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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Multiple highly expressed phospho enol pyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses

Abstract Background and Aims Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme’s amino acid structure influences its function. Methods Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. Key Results The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. Conclusions The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC’s sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.

DiMario, Robert J. (ORCID:0000000250566868)↗
DOE OSTI2021

Integrating continuous hypermutation with high–throughput screening for optimization of cis,cis –muconic acid production in yeast

Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Reconstruction of fast neutron direction in segmented organic detectors using deep learning

A method for reconstructing the direction of a fast neutron source using a segmented organic scintillator-based detector and deep learning model is proposed and analyzed. Here, the model is based on recurrent neural network, which can be trained by a sequence of data obtained from an event recorded in the detector and suitably pre-processed. The performance of deep learning-based model is compared with the conventional double-scatter detection algorithm in reconstructing the direction of a fast neutron source. With the deep learning model, the uncertainty in source direction of 0.301 rad is achieved with 100 neutron detection events in a segmented cubic organic scintillator detector with a side length of 46 mm. To reconstruct the source direction with the same angular resolution as the double-scatter algorithm, the deep learning method requires 75% fewer events. Application of this method could augment the operation of segmented detectors operated in the neutron scatter camera configuration for applications such as special nuclear material detection.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Atmospheric pressure plasmas interacting with wet and dry microchannels: reverse surface ionization waves

Atmospheric pressure plasma jets (APPJs) are increasingly being used to functionalize polymers and dielectric materials for biomedical and biotechnology applications. Once such application is microfluidic labs-on-a-chip consisting of dielectric slabs with microchannel grooves hundreds of microns in width and depth. The periodic channels, an example of a complex surface, present challenges in terms of directly and uniformly exposing the surface to the plasma. In this paper, we discuss results from computational and experimental investigations of negative APPJs sustained in Ar/N 2 mixtures flowing into ambient air and incident onto a series of microchannels. Results from two-dimensional plasma hydrodynamics modeling are compared to experimental measurements of electric field and fast-camera imaging. The propagation of the plasma across dry microchannels largely consists of a sequence of surface ionization waves (SIWs) on the top ridges of the channels and bulk ionization waves (IWs) crossing over the channels. The IWs are directed into electric field enhanced vertices of the next ridge. The charging of these ridges produce reverse IWs responsible for the majority of the ionization. The propagation of the plasma across water filled microchannels evolve into hopping SIWs between the leading edges of the water channels, regions of electric enhancement due to polarization of the water. Positive, reverse IWs follow the pre-ionized path of the initial negative waves.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals

Abstract Background Hepatitis C virus (HCV) has high genetic diversity and is classified into 8 genotypes and >90 subtypes, with some endemic to specific world regions. This could compromise direct-acting antiviral efficacy and global HCV elimination. Methods We characterized HCV subtypes “rare” in the United Kingdom (non-1a/1b/2b/3a/4d) by means of whole-genome sequencing via a national surveillance program. Genetic analyses to determine the genotype of samples with unresolved genotypes were undertaken by comparison with International Committee on Taxonomy of Viruses HCV reference sequences. Results Two HCV variants were characterized as being closely related to the recently identified genotype (GT) 8, with >85% pairwise genetic distance similarity to GT8 sequences and within the typical intersubtype genetic distance range. The individuals infected by the variants were UK residents originally from Pakistan and India. In contrast, a third variant was only confidently identified to be more similar to GT6 compared with other genotypes across 6% of the genome and was isolated from a UK resident originally from Guyana. All 3 were cured with pangenotypic direct-acting antivirals (sofosbuvir-velpatasvir or glecaprevir-pibrentasvir) despite the presence of resistance polymorphisms in NS3 (80K/168E), NS5A (28V/30S/62L/92S/93S) and NS5B (159F). Conclusions This study expands our knowledge of HCV diversity by identifying 2 new GT8 subtypes and potentially a new genotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

FutureTense

Protective vaccines and reliable diagnostics are essential tools for controlling viral diseases. However, the efficacy of these tools can be diminished by mutations in viral genomes. The delay between the emergence of new viral strains and the redesign of vaccines and diagnostics allows for continued viral transmission. Is it possible to address this challenge by computationally predicting viral genome sequence evolution? Can we “future-proof” vaccines and diagnostics by targeting both current and anticipated future sequence variants? While predicting viral evolution is still an unsolved, “grand challenge” problem in biology, the large, and rapidly growing, number of SARS-CoV-2 genome sequences provide an opportunity to quantify the ability of machine learning to predict viral genome sequence evolution. Towards this end, we have developed a simple computational model for predicting viral evolution at the level of individual nucleotides. The key metric for quantifying the per-base, prediction accuracy for viral evolution is the Mann-Whitney U statistic (or, equivalently, the area under the receiver operator curve). Since the Mann-Whitney U statistic is not a differentiable function, existing deep leaning packages (like Pytorch and Keras/TensorFlow) are not useful, as they require that the accuracy metric/objective function be analytically differentiable with respect to the model parameters. To overcome this challenge, we have implemented custom software, “FutureTense”, that can train a machine learning model by maximizing the non-differentiable Mann-Whitney U statistic. This software trains a machine learning model by exploring along the direction of the discrete gradient of the Mann-Whitney U statistic in the model parameter space. Parallel computing and genome sequence-specific optimizations are used to accelerate model training. The resulting machine learning model learns the observed high C->U mutation rates in the SARS-CoV-2 genome (which are potentially induced by host defenses) and provides prediction accuracies that are significantly better than one would expect from random chance. While predicting viral evolution is still quite far from a solved problem, the surprising performance of this simple model gives hope that the accuracy of predicting viral genome evolution can be further increased by more sophisticated approaches.

Gans, Jason↗
DOE OSTI2023

Natural transformation as a tool in Acinetobacter baylyi : Streamlined engineering and mutational analysis

Natural transformation and homologous recombination in a soil bacterium, Acinetobacter baylyi ADP1, occur with exceptionally high efficiency. These genetic features can be harnessed to address a wide variety of fundamental and applied scientific topics. Recent advances in synthetic biology and laboratory evolution have led to renewed appreciation for the use of A. baylyi as a model organism. To complement several review articles that highlight new tool sets, this chapter focuses on simple protocols and examples of transformation assays that facilitate genetic analysis and engineering. Whole genome sequencing often reveals extensive genetic variation among closely related isolates that can confound the association of genotypic and phenotypic changes. In A. baylyi, such associations can be deciphered in unique ways by directly transforming cells with linear DNA fragments. The resulting allelic replacement, which occurs at high frequency, rapidly generates desired mutants via targeted chromosomal editing. Diverse screening and selection methods can be used to test hypotheses and streamline experimental strategies to reveal the significance of specific DNA sequences. Moreover, large procedural variations are well tolerated, and techniques can be readily adapted for new purposes. Furthermore, one goal of highlighting natural transformation methodology in A. baylyi is to expand the community of researchers using this versatile bacterial host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome

Viruses are an understudied component of plant microbiomes. Identifying viruses that are shared between individual plants, or members of the “core virome”, could reveal stable viral populations with the potential to modulate the composition and function of the microbiome. Here, we examined the virome associated with Sphagnum mosses, a keystone species that has direct influence over the fate of peatland carbon stores. We analyzed bulk metagenomes and metatranscriptomes generated from Sphagnum field samples collected over a ten-month period to identify virus-like sequences shared among plants. Individual Sphagnum samples harbored distinct DNA and RNA viromes where only a small percentage (< 1%) of the total number of identified viral contigs were shared among all samples. Based on taxonomic classification, the shared viral contigs represent bacterial viruses, or phage (Caudoviricetes), as well as viruses of eukaryotes, namely nucleocytoplasmic large DNA viruses (Nucleocytoviricota) and RNA viruses (Riboviria). We linked the shared phage-like contigs to viral regions within sequenced genomes of bacterial taxa that are members of the Sphagnum core microbiome, suggesting that these contigs represent temperate phage or degraded prophage. The putative nucleocytoplasmic large DNA viruses and RNA viruses were phylogenetically diverse and showed sequence similarity to viruses associated with a broad range of hosts and environmental sources. The identification of shared viral contigs suggested that, despite the compositional heterogeneity between samples, Sphagnum mosses may harbor a core virome. Future work validating the presence of the core virome is warranted as it may aid in understanding how persistent viruses impact microbiome ecology and symbiont evolution within this climatically relevant keystone species.

Metagenomics↗
DOE OSTI2022

“Multiagent” Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations

Enzyme evolution has enabled numerous advances in biotechnology and synthetic biology, yet still requires many iterative rounds of screening to identify optimal mutant sequences. This is due to the sparsity of the fitness landscape, which is caused by epistatic mutations that only offer improvements when combined with other mutations. We report an approach that incorporates diverse substrate analogues in the screening process, where multiple substrates act like multiple agents navigating the fitness landscape, identifying epistatic mutant residues without a need for testing the entire combinatorial search space. We initially validate this approach by engineering a malonyl-CoA synthetase and identify numerous epistatic mutations improving activity for several diverse substrates. The majority of these mutations would have been missed upon screening for a single substrate alone. We expect that this approach can accelerate a wide array of enzyme engineering programs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Probing the Consequences of Cubic Particle Shape and Applied Field on Colloidal Crystal Engineering with DNA

Abstract In a magnetic field, cubic Fe 3 O 4 nanoparticles exhibit assembly behavior that is a consequence of a competition between magnetic dipole–dipole and ligand interactions. In most cases, the interactions between short hydrophobic ligands dominate and dictate assembly outcome. To better tune the face‐to‐face interactions, cubic Fe 3 O 4 nanoparticles were functionalized with DNA. Their assembly behaviors were investigated both with and without an applied magnetic field. Upon application of a field, the tilted orientation of cubes, enabled by the flexible DNA ligand shell, led to an unexpected crystallographic alignment of the entire superlattice, as opposed to just the individual particles, along the field direction as revealed by small and wide‐angle X‐ray scattering. This observation is dependent upon DNA length and sequence and cube dimensions. Taken together, these studies show how combining physical and chemical control can expand the possibilities of crystal engineering with DNA.

Urbach, Zachary J.↗
DOE OSTI2024

Ensuring Solution Uniqueness in Three-Phase Power System State Estimation

This paper is concerned with the issue of potential non-unique solutions in three-phase state estimation. Theory of observability analysis for positive sequence power system state estimation is based on certain assumptions that avoid possibility of multiple solutions. Also, it is shown that observability of a positive sequence network remains independent of the network parameters or the operating state. When extending single-phase observability analysis directly to the three-phase case, this paper considers the possibility of converging to multiple solutions, i.e. solution non-uniqueness, even for cases where state estimator successfully converges. The study illustrates via numerical examples the likelihood of converging to entirely different solutions for certain network parameters. It also examines how the operating state, particularly under unbalanced loading, leads to solution non-uniqueness. The paper then describes an alternative approach to ensure a unique solution in three-phase state estimation. This method aims to accurately and uniquely estimate the state of any unbalanced three-phase system, irrespective of load imbalance, network configuration, existence of synchronous generators or transformers.

Power System State Estimation, Three-Phase, Distri↗
DOE OSTI2025

Generalizing multiple memories from a single drive: The hysteron latch

Far-from-equilibrium systems can form memories of previous deformations or driving. In systems from sheared glassy materials to buckling beams to crumpled sheets, this behavior is dominated by return-point memory, in which revisiting a past extremum of driving restores the system to a previous state. Cyclic driving with both positive and negative strains forms multiple nested memories, as in a single-dial combination lock, while asymmetric driving (only positive strain) cannot. We study this case in a general model of hysteresis that considers discrete elements called hysterons. We show how two hysterons with a frustrated interaction can violate return-point memory, realizing multiple memories of asymmetric driving. This reveals a general principle for designing systems that store sequences of cyclic driving, whether symmetric or asymmetric. In disordered systems, asymmetric driving is a sensitive tool for the direct measurement of frustration.

Science & Technology - Other Topics↗
DOE OSTI2020

Interpreting pre-vegetation landscape dynamics: The Cambrian Lower Mount Simon Sandstone, Illinois, U.S.A.

ABSTRACT The Cambrian Mount Simon Sandstone has been the subject of extensive study and multiple industrial-scale carbon storage demonstrations at Decatur, Illinois, USA. The development of a reliable paleoenvironmental model is critical to successful large-scale carbon dioxide (CO2) storage, but is complicated by the need to interpret pre-vegetation sedimentation processes. The present study presents a paleoenvironmental model of the Lower Mount Simon Sandstone, based on analysis of primary sedimentary structures in two cores and four complete high-resolution resistivity logs (FMI). The Lower Mount Simon Sandstone represents a vertical “drying-up” sequence composed of three associated depositional units: a north–south oriented coastal system at the base, an eastward-directed fluvial unit in the middle, and a westward-directed eolian system at the top that recycled medium- and fine-grained sand in the basin. Quantitative analysis of fluvial cross-strata indicates that the perennial river system was shallow (c. 1 m deep) with relatively narrow channel belts (c. 1 km). Adjacent sandy eolian-floodplain deposits contain abundant thin, crinkly planar laminae that are enriched in fines and are interpreted as cementation surfaces, likely of biological origin. Deflation lags and wind-ripple strata are commonly interbedded with the crinkly strata, suggesting that the recurrence of erosion and deposition that controlled sedimentary preservation on the floodplain were dominated by eolian transport, re-wetting, and (bio-) cementation. Such a prominent role of exposure to the wind, basin-scale sediment recycling, and eolian removal of fine-grained sediment would have ceased to exist for most climates after the development of vegetation on land, yet, may well be key to understanding the environmental context for early life on Earth.

Geology↗
DOE OSTI2021

Building Neutron Scattering Infrastructure in Louisiana for Advanced Materials (Final Report)

The main objective of the Louisiana Consortium for Neutron Scattering (LaCNS) is to build a major neutron scattering infrastructure capable of treating both soft and hard materials. The goal is to create a sustainable effort having the quality, breadth, and depth necessary to produce competitive proposals including collaborative and center type proposals. Our scientific aim is to understand the role of coupling in emergent complex materials and its impact on the structure/property relationship and to explore how to tune the key couplings to guide the design of materials with the desired properties. This naturally includes building a base of users of the Spallation Neutron Source (SNS) and the High Flux Isotope Reactor (HFIR) in Louisiana; to train highly talented graduate and post-doctoral students in synthesis, neutron scattering, and simulation and modeling techniques, thereby helping to produce the next generation of scientist who use neutron scattering techniques as a crucial part of their research. The goal of our hard matter program is to understand the interplay between spin, charge, orbital, and lattice degrees of freedom in carefully selected complex materials. We have made considerable progress on number of complex systems including the oxide Sr3(Ru1-xMnx)2O7 where short-range magnetic ordering with anisotropic spin texture is initiated at the metal-insulator transition that clearly indicates a strong spin-charge coupling. Another critical area is in quantum materials. For example, in the topological semimetal BaMnSb2, we found a 3D canted antiferromagnetic Weyl semimetal with a 2D electronic structure and a nontrivial Berry phase. In addition, in the hexagonal chiral Mn1/3NbS2 system, we found soliton/soliton and soliton/antisoliton domain walls where the application of small fields or small currents can be used to control nanoscopic magnetic domains where the control of domain walls is crucially important for information storage. In addition, chemical transformation investigations were performed on the VISION instrument at Spallation Neutron Source (SNS). The soft matter effort was focused on understanding the role of non-covalent interactions on the structure and dynamics of fluid-based soft matter. One key focus was on sequence-defined (SD) amphiphilic peptoid polymers that allow encoding of molecular interactions and thereby systematic investigations of how charge directs the solution self-assembly of amphiphilic polymers in water. Another important area was on the dynamics of lipids self-assembled into membranes for exploring the permeability and mechanical using both neutron spin echo (NSE) spectroscopy and quasielastic neutron scattering (QENS) to distinguished between viscoelasticity and permeability at the molecular scale. Overall, the LaCNS project was quite successful, generating 145 publications and 245 presentations. Our graduate and post-doctoral students were well trained resulting in positions in national laboratories (Oak Ridge National Laboratory (ORNL), Argonne National Laboratory and Los Alamos National Laboratory), major research universities, and industry. We also developed a uniaxial pressure cell along with ORNL for SNS. A critical goal of this project was to establish a foundation for competing nationally in federally funded research programs. To this end, we were quite successful in generating over twenty-two federally and non-federally funded grants including awards from NSF, DOE, and DOD, and two early career awards. Equally important, we were able to secure a key major piece of instrumentation via a large ARO grant for a state-of-the-art electron microscope.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Direct local parametrization of nuclear state densities using the back-shifted Bethe formula

Level densities are often parametrized using the back-shifted Bethe formula (BBF) for nuclei that possess experimental data for s-wave neutron resonance average spacings and a complete discrete level sequence at low excitation energies. However, these parametrizations require the additional modeling of the dependence of the spin-cutoff parameter on excitation energy. Here, in this work, we avoid the need to model the spin distribution of level densities by using the experimental data to parametrize directly the state densities, for which the BBF does not depend on the spin-cutoff parameter. This approach allows for a local parameterization of state densities that is independent of the spin-cutoff parameter. We provide these parameters in a tabulated form for applications in nuclear reaction calculations and for testing microscopic approaches to state densities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Peptoid-Directed Formation of Five-Fold Twinned Au Nanostars through Particle Attachment and Facet Stabilization

While bio-inspired synthesis offers great potential for controlling nucleation and growth of inorganic particles, precisely tuning biomolecule-particle interactions is a long-standing challenge. Herein, we used variations in peptoid sequence to manipulate peptoid-Au interaction, leading to synthesis of concave five-fold twinned, five-pointed Au nanostars via a process of repeated particle attachment and facet stabilization. Ex situ and liquid-phase TEM observations show that a balance between particle attachment biased to occur near the star points, preferential growth along the [100] direction, and stabilization of (111) facets is critical to forming star-shaped particles. Molecular simulations predict that interaction strengths between peptoids and distinct Au facets differ significantly and thus can alter attachment kinetics and surface energies to form the stars. This work provides new insights into how sequence-defined ligands affect particle growth to regulate crystal morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗