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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 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism

ABSTRACT Trichoderma species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism, Trichoderma spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host’s cell wall. Here, we explored the participation of the Trichoderma atroviride RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the T. atroviride -RNAi when interacting with Alternaria alternata, Rhizoctonia solani AG2 , and R. solani AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the Trichoderma -host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition ( het ) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in T. atroviride dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established. IMPORTANCE There is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing Trichoderma species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by Trichoderma species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of Trichoderma species, there are still unsolved questions related to how Trichoderma regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by Trichoderma atroviride .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Scalable Causal Graph Learning through a Deep Neural Network

Learning the causal graph in a complex system is crucial for knowledge discovery and decision making, yet it remains a challenging problem because of the unknown nonlinear interaction among system components. Most of the existing methods either rely on predefined kernel or data distribution, or they focus simply on the causality between a single target and the remaining system. This work presents a deep neural network for scalable causal graph learning (SCGL) through low-rank approximation. The SCGL model can explore nonlinearity on both temporal and intervariable relationships without any predefined kernel or distribution assumptions. Through low-rank approximation, the noise influence is reduced, and better accuracy and high scalability are achieved. Experiments using synthetic and real-world datasets show that our SCGL algorithm outperforms existing state-of-the-art methods for causal graph learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Site-specific programming of the host epithelial transcriptome by the gut microbiota

The intestinal epithelium separates us from the microbiota but also interacts with it and thus affects host immune status and physiology. Previous studies investigated microbiota-induced responses in the gut using intact tissues or unfractionated epithelial cells, thereby limiting conclusions about regional differences in the epithelium. Here, we sought to investigate microbiota-induced transcriptional responses in specific fractions of intestinal epithelial cells. To this end, we used microarray analysis of laser capture microdissection (LCM)-harvested ileal and colonic tip and crypt epithelial fractions from germ-free and conventionally raised mice and from mice during the time course of colonization. We found that about 10% of the host’s transcriptome was microbially regulated, mainly including genes annotated with functions in immunity, cell proliferation, and metabolism. The microbial impact on host gene expression was highly site specific, as epithelial responses to the microbiota differed between cell fractions. Specific transcriptional regulators were enriched in each fraction. In general, the gut microbiota induced a more rapid response in the colon than in the ileum. Our study indicates that the microbiota engage different regulatory networks to alter host gene expression in a particular niche. Understanding host-microbiota interactions on a cellular level may facilitate signaling pathways that contribute to health and disease and thus provide new therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass

Abstract Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost‐effective 3′‐Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C 4 perennial grass, Panicum hallii . We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine‐scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis ‐regulatory elements and biological processes under short‐ and long‐day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod‐dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well‐known GI‐interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.

Weng, Xiaoyu↗
DOE OSTI2023

Multiple incommensurate magnetic states in the kagome antiferromagnet Na 2 Mn 3 Cl 8

The kagome lattice can host exotic magnetic phases arising from frustrated and competing magnetic interactions. However, relatively few insulating kagome materials exhibit incommensurate magnetic ordering. Here, we present a study of the magnetic structures and interactions of antiferromagnetic Na 2 Mn 3 Cl 8 with an undistorted Mn 2+ kagome network. Using neutron-diffraction and bulk magnetic measurements, we show that Na 2 Mn 3 Cl 8 hosts two different incommensurate magnetic states, which develop at T N1 = 1.6 K and T N2 = 0.6 K. Magnetic Rietveld refinements indicate magnetic propagation vectors of the form q=(q x , q y , $\frac{3}{2}$), and our neutron-diffraction data can be well described by cycloidal magnetic structures. By optimizing exchange parameters against magnetic diffuse-scattering data, we show that the spin Hamiltonian contains ferromagnetic nearest-neighbor and antiferromagnetic third-neighbor Heisenberg interactions, with a significant contribution from long-ranged dipolar coupling. This experimentally determined interaction model is compared with density-functional-theory simulations. Using classical Monte Carlo simulations, we show that these competing interactions explain the experimental observation of multiple incommensurate magnetic phases and may stabilize multi-q states. Here, our results expand the known range of magnetic behavior on the kagome lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Controllable growth of interpenetrating or random copolymer networks

Interpenetrating and random copolymer networks are vital in a number of industrial applications, including the fabrication of automotive parts, damping materials, and tissue engineering scaffolds. We develop a theoretical model for a process that enables the controlled growth of interpenetrating network (IPNs), or a random copolymer network (RCN) of specified size and mechanical properties. In this process, a primary gel “seed” is immersed into a solution containing the secondary monomer and crosslinkers. After the latter species are absorbed into the primary network, the absorbed monomers are polymerized to form the secondary polymer chains, which then can undergo further crosslinking to form an IPN, or undergo inter-chain exchange with the existing network to form a RCN. The swelling and elastic properties of the IPN and RCN networks can be tailored by modifying the monomer and crosslinker concentrations in the surrounding solution, or by tuning the enthalpic interactions between the primary polymer, secondary monomer and solvent through a proper choice of chemistry. This process can be used repeatedly to fabricate gels with a range of mechanical properties from stiff, rigid materials to soft, flexible networks, allowing the method to meet the materials requirements of a variety of applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Latent map Gaussian processes for mixed variable metamodeling

Gaussian processes (GPs) are ubiquitously used in sciences and engineering as metamodels. Standard GPs, however, can only handle numerical or quantitative variables. Here we introduce latent map Gaussian processes (LMGPs) that inherit the attractive properties of GPs and are also applicable to mixed data which have both quantitative and qualitative inputs. The core idea behind LMGPs is to learn a continuous, low-dimensional latent space or manifold which encodes all qualitative inputs. To learn this manifold, we first assign a unique prior vector representation to each combination of qualitative inputs. We then use a low-rank linear map to project these priors on a manifold that characterizes the posterior representations. As the posteriors are quantitative, they can be directly used in any standard correlation function such as the Gaussian or Matern. Hence, the optimal map and the corresponding manifold, along with other hyperparameters of the correlation function, can be systematically learned via maximum likelihood estimation. Through a wide range of analytic and real-world examples, we demonstrate the advantages of LMGPs over state-of-the-art methods in terms of accuracy and versatility. In particular, we show that LMGPs can handle variable-length inputs, have an explainable neural network interpretation, and provide insights into how qualitative inputs affect the response or interact with each other. We also employ LMGPs in Bayesian optimization and illustrate that they can discover optimal compound compositions more efficiently than conventional methods that convert compositions to qualitative variables via manual featurization.

42 ENGINEERING↗
DOE OSTI2012

Mechanistic and Structural Analyses of the Role of His67 in the Yeast Polyamine Oxidase Fms1

The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N1-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N1-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2-3 orders of magnitude, with the H67Q mutation having the smallest effect and H67N the largest. The k{sub cat}/K{sub O2} value changes very little upon mutation with N{sup 1}-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The k{sub cat}/K{sub M}-pH profiles with N{sup 1}-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pK{sub a} values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pK{sub a} as wild-type Fms1, about {approx}7.4; this pK{sub a} is assigned to the substrate N4. The k{sub cat}/K{sub O2}-pH profiles for wild-type Fms1 and the H67A enzyme both show a pK{sub a} of about {approx}6.9; this suggests His67 is not responsible for this pH behavior. With the H67Q, H67N, and H67A enzymes the k{sub cat} value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 {angstrom}. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure.

08 HYDROGEN↗
DOE OSTI2011

Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the “Hydrophobic Wall” of Carbonic Anhydrase

The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H{sub 2}NSO{sub 2}C{sub 6}H{sub 4}-CONHCH{sub 2}(CX{sub 2}){sub n}CX{sub 3}, n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).

08 HYDROGEN↗
DOE OSTI2024

Integrating Tide‐Driven Wetland Soil Redox and Biogeochemical Interactions Into a Land Surface Model

Abstract Redox processes, aqueous and solid‐phase chemistry, and pH dynamics are key drivers of subsurface biogeochemical cycling and methanogenesis in terrestrial and wetland ecosystems but are typically not included in terrestrial carbon cycle models. These omissions may introduce errors when simulating systems where redox interactions and pH fluctuations are important, such as wetlands where saturation of soils can produce anoxic conditions and coastal systems where sulfate inputs from seawater can influence biogeochemistry. Integrating cycling of redox‐sensitive elements could therefore allow models to better represent key elements of carbon cycling and greenhouse gas production. We describe a model framework that couples the Energy Exascale Earth System Model (E3SM) Land Model (ELM) with PFLOTRAN biogeochemistry, allowing geochemical processes and redox interactions to be integrated with land surface model simulations. We implemented a reaction network including aerobic decomposition, fermentation, sulfate reduction, sulfide oxidation, methanogenesis, and methanotrophy as well as pH dynamics along with iron oxide and iron sulfide mineral precipitation and dissolution. We simulated biogeochemical cycling in tidal wetlands subject to either saltwater or freshwater inputs driven by tidal hydrological dynamics. In simulations with saltwater tidal inputs, sulfate reduction led to accumulation of sulfide, higher dissolved inorganic carbon concentrations, lower dissolved organic carbon concentrations, and lower methane emissions than simulations with freshwater tidal inputs. Model simulations compared well with measured porewater concentrations and surface gas emissions from coastal wetlands in the Northeastern United States. These results demonstrate how simulating geochemical reaction networks can improve land surface model simulations of subsurface biogeochemistry and carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Magnetic field-temperature phase diagram of multiferroic (NH4)2FeCl5·H2O

Abstract Owing to their overall low energy scales, flexible molecular architectures, and ease of chemical substitution, molecule-based multiferroics are extraordinarily responsive to external stimuli and exhibit remarkably rich phase diagrams. Even so, the stability and microscopic properties of various magnetic states in close proximity to quantum critical points are highly under-explored in these materials. Inspired by these opportunities, we combined pulsed-field magnetization, first-principles calculations, and numerical simulations to reveal the magnetic field–temperature ( B – T ) phase diagram of multiferroic (NH 4 ) 2 FeCl 5 ⋅H 2 O. In this system, a network of intermolecular hydrogen and halogen bonds creates a competing set of exchange interactions that generates additional structure in the phase diagram—both in the vicinity of the spin flop and near the 30 T transition to the fully saturated state. Consequently, the phase diagrams of (NH 4 ) 2 FeCl 5 ⋅H 2 O and its deuterated analog are much more complex than those of other molecule-based multiferroics. The entire series of coupled electric and magnetic transitions can be accessed with a powered magnet, opening the door to exploration and control of properties in this and related materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Correlating structural changes in thermoresponsive hydrogels to the optical response of embedded plasmonic nanoparticles

Stimuli-responsive microgels, composed of small beads with soft, deformable polymer networks swollen through a combination of synthetic control over the polymer and its interaction with water, form a versatile platform for development of multifunctional and biocompatible sensors. The interfacial structural variation of such materials at a nanometer length scale is essential to their function, but not yet fully comprehended. Here, we take advantage of the plasmonic response of a gold nanorod embedded in a thermoresponsive microgel (AuNR@PNIPMAm) to monitor structural changes in the hydrogel directly near the nanorod surface. By direct comparison of the plasmon response against measurements of the hydrogel structure from dynamic light scattering and nuclear magnetic resonance, we find that the microgel shell of batch-polymerized AuNR@PNIPMAm exhibits a heterogeneous volume phase transition reflected by different onset temperatures for changes in the hydrodyanmic radius (R H ) and plasmon resonance, respectively. The new approach of contrasting plasmonic response (a measure of local surface hydrogel structure) with R H and relaxation times paves a new path to gain valuable insight for the design of plasmonic sensors based on stimuli-responsive hydrogels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Probing itinerant carrier dynamics at the diamond surface using single nitrogen vacancy centers

Color centers in diamond are widely explored for applications in quantum sensing, computing, and networking. Their optical, spin, and charge properties have extensively been studied, while their interactions with itinerant carriers are relatively unexplored. Here, we show that NV centers situated 10 ± 5 nm of the diamond surface can be converted to the neutral charge state via hole capture. By measuring the hole capture rate, we extract the capture cross section, which is suppressed by proximity to the diamond surface. The distance dependence is consistent with a carrier diffusion model, indicating that the itinerant carrier lifetime can be long, even at the diamond surface. Measuring dynamics of near-surface NV centers offers a tool for characterizing the diamond surface and investigating charge transport in diamond devices.

Physics↗
DOE OSTI2017

Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyl transfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Continuous Spin Excitations in the Three-Dimensional Frustrated Magnet K 2 Ni 2 ⁢(SO 4 ) 3

Continuous spin excitations are widely recognized as one of the hallmarks of novel spin states in quantum magnets, such as quantum spin liquids (QSLs). Here, we report the observation of such kind of excitations in K 2 Ni 2 (SO 4 ) 3 , which consists of two sets of intersected spin-1 (Ni 2+ ) trillium lattices. Our inelastic neutron scattering measurement on single crystals clearly shows a dominant excitation continuum, which exhibits a distinct temperature-dependent behavior from that of spin waves and is rooted in strong quantum spin fluctuations. Further using the self-consistent-Gaussian-approximation method, we determine that the fourth- and fifth nearest-neighbor exchange interactions are dominant. These two bonds together form a unique three-dimensional network of corner-sharing tetrahedra, which we name as a “hypertrillium” lattice. In conclusion, our results provide direct evidence for the existence of QSL features in K 2 Ni 2 (SO 4 ) 3 and highlight the potential for the hypertrillium lattice to host frustrated quantum magnetism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Nonthermal Bonding Origin of a Novel Photoexcited Lattice Instability in SnSe

Lattice dynamics measurements are often crucial tools for understanding how materials transform between different structures. Here, we report time-resolved x-ray scattering-based measurements of the nonequilibrium lattice dynamics in SnSe, a monochalcogenide reported to host a novel photoinduced lattice instability. By fitting interatomic force models to the fluence dependent excited-state dispersion, we determine the nonthermal origin of the lattice instability to be dominated by changes of interatomic interactions along a bilayer-connecting bond, rather than of an intralayer bonding network that is of primary importance to the lattice instability in thermal equilibrium.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A graphical user interface platform to support power electronic converters and integrated systems

Power Electronic Systems have grown in size and complexity over the past years. Therefore, users require interfaces to properly configure, develop, and deploy these systems. This work presents a Graphical User Interface that dynamically adapts to the system and allows the user to control and monitor its operation. This GUI uses networked communication and open-source Python libraries to allow the user to interact with the system at its different hierarchical layers, as well as visualize the interconnection of the full system. This is demonstrated by showing the user interface applied to a megawatt class charging station that consists of various energy resources.

Dean, Ben↗
DOE OSTI2014

Molecular Mimicry Regulates ABA Signaling by SnRK2 Kinases and PP2C Phosphatases

Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, while the conserved ABA-sensing tryptophan of PP2C inserts into the kinase catalytic cleft, thus mimicking receptor-PP2C interactions. These structural results provide a simple mechanism that directly couples ABA binding to SnRK2 kinase activation and highlight a new paradigm of kinase-phosphatase regulation through mutual packing of their catalytic sites.

59 BASIC BIOLOGICAL SCIENCES↗