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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps

Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. Here, we quantify the impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.

3D alignment↗
DOE OSTI2023

Development of Scalable Reactive Transport Framework for PFAS

Research on PFAS chemicals is extensive and covers all aspects, including analytical quantification, determination of properties, toxicology, ex situ treatment, and in situ remediation. PFAS chemicals are very stable and thus persistent/recalcitrant in the environment. Although there are many unknowns about PFAS chemicals, degradation pathways, reaction rates, etc., many different sorption, oxidation, reduction, biological, and innovative treatment approaches are being developed. Sorption with activated carbon is currently the only fully available in situ treatment technology for PFAS-impacted groundwater. Given the wide array of PFAS chemicals and transformation products, remediation may need multi-step treatment trains to fully address the PFAS contamination. The work here provides kinetic reaction modules that represent an initial cut at functionality representing PFAS migration and reaction in groundwater aquifer flow and transport models. One reaction kinetics module provides a method to model kinetically limited adsorption using a mass transfer model. The second reaction module represents biological transformation of 8:2 FTOH and daughter species, illustrating how a complex reaction pathway network can be represented. Both reaction modules allow for spatially variable parameter values so that a variety of remediation approaches (e.g., a PRB or volumetric treatment or variations in geochemical conditions) can be simulated. The intent with these PFAS reaction modules is to provide tools for practitioners to aid in the selection, design, and assessment of potential in situ PFAS remediation strategies. It is anticipated that, as PFAS remediation technologies and scientific understanding advances, these modules would be refined or replaced to match new knowledge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Atmospheric Transport of North African Dust-Bearing Supermicron Freshwater Diatoms to South America: Implications for Iron Transport to the Equatorial North Atlantic Ocean

The equatorial North Atlantic Ocean (NAO) is a nutrient-limited ecosystem that relies on the deposition of long-range transported iron (Fe)-containing aerosols to stimulate primary productivity. Using microscopy, we characterized supermicron and supercoarse mode African aerosols transported to the western NAO in boreal winter/spring. In this work, we detected three particle types including African dust, primary biological aerosol particles, and freshwater diatoms (FDs). FDs contained 4% Fe by weight due to surficial dust inclusions that may be susceptible to chemical processing and dissolution. FDs were typically larger than dust particles and comprised 38% of particles between 10 and 18 μm in diameter. The low density, high surface-area-to-volume ratio, and large aspect ratios of FD particles suggest a mechanism by which they can be carried great distances aloft. These same properties likely increase the residence time of FDs in surface waters thereby increasing the time for Fe dissolution and their potential impact on marine biogeochemical cycles.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

A Maize GT14 Family Glycosyltransferase Affects Cell Wall Composition and Carbohydrate Export from Source Leaves

Sucrose translocation from photosynthetic leaves to distant parts of a plant, such as seeds and roots, is a critical aspect of plant growth and development and a major determinant of crop yield. To identify genes contributing to this process in maize (Zea mays), we isolated four allelic mutants, carbohydrate partitioning defective7, 48, 49 (cpd7, cpd48, cpd49) and a UniformMu insertion (mu1049954), all of which exhibited reduced growth and fertility and hyperaccumulation of starch and soluble sugars in mature leaves. Consistent with carbohydrate accumulation, cpd7 mutants exhibited reduced sucrose export from mature leaves. Cpd7 encodes a Golgi-resident glucuronosyltransferase belonging to the Glycosyltransferase14 (GT14) family, which is involved in decoration of type II arabinogalactan proteins. No previously described GT14 mutants exhibit reduced sucrose transport or carbohydrate partitioning defects. Additionally, we show that mature leaves of cpd7 mutants have reduced cellulose content and an altered cell wall composition. Further, cpd7 mutants exhibit ectopic phloem lignification likely as a compensatory mechanism for reduced cell wall integrity. Collectively, our data suggest that Cpd7 functions to facilitate cell wall development in the phloem, which is required for efficient sucrose export from mature maize leaves.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Regulation of L - and D -Aspartate Transport and Metabolism in Acinetobacter baylyi ADP1

Here, the regulated uptake and consumption of d-amino acids by bacteria remain largely unexplored, despite the physiological importance of these compounds. Unlike other characterized bacteria, such as Escherichia coli, which utilizes only l-Asp, Acinetobacter baylyi ADP1 can consume both d-Asp and l-Asp as the sole carbon or nitrogen source. As described here, two LysR-type transcriptional regulators (LTTRs), DarR and AalR, control d- and l-Asp metabolism in strain ADP1. Heterologous expression of A. baylyi proteins enabled E. coli to use d-Asp as the carbon source when either of two transporters (AspT or AspY) and a racemase (RacD) were coexpressed. A third transporter, designated AspS, was also discovered to transport Asp in ADP1. DarR and/or AalR controlled the transcription of aspT, aspY, racD, and aspA (which encodes aspartate ammonia lyase). Conserved residues in the N-terminal DNA-binding domains of both regulators likely enable them to recognize the same DNA consensus sequence (ATGC-N7-GCAT) in several operator-promoter regions. In strains lacking AalR, suppressor mutations revealed a role for the ClpAP protease in Asp metabolism. In the absence of the ClpA component of this protease, DarR can compensate for the loss of AalR. ADP1 consumed l- and d-Asn and l-Glu, but not d-Glu, as the sole carbon or nitrogen source using interrelated pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Using Complex Probability Amplitudes to Simulate Solute Transport in Composite Porous Media

Probability amplitudes are fundamental to quantum mechanics and offer robust descriptions of complicated systems, which have allowed physicists to explain behaviors inaccessible to classical physics. This article ponders how some of the same conceptual underpinnings of the mathematics used for modeling quantum systems might be applied to subsurface water resources problems and speculates how these tools could facilitate applications on quantum computers. A probability amplitude-based model for describing advective-dispersive transport in porous media using linear operators is investigated. The proposed complex valued model decomposes spreading into two “sub-continuum partial dispersion” coefficients, and this recovers classical spreading when the sum of these coefficients is the Fickian dispersion coefficient. However, the probability amplitudes have a manyto-one relationship to a probability distribution, so it embeds a level of heterogeneity into seemingly equivalent functions. Two propagators with different sub-continuum coefficients may have the same macroscopic behavior when either is considered in isolation, but when they act on the other the system’s behavior changes. Additionally, differences in the amplitudes cause a reduction in spreading as velocity correlations are disrupted, despite both propagators having identical dispersion coefficients, and this cannot be achieved using classical methods without changing the dispersion coefficient. The main point is that these amplitude-based models offer a way to embed information about the system into the propagators, instead of just “averaging it out” when making an upscaled model.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A systems genetic analysis identifies putative mechanisms and candidate genes regulating vessel traits in poplar wood

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Large-scale prediction of outer-membrane multiheme cytochromes uncovers hidden diversity of electroactive bacteria and underlying pathways

Multi-heme cytochromes (MHCs), together with accessory proteins like porins and periplasmic cytochromes, enable microbes to transport electrons between the cytoplasmic membrane and extracellular substrates (e.g., minerals, electrodes, other cells). Extracellular electron transfer (EET) has been described in multiple systems; yet, the broad phylogenetic and mechanistic diversity of these pathways is less clear. One commonality in EET-capable systems is the involvement of MHCs, in the form of porin-cytochrome complexes, pili-like cytochrome polymers, and lipid-anchored extracellular cytochromes. Here, we put forth MHCscan—a software tool for identifying MHCs and identifying potential EET capability. Using MHCscan, we scanned ~60,000 bacterial and 2,000 archaeal assemblies, and identify a diversity of MHCs, many of which represent enzymes with no known function, and many found within organisms not previously known to be electroactive. In total, our scan identified ~1,400 unique enzymes, each encoding more than 10 heme-binding motifs. In our analysis, we also find evidence for modularity and flexibility in MHC-dependent EET pathways, and suggest that MHCs may be far more common than previously recognized, with many facets yet to be discovered. We present MHCscan as a lightweight and user-friendly software tool that is freely available: https://github.com/Arkadiy-Garber/MHCscan.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Biological and Environmental Research Network Requirements Review (Final Report)

The Energy Sciences Network (ESnet) is the high-performance network user facility for the US Department of Energy (DOE) Office of Science (SC) and delivers highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the DOE science mission by connecting all its laboratories and facilities in the US and abroad. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education (R&E) networking community. Between August 2022 and April 2023, ESnet and the Office of Biological and Environmental Research (BER) of the DOE SC organized an ESnet requirements review of BER-supported activities. Preparation for these events included identification of key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare formal case study documents about its relationship to the BER ESS program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward. A series of pre-planning meetings better prepared case study authors for this task, along with guidance on how the review would proceed in a virtual fashion.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar ( Populus trichocarpa ). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Polyketide synthase-based controlled synthesis of polycyclopropanated fuel molecules

Reducing carbon emissions from aviation and long-distance transportation sectors requires the development of sustainable biofuels with suitable energy density, freezing point, and other physical properties. We previously demonstrated biological production of high energy polycyclopropanated fatty acids (POP-FAs, class I) using an iterative polyketide synthase (iPKS) pathway in a Streptomyces host. Here, we used a computational model of fuel properties to identify chain length and cyclopropanation control as critical steps to engineer this iPKS for biofuel applications. We next explored the natural diversity of POP biosynthesis by investigating homologous pathways. Then, by in vivo gene exchange, we determined cyclopropanase (CP) catalysis to be key for POP-FA engineering. Leveraging both natural and engineered pathway product diversity, we demonstrate targeted production of improved POP-FAs, namely shortened POP-FAs with predicted superior freezing point properties for aviation, as well as fully cyclopropane-saturated POP-FAs which should have superior energy-density. These precise and controllable modifications to POP-FA structure open the door for bioproduction of designer POP fuels.

Yin, Kevin↗
DOE OSTI2023

Sucrose transport inside the phloem: Bridging hydrodynamics and geometric characteristics

In plants, the delivery of the products of photosynthesis is achieved through a hydraulic system labeled as phloem. This semi-permeable plant tissue consists of living cells that contract and expand in response to fluid pressure and flow velocity fluctuations. The Münch pressure flow theory, which is based on osmosis providing the necessary pressure gradient to drive the mass flow of carbohydrates, is currently the most accepted model for such sucrose transport. When this hypothesis is combined with the conservation of fluid mass and momentum as well as sucrose mass, many simplifications must be invoked to mathematically close the problem and to resolve the flow. Here this study revisits such osmotically driven flows by developing a new two-dimensional numerical model in cylindrical coordinates for an elastic membrane and a concentration-dependent viscosity. It is demonstrated that the interaction between the hydrodynamic and externally supplied geometrical characteristic of the phloem has a significant effect on the front speed of sucrose transport. These results offer a novel perspective about the evolutionary adaptation of plant hydraulic traits to optimize phloem soluble compounds transport efficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Electrochromic shift supports the membrane destabilization model of Tat-mediated transport and shows ion leakage during Sec transport

Significance Due to the transient nature of the active Tat complex, much of the knowledge available has been hard won. Electric-field-indicating absorbance transients allow investigation of transmembrane ion movement using native electric potential in thylakoids while circumventing challenges of reconstitution. Electrical behavior of transiently and/or constitutively assembled complexes suggests that Sec translocation occurs through a barrel-stave-type proteinaceous pore, while Tat translocation likely occurs through a toroidal pore. This would be the first instance of toroidal pores being exploited by a general protein translocation system. Our electrochemical analysis offers insight into how protein transport might be linked to light stimulation. Localized membrane destabilization presents a rational link between the proton motive force, membrane thinning, and Tat-mediated transport of substrates critical to photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure and intermolecular organization. Synthetic rings are hybrid objects with conformations that display both ideal random walk and compact globular features, which can serve as models of genomic DNA. To date, emphasis has been placed on the effect of ring molecular weight on their unusual behaviors. Here, we combine simulations and a microscopic force-level theory to build a unified understanding for how key aspects of ring dynamics depend on different tunable molecular properties including backbone rigidity, monomer concentration, degree of traditional entanglement, and molecular weight. Our large-scale molecular dynamics simulations of ring melts with very different backbone stiffnesses reveal unanticipated behaviors which agree well with our generalized theory. This includes a universal master curve for center-of-mass diffusion constants as a function of molecular weight scaled by a chemistry and thermodynamic state-dependent critical molecular weight that generalizes the concept of an entanglement cross-over for linear chains. The key physics is how backbone rigidity and monomer concentration induced changes of the entanglement length, interring packing, degree of interpenetration, and liquid compressibility slow down space-time dynamic-force correlations on macromolecular scales. A power law decay of the center-of-mass diffusion constant with inverse molecular weight squared is the first consequence, followed by an ultraslow activated hopping transport regime. Our results set the stage to address slow dynamics and kinetic arrest in different families of compact synthetic and biological polymeric systems.

Science & Technology - Other Topics↗
DOE OSTI2023

The molecular mechanism of sialic acid transport mediated by Sialin

Malfunction of the sialic acid transporter caused by various genetic mutations in the SLC17A5 gene encoding Sialin leads to a spectrum of neurodegenerative conditions called free sialic acid storage disorders. Unfortunately, how Sialin transports sialic acid/proton (H + ) and how pathogenic mutations impair its function are poorly defined. Here, we present the structure of human Sialin in an inward-facing partially open conformation determined by cryo–electron microscopy, representing the first high-resolution structure of any human SLC17 member. Our analysis reveals two unique features in Sialin: (i) The H + coupling/sensing requires two highly conserved Glu residues (E171 and E175) instead of one (E175) as implied in previous studies; and (ii) the normal function of Sialin requires the stabilization of a cytosolic helix, which has not been noticed in the literature. By mapping known pathogenic mutations, we provide mechanistic explanations for corresponding functional defects. We propose a structure-based mechanism for sialic acid transport mediated by Sialin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Arabidopsis thaliana nucleotide sugar transporter GONST2 is a functional homolog of GONST1

Abstract Glycosylinositolphosphorylceramides (GIPCs) are the predominant lipid in the outer leaflet of the plasma membrane. Characterized GIPC glycosylation mutants have severe or lethal plant phenotypes. However, the function of the glycosylation is unclear. Previously, we characterized Arabidopsis thaliana GONST1 and showed that it was a nucleotide sugar transporter which provides GDP‐mannose for GIPC glycosylation. gonst1 has a severe growth phenotype, as well as a constitutive defense response. Here, we characterize a mutant in GONST1’s closest homolog, GONST2. The gonst2‐ 1 allele has a minor change to GIPC headgroup glycosylation. Like other reported GIPC glycosylation mutants, gonst1‐1gonst2‐1 has reduced cellulose, a cell wall polymer that is synthesized at the plasma membrane. The gonst2‐1 allele has increased resistance to a biotrophic pathogen Golovinomyces orontii but not the necrotrophic pathogen Botrytis cinerea . Expression of GONST2 under the GONST1 promoter can rescue the gonst1 phenotype, indicating that GONST2 has a similar function to GONST1 in providing GDP‐D‐Man for GIPC mannosylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary

Significance Biomolecules, such as proteins or nucleic acids, can condense into liquid droplets whose biological or technological function depends on interactions with other solutes. We explore such interactions using a system of self-assembled DNA particles that forms liquid droplets which are degraded by an active solute, a restriction enzyme. We find that enzymes are able to penetrate the droplets when the liquid is poised near the phase boundary, enhancing the degradation rate and, in certain cases, causing internal bubbling. These results point to a complex interplay of phase stability and solute transport in liquid–liquid phase-separating macromolecular systems.

59 BASIC BIOLOGICAL SCIENCES↗