify chemicals in terms of agonist potency, distinguish ER agonists from antagonists, and cluster chemicals with similar activities as predicted by the ToxCast ER Pathway model. Uniform manifold approximation and projection (UMAP) embedding of signature-level results identified novel ER modulators with no ToxCast ER Pathway model predictions. Finally, UMAP combined with ToxPrint chemotype enrichment was used to explore the biological activity of structurally related chemicals. The study demonstrates that HTTr can be used to inform chemical risk assessment by determining in vitro points of departure, predicting chemicals’ MeOA and grouping chemicals with similar bioactivity profiles.

Toxicology↗
DOE OSTI2025

Spatial String Tension and Its Effects on Screening Correlators in a Thermal QCD Plasma

We calculate the spatial Wilson line correlator for 2 +1 flavor QCD using highly improved staggered quark discretization for fermions and in quenched QCD for a wide range of temperatures, from the chiral crossover temperature 𝑇 pc ≃ 156 MeV or the deconfinement temperature ≃300 MeV, respectively, up to 2 GeV. Extracting the spatial string tension for different lattice cutoffs and by performing a continuum extrapolation of this observable, we show that the soft (magnetic) gluons interact nonperturbatively even at temperatures ≳1 GeV. We provide incriminating evidences to demonstrate that dimensionally reduced effective theories can describe these soft quark and gluon quasi-particles for both quenched and 2 +1 flavor QCD, at temperatures 𝑇 ≳ 5⁢𝑇 pc . We also show for the first time the imprints of the nonperturbative pseudopotential in the properties of mesonic screening masses for temperatures ranging from 0.8 to 164 GeV in the quark-gluon plasma.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗