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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Improving operational flexibility of integrated energy system with uncertain renewable generations considering thermal inertia of buildings

Insufficient flexibility in system operation caused by traditional "heat-set" operating modes of combined heat and power (CHP) units in winter heating periods is a key issue that limits renewable energy consumption. In order to reduce the curtailment of renewable energy resources through improving the operational flexibility, a novel optimal scheduling model based on chance-constrained programming (CCP), aiming at minimizing the lowest generation cost, is proposed for a small-scale integrated energy system (IES) with CHP units, thermal power units, renewable generations and representative auxiliary equipments. In this model, due to the uncertainties of renewable generations including wind turbines and photovoltaic units, the probabilistic spinning reserves are supplied in the form of chance-constrained; from the perspective of user experience, a heating load model is built with consideration of heat comfort and inertia in buildings. To solve the model, a solution approach based on sequence operation theory (SOT) is developed, where the original CCP-based scheduling model is tackled into a solvable mixed-integer linear programming (MILP) formulation by converting a chance constraint into its deterministic equivalence class, and thereby is solved via the CPLEX solver. We report the simulation results on the modified IEEE 30-bus system demonstrate that the presented method manages to improve operational flexibility of the IES with uncertain renewable generations by comprehensively leveraging thermal inertia of buildings and different kinds of auxiliary equipments, which provides a fundamental way for promoting renewable energy consumption.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2024

Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance

Abstract A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron . From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a d -glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Elimination of homogeneous broadening in 1 H solid-state NMR

1 H solid-state NMR spectra are plagued by low resolution, necessitating the use of complex pulse sequences or specialized equipment. Here, we introduce a new resolution enhancement method, inspired by super-resolution microscopy, that uses a 2D Hahn-echo experiment to constrain deconvolution. The result is an effective doubling of the MAS frequency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Determination of a macro- to micro-scale progression leading to a magnetized plasma disruption

We report here the observations of a plasma jet evolving through a macro- to micro-scale progression sequence. This leads to a fast magnetic reconnection that results in the jet breaking off from its originating electrode and forming a force-free state. A sausage-like pinching occurs first and squeezes an initially fat, short magnetized jet so that it becomes thin. The thin jet then becomes kink unstable. The lengthening of the jet by the kinking thins the jet even more since the kink is an incompressible instability. When the jet radius becomes comparable to the ion-skin depth, Hall and electron inertial physics become important and establish the environment for a fast magnetic reconnection. This fast reconnection occurs, disrupting the jet and establishing a force-free state. X-ray bursts and whistler waves, evidence of a magnetic reconnection, are observed when the plasma jet breaks off from the electrode. This experimentally confirmed sequence of successive thinning from pinching followed by kinking is reproduced in a three-dimensional ideal Magnetohydrodynamic (MHD) numerical simulation. The results of the experiment and the numerical simulation, together demonstrate a viable path from macro-scale MHD physics to micro-scale non-MHD physics where fast reconnection occurs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Feedforward equilibrium trajectory optimization with GSPulse

One of the common tasks required for designing new plasma scenarios or evaluating capabilities of a tokamak is to design the desired equilibria using a Grad-Shafranov (GS) equilibrium solver. However, most standard equilibrium solvers are time-independent and do not include dynamic effects such as plasma current flux consumption, induced vessel currents, or voltage constraints. Another class of tools, plasma equilibrium evolution simulators, do include time-dependent effects. These are generally structured to solve the forward problem of evolving the plasma equilibrium given feedback-controlled voltages. In this work, we introduce GSPulse, a novel algorithm for equilibrium trajectory optimization, that is more akin to a pulse planner than a pulse simulator. GSPulse includes time-dependent effects and solves the inverse problem: given a user-specified set of target equilibrium shapes, as well as limits on the coil currents and voltages, the optimizer returns trajectories of the voltages, currents, and achievable equilibria. This task is useful for scoping performance of a tokamak and exploring the space of achievable pulses. The computed equilibria satisfy both Grad-Shafranov force balance and axisymmetric circuit dynamics. The optimization is performed by restructuring the free-boundary equilibrium evolution equations into a form where it is computationally efficient to optimize the entire dynamic sequence. GSPulse can solve for hundreds of equilibria simultaneously within a few minutes. GSPulse has been validated against NSTX-U and MAST-U experiments and against SPARC feedback control simulations, and is being used to perform scenario design for SPARC. The computed trajectories can be used as feedforward inputs that are connected to the feedback controller to inform and improve feedback performance. The code for GSPulse is available open-source at github.com/jwai-cfs/GSPulse_public.

equilibrium↗
DOE OSTI2017

ClusterCAD: a computational platform for type I modular polyketide synthase design

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Navigating the maze: the impact of configurability in bioinformatics software

The bioinformatics software domain contains thousands of applications for automating tasks such as the pairwise alignment of DNA sequences, building and reasoning about metabolic models or simulating growth of an organism. Its end users range from sophisticated developers to those with little computational experience. In response to their needs, developers provide many options to customize the way their algorithms are tuned. Yet there is little or no automated help for the user in determining the consequences or impact of the options they choose. In this paper we describe our experience working with configurable bioinformatics tools. We find limited documentation and help for combining and selecting options along with variation in both functionality and performance. We also find previously undetected faults. We summarize our findings with a set of lessons learned, and present a roadmap for creating automated techniques to interact with bioinformatics software. We believe these will generalize to other types of scientific software.

McDevitt, Mikaela Cashman↗
DOE OSTI2014

Efficient prediction of human protein-protein interactions at a global scale

Background: Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. Results: On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments. Conclusions: The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Measurement of the bulk radioactive contamination of detector-grade silicon with DAMIC at SNOLAB

We present measurements of bulk radiocontaminants in the high-resistivity silicon CCDs from the DAMIC experiment at SNOLAB. We utilize the exquisite spatial resolution of CCDs to discriminate between α and β decays, and to search with high efficiency for the spatially-correlated decays of various radioisotope sequences. Using spatially-correlated β decays, we measure a bulk radioactive contamination of 32 Si in the CCDs of 140 ± 30 μBq/kg, and place an upper limit on bulk 210 Pb of < 160 μBq/kg. Using similar analyses of spatially-correlated α and β decays, we set upper limits of < 11 μBq/kg (0.9 ppt) on 238 U and < 7.3 μBq/kg (1.8 ppt) on 232 Th in the bulk silicon. The ability of DAMIC CCDs to identify and reject spatially-coincident backgrounds, particularly from 32 Si, has significant implications for the next generation of silicon-based dark matter experiments, where β's from 32 Si decay will likely be a dominant background.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V-Type ATPases

ATP synthase is the most prominent bioenergetic macromolecular motor in all life forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 μs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein–protein interfaces in the V1-ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. However, in a complete V1-ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP + Pi) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments.

Chemistry↗
DOE OSTI2015

Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii

Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. In this paper, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C. torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Finally, our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

A comparison of acceleration methods for solving the neutron transport k-eigenvalue problem

Over the past several years a number of papers have been written describing modern techniques for numerically computing the dominant eigenvalue of the neutron transport criticality problem. These methods fall into two distinct categories. The first category of methods rewrite the multi-group k-eigenvalue problem as a nonlinear system of equations and solve the resulting system using either a Jacobian-Free Newton–Krylov (JFNK) method or Nonlinear Krylov Acceleration (NKA), a variant of Anderson Acceleration. These methods are generally successful in significantly reducing the number of transport sweeps required to compute the dominant eigenvalue. The second category of methods utilize Moment-Based Acceleration (or High-Order/Low-Order (HOLO) Acceleration). These methods solve a sequence of modified diffusion eigenvalue problems whose solutions converge to the solution of the original transport eigenvalue problem. This second class of methods is, in our experience, always superior to the first, as most of the computational work is eliminated by the acceleration from the LO diffusion system. In this paper, we review each of these methods. Our computational results support our claim that the choice of which nonlinear solver to use, JFNK or NKA, should be secondary. The primary computational savings result from the implementation of a HOLO algorithm. We display computational results for a series of challenging multi-dimensional test problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

LncRNA DLEU2 promotes cervical cancer cell proliferation by regulating cell cycle and NOTCH pathway

Highlights: • LncRNA DLEU2 is upregulated and related to tumor topography in cervical cancer. • LncRNA DLEU2 promotes cervical cancer cell proliferation. • LncRNA DLEU2 promotes the progression of the cell cycle. • LncRNA DLEU2 inhibits the activity of the Notch signaling pathway. Long noncoding RNAs (lncRNAs) are known to play a crucial role in the onset and progression of cervical cancer (CC). Here, the results of RNA microarray and RNA-sequencing dataset analysis showed that lncRNA DLEU2 was significantly upregulated in CC tissues. Clinicopathologic analysis indicated that lncRNA DLEU2 was closely related to tumor topography. Functional experiments and bioinformatics analysis revealed that lncRNA DLEU2 promoted CC cell proliferation and accelerated the cell cycle. Mechanistically, lncRNA DLEU2 promoted the progression of the cell cycle and inhibited the activity of the Notch signaling pathway by inhibiting p53 expression. Additionally, lncRNA DLEU2 probably interacted with ZFP36 Ring Finger Protein (ZFP36) to inhibit the expression of p53. In conclusion, this study revealed the function of lncRNA DLEU2 in CC tumorigenesis, suggesting new therapeutic targets in CC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Guide-bound structures of an RNA-targeting A-cleaving CRISPR–Cas13a enzyme

CRISPR adaptive immune systems protect bacteria from infections by deploying CRISPR RNA (crRNA)-guided enzymes to recognize and cut foreign nucleic acids. Type VI-A CRISPR–Cas systems include the Cas13a enzyme, an RNA-activated RNase capable of crRNA processing and single-stranded RNA degradation upon target-transcript binding. Here we present the 2.0-Å resolution crystal structure of a crRNA-bound Lachnospiraceae bacterium Cas13a (LbaCas13a), representing a recently discovered Cas13a enzyme subtype. This structure and accompanying biochemical experiments define the Cas13a catalytic residues that are directly responsible for crRNA maturation. In addition, the orientation of the foreign-derived target-RNA-specifying sequence in the protein interior explains the conformational gating of Cas13a nuclease activation. These results describe how Cas13a enzymes generate functional crRNAs and how catalytic activity is blocked before target-RNA recognition, with implications for both bacterial immunity and diagnostic applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Angular momentum transport within evolved low-mass stars

Asteroseismology of 1.0-2.0 M {sub ☉} red giants by the Kepler satellite has enabled the first definitive measurements of interior rotation in both first ascent red giant branch (RGB) stars and those on the helium burning clump. The inferred rotation rates are 10-30 days for the ≈0.2 M {sub ☉} He degenerate cores on the RGB and 30-100 days for the He burning core in a clump star. Using the Modules for Experiments in Stellar Evolution code, we calculate state-of-the-art stellar evolution models of low mass rotating stars from the zero-age main sequence to the cooling white dwarf (WD) stage. We include transport of angular momentum due to rotationally induced instabilities and circulations, as well as magnetic fields in radiative zones (generated by the Tayler-Spruit dynamo). We find that all models fail to predict core rotation as slow as observed on the RGB and during core He burning, implying that an unmodeled angular momentum transport process must be operating on the early RGB of low mass stars. Later evolution of the star from the He burning clump to the cooling WD phase appears to be at nearly constant core angular momentum. We also incorporate the adiabatic pulsation code, ADIPLS, to explicitly highlight this shortfall when applied to a specific Kepler asteroseismic target, KIC8366239.

79 ASTRONOMY AND ASTROPHYSICS↗