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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 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells

Chronic bacterial infections are difficult to eradicate, though they are caused primarily by drug-susceptible pathogens. Antibiotic-tolerant persisters largely account for this paradox. In spite of their significance in the recalcitrance of chronic infections, the mechanism of persister formation is poorly understood. We previously reported that a decrease in ATP levels leads to drug tolerance in Escherichia coli , Pseudomonas aeruginosa , and Staphylococcus aureus . We reasoned that stochastic fluctuation in the expression of tricarboxylic acid (TCA) cycle enzymes can produce cells with low energy levels. S. aureus knockouts in glutamate dehydrogenase, 2-oxoketoglutarate dehydrogenase, succinyl coenzyme A (CoA) synthetase, and fumarase have low ATP levels and exhibit increased tolerance of fluoroquinolone, aminoglycoside, and β-lactam antibiotics. Fluorescence-activated cell sorter (FACS) analysis of TCA genes shows a broad Gaussian distribution in a population, with differences of over 3 orders of magnitude in the levels of expression between individual cells. Sorted cells with low levels of TCA enzyme expression have an increased tolerance of antibiotic treatment. Here, these findings suggest that fluctuations in the levels of expression of energy-generating components serve as a mechanism of persister formation. Persister cells are rare phenotypic variants that are able to survive antibiotic treatment. Unlike resistant bacteria, which have specific mechanisms to prevent antibiotics from binding to their targets, persisters evade antibiotic killing by entering a tolerant nongrowing state. Persisters have been implicated in chronic infections in multiple species, and growing evidence suggests that persister cells are responsible for many cases of antibiotic treatment failure. New antibiotic treatment strategies aim to kill tolerant persister cells more effectively, but the mechanism of tolerance has remained unclear until now.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Advancing Genome-Resolved Metagenomics beyond the Shotgun

Exploration of environmental microbiomes has shed light on the ecological and evolutionary principles at play in natural ecosystems and has been further accelerated through the reconstruction of population genomes to provide genome-centric context. Yet technical challenges with traditional shotgun metagenomics remain for computationally intense short-read assembly, strain heterogeneity within communities, and depth of coverage required for low-abundance microbes. In this Perspective, we highlight three main avenues for promising future developments, including coupling stable isotope probing and genome-resolved metagenomics, applying fluorescence-activated cell sorting approaches to target mini-metagenomes within a larger community, and utilizing single-molecule long-read and synthetic long-read technology to link mobile elements to host microbial cells. These developments on the horizon will undoubtedly advance genome-resolved metagenomic approaches and enable a better understanding of uncultivated microbes in their natural environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis

Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In bacterial pathogens, persisters are able to survive antibiotic treatment and reinfect patients in a frustrating cycle of chronic infection. To better define core persistence mechanisms for therapeutics development, we performed transcriptomics analyses of Burkholderia thailandensis populations enriched for persisters via three methods: flow sorting for low proton motive force, meropenem treatment, and culture aging. Although the three persister-enriched populations generally displayed divergent gene expression profiles that reflect the multimechanistic nature of stress adaptations, there were several common gene pathways activated in two or all three populations. These include polyketide and nonribosomal peptide synthesis, Clp proteases, mobile elements, enzymes involved in lipid metabolism, and ATP binding cassette (ABC) transporter systems. In particular, identification of genes that encode polyketide synthases (PKSs) and fatty acid catabolism factors indicates that generation of secondary metabolites, natural products, and complex lipids could be part of the metabolic program that governs the persistence state. We also found that loss-of-function mutations in the PKS-encoding gene locus BTH_I2366, which plays a role in biosynthesis of histone deacetylase (HDAC) inhibitors, resulted in increased sensitivity to antibiotics targeting DNA replication. Furthermore, treatment of multiple bacterial pathogens with a fatty acid synthesis inhibitor, CP-640186, potentiated the efficacy of meropenem against the persister populations. Altogether, our results suggest that bacterial persisters may exhibit an outwardly dormant physiology but maintain active metabolic processes that are required to maintain persistence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

INTERDUNE DEPOSITS AND STRATIGRAPHIC FRAMEWORK OF THE NAVAJO SANDSTONE IN THE LAKE POWELL AREA, UTAH, USA

The Western Interior of the USA was dominated by desert environments for much of the Jurassic. Of these desert environments, the most extensive by far was the Navajo Sandstone erg, which, in conjunction with its correlative Nugget and Aztec Sandstones, is thought to have covered well over 500,000 km2, and is one of the largest ergs preserved in the rock record. The Navajo Sandstone is also one of a few geologic units which show promise as a potential CO2 sequestration reservoir in Utah. It outcrops along the eastern and southern margin of the state, and subcrops throughout most of the central area. The Navajo Sandstone consists of stacked eolian deposits, composed of well sorted, clean sandstone, deposited in commonly tabular, high angle cross bedded paleodunes, which are on average 15 m thick. Interspersed between these paleodunes are interdune deposits. Interdune deposits consist of sandy to calcareous, predominantly planar bedded, lensoid units, ranging from <1 m up to 7 m thick. In some cases, these interdune deposits occur along more extensive stratigraphic bounding surfaces. Dating within the Navajo Sandstone has historically been very difficult, as a result of its predominantly clean, aeolian sandstone composition. In addition, complexity of internal stratigraphic surfaces coupled with a low structural dip and generally flat topography has resulted in a poor understanding of the internal stratigraphy of the Navajo Sandstone. Exceptional three-dimensional exposures of the Navajo Sandstone in the upper portions of Lake Powell permit us to relate interdune carbonates to a hierarchical bounding surfaces model. Here we use this combined approach to interpret the internal stratigraphy of the Navajo Sandstone in this region. This work forms part of a larger study of the Navajo Sandstone across Utah and its potential as a CO2 reservoir, by developing a more comprehensive stratigraphic framework, and increasing understanding of stratigraphic complexity within one of the most significant eolian systems in the world.

Mahon, Elizabeth↗
DOE OSTI2016

Submarine deposits from pumiceous pyroclastic density currents traveling over water: An outstanding example from offshore Montserrat (IODP 340)

Pyroclastic density currents have been observed to both enter the sea, and to travel over water for tens of kilometers. Here, we identified a 1.2-m-thick, stratified pumice lapilli-ash cored at Site U1396 offshore Montserrat (Integrated Ocean Drilling Program [IODP] Expedition 340) as being the first deposit to provide evidence that it was formed by submarine deposition from pumice-rich pyroclastic density currents that traveled above the water surface. The age of the submarine deposit is ca. 4 Ma, and its magma source is similar to those for much younger Soufrière Hills deposits, indicating that the island experienced large-magnitude, sub-aerial caldera-forming explosive eruptions much earlier than recorded in land deposits. The deposit's combined sedimentological characteristics are incompatible with deposition from a submarine eruption, pyroclastic fall over water, or a submarine seafloor-hugging turbidity current derived from a subaerial pyroclastic density current that entered water at the shoreline. The stratified pumice lapilli-ash unit can be subdivided into at least three depositional units, with the lowermost one being clast supported. The unit contains grains in five separate size modes and has a >12 phi range. Particles are chiefly sub-rounded pumice clasts, lithic clasts, crystal fragments, and glass shards. Pumice clasts are very poorly segregated from other particle types, and lithic clasts occur throughout the deposit; fine particles are weakly density graded. We interpret the unit to record multiple closely spaced (< 2 d) hot pyroclastic density currents that flowed over the ocean, releasing pyroclasts onto the water surface, and settling of the various pyroclasts into the water column. Our settling and hot and cold flotation experiments show that waterlogging of pumice clasts at the water surface would have been immediate. The overall poor hydraulic sorting of the deposit resulted from mixing of particles from multiple pulses of vertical settling in the water column, attesting to complex sedimentation. Slow-settling particles were deposited on the seafloor together with faster-descending particles that were delivered at the water surface by subsequent pyroclastic flows. The final sediment pulses were eventually deflected upon their arrival on the seafloor and were deposited in laterally continuous facies. This study emphasizes the interaction between products of explosive volcanism and the ocean and discusses sedimentological complexities and hydrodynamics associated with particle delivery to water.

58 GEOSCIENCES↗
DOE OSTI2017

Structure of complexes of uranyl succinate with carbamide and dimethylurea

Three new succinate-containing complexes of uranyl with carbamide (Urea) and N,N'-dimethylurea (s-Dmur) are synthesized and studied by IR spectroscopy and X-ray diffraction. Structures of the same type, [UO{sub 2}(Urea){sub 4}(H{sub 2}O)][(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4})3] · 3H{sub 2}О and [UO{sub 2}(Urea){sub 4}(H{sub 2}O)][(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4})3] · 2Urea contain two sorts of uranium-containing complex groups, namely, mononuclear [UO{sub 2}(Urea){sub 4}(H{sub 2}O)]{sup 2+} cations and two-dimensional [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2–} anions described by crystal-chemical formulas AМ{sub 5}{sup 1} and A{sub 2}Q{sub 3}{sup 02}, respectively (A = UO{sub 2}{sup 2+}, M{sup 1} = Urea or H{sub 2}O, Q{sup 02} = C{sub 4}H{sub 4}O{sub 4}{sup 2-}), and differ only in the nature of noncoordinated molecules—water and carbamide. The main structural groups of the [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 2}(s-Dmur){sub 3}] crystals are [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 2}(s-Dmur){sub 3}] chains belonging to the А{sub 2}Q{sub 2}{sup 02}M{sub 3}{sup 1} (A = UO{sub 2}{sup 2+}, Q{sup 02} = C{sub 4}H{sub 4}O{sub 4}{sup 2-}, M{sup 1} = s-Dmur) crystal-chemical group. Specific features of intermolecular interactions in the crystal structures are revealed using the Voronoi–Dirichlet method of molecular polyhedra.

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

Collective state of electrons and impurities with a spin

The problem of states of an electron system interacting with impurities that have a spin of 1/2 is considered. It is shown that in the calculation of the energy of the system, the electron spin-flip processes and the formation of electron–hole–impurity flip spin (hole against the background of electrons with another spin projection) play the major role. Such complexes are accumulated in the system (a sort of Bose condensate of complexes is formed); this reduces the energy of the system, which is a linear function of the initial interaction of an electron with the impurity spin (in contrast, for example, to the result obtained in perturbation theory). The hole-type excitation and the spin excitation have a gap in the spectrum. Small parameters of the problem are the interaction of electrons with impurity spins and the number of impurities. The electron–electron interaction is not taken into account. Impurities are assumed to be distributed at random, and calculations are performed using the known averaging over the positions of impurities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Spherical nuclei near the stability line and far from it

Results of microscopic and semiphenomenological calculations of features of spherical nuclei lying near the stability line and far from it are presented. The reason why the nuclei being considered are spherical is that they are magic at least in one nucleon sort. The present analysis is performed for Z = 50 and Z = 28 isotopes and for N = 50 isotones, the region extending from neutron-rich to neutron-deficient nuclei being covered. The isotopic dependence of the mean-field spin–orbit nuclear potential is revealed; systematics of energies of levels and probabilities for electromagnetic transitions is examined; and root-mean-square radii of nuclei are calculated, along with the proton- and neutron-density distributions in them. Nuclei in the vicinity of closed shells are considered in detail, and the axial-vector weak coupling constant in nuclei is evaluated. A systematic comparison of the results of calculations with experimental data is performed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Photoneutron reactions in the range of giant dipole resonance

The well-known significant systematic disagreements between data on partial photoneutron reaction cross sections obtained in experiments using quasimonoenergetic annihilation photons and bremsstrahlung were investigated using objective physical criteria of data reliability. It was shown that many data are not reliable because of significant systematic uncertainties of the photoneutron multiplicity sorting methods used. The experimental-theoretical method for evaluation of reliable partial reaction cross sections was proposed and many new data were obtained.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Erosion of the Leading Edge of a Low-Energy High-Current Electron Beam Injected into Gas in the Absence of an External Magnetic Field

Erosion of the leading edge a low-energy high-current electron beam injected into a low-pressure neutral gas under conditions of virtual cathode formation in the absence of an external magnetic field is studied theoretically. Beam losses are calculated as functions of the pressure and sort of gas, beam electron energy, and system geometry. The dependence of the duration of the leading edge erosion on the system parameters is analyzed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

High-Performance Sparse Matrix-Matrix Products on Intel KNL and Multicore Architectures

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is vastly used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. While many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. We firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting multi- and many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. We investigate their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. In conclusion, a critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗
DOE OSTI2025

Position-Enhanced Gradient Attack (PEGA) on Medical Language Models

Federated Learning (FL) enables collaborative training of language models on sensitive clinical notes without sharing the data. However, this paradigm is vulnerable to gradient inversion attacks that can reconstruct private data from shared gradients. We find that state-of-the-art attacks are less effective in the medical domain, failing to overcome the unique challenges posed by its specialized vocabulary and unstructured format. To address this, we introduce the Position-Enhanced Gradient Attack (PEGA), a novel attack that makes gradients position-aware by optimizing token and position embeddings simultaneously. PEGA employs two key innovations: a periodic sorting of positional embeddings to resolve token order ambiguity and a late-stage embedding replacement strategy to correct hard-to-recover critical tokens. To evaluate the leakage of sensitive data more directly, we also propose the Unified PHI-Recall (UPHI), a new metric measuring the recovery of Protected Health Information. Experiments on the MIMIC-III dataset show that PEGA significantly outperforms leading attacks like TAG and LAMP, particularly in its ability to reconstruct identifiable patient information, exposing a more severe and nuanced privacy risk in federated medical NLP.

Xu, Nuo [University of Minnesota]↗
DOE OSTI2016

Ratchet Effects in Active Matter Systems

Ratchet effects can arise for single or collectively interacting Brownian particles on an asymmetric substrate when a net dc transport is produced by an externally applied ac driving force or by periodically flashing the substrate. Recently, a new class of active ratchet systems that do not require the application of external driving has been realized through the use of active matter; they are self-propelled units that can be biological or nonbiological in nature. When active materials such as swimming bacteria interact with an asymmetric substrate, a net dc directed motion can arise even without external driving, opening a wealth of possibilities such as sorting, cargo transport, or micromachine construction. We review the current status of active matter ratchets for swimming bacteria, cells, active colloids, and swarming models, focusing on the role of particle-substrate interactions. Here, we describe ratchet reversals produced by collective effects and the use of active ratchets to transport passive particles. We discuss future directions including deformable substrates or particles, the role of different swimming modes, varied particle–particle interactions, and nondissipative effects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Futility

The Futility package contains the following: 1) Definition of the size of integers and real numbers; 2) A generic Unit test harness; 3) Definitions for some basic extensions to the Fortran language: arbitrary length strings, a parameter list construct, exception handlers, command line processor, timers; 4) Geometry definitions: point, line, plane, box, cylinder, polyhedron; 5) File wrapper functions: standard Fortran input/output files, Fortran binary files, HDF5 files; 6) Parallel wrapper functions: MPI, and Open MP abstraction layers, partitioning algorithms; 7) Math utilities: BLAS, Matrix and Vector definitions, Linear Solver methods and wrappers for other TPLs (PETSC, MKL, etc), preconditioner classes; 8) Misc: random number generator, water saturation properties, sorting algorithms.

Collins, BenjaminS.↗
DOE OSTI2018

miniGraphics v. 1.0

The miniGraphics package provides a collection of reference implementations for parallel rendering. In particular, miniGraphics is focused on sort-last parallel rendering, which is the rendering algorithm of choice for HPC rendering. The miniGraphics package provides a collection of simple serial rendering systems and a collection of parallel image compositing methods, which can be combined to test the behavior of parallel rendering under different conditions.

Peterson, MatthewG.↗
DOE OSTI2019

numericalFunctions

The numericalFunction C library is designed to handle point-wise interpolative data representing a mathematical function. The library currently handles 1-d functions (i.e., functions of the format f(x)). The main object is the ptwXYPoints C struct that holds list of x,y pairs sorted by ascending x-values with an interpolation rule. That is, it contains the 1-d function f(x) = y(x). Functions are included that support common unitary and binary operations (e.g., negation, addition, multiplication). As example, if f(x) and g(x) are two ptwXYPoints instances, then routines to calculate f(x) + g(x) and f(x) * g(x) are included. The library support storage of data with lin-lin, lin-log, log-lin, log-log and flat (or histogram) interpolation. Functions to convert any of the supported interpolation to lin-lin are included. However, many of the binary functions only support lin-lin interpolation. The library also contains a C struct for storing a Legendre series representation of a 1-d function, and functions to convert Legendre series to and from a ptwXYPoints instance. A python interface to the library is included, with the ptwXYPoints C struct treated as a class. This class has many of the standard python math methods (e.g., __add__, __mul__).

Beck, Bret↗
DOE OSTI2016

LabVIEW Task Manager v. 1.10.0

LabVIEW Task Manager is a debugging tool for use during code development in the National Instruments (NI) LabVIEW® IDE. While providing a dynamic & big-picture view of running code, an expandable/collapsible tree diagram displays detailed information (both static and dynamic) on all VIs in memory, belonging to a selected project/target. It allows for interacting with single or multiple selected VIs at a time, providing significant benefits while troubleshooting, and has the following features: Look & Feel similar to Windows® Task Manager; Selection of project/target; Lists all VIs in memory, grouped by class/library; Searches for and enumerates clones in memory; DropIn VI for including dynamically referenced clones (Clone Beacon); 'Refresh Now' (F5) re-reads all VIs in memory and adds new ones to the tree; Displays VI name, owning class/library, state, path, data size & code size; Displays VI FP Behavior, Reentrant?, Reentrancy Type, Paused? & Highlight?; Sort by any column, including by library name; Filter by item types vi, ctl, and vit/ctt; Filter out vi.lib and global VIs; Tracking of, and ability to toggle, execution highlighting on multiple selected VIs; Tracking of paused VIs with ability to Pause/Resume/TogglePause multiple selected VIs; DropIn VI for pausing on a condition; If a clone initiates a pause, a different pause symbol is used for all clones of that same reentrant original VI; Select multiple VIs and open or close their FPs or BDs; Double Click a VI from the tree to bring the BD (first choice) or FP to front, if already open; and Select multiple top-level VIs and Abort them.

Vargo, TimothyD.↗