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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗
DOE OSTI2022

Seeking regularity from irregularity: unveiling the synthesis–nanomorphology relationships of heterogeneous nanomaterials using unsupervised machine learning

Nanoscale morphology of functional materials determines their chemical and physical properties. However, despite increasing use of transmission electron microscopy (TEM) to directly image nanomorphology, it remains challenging to quantify the information embedded in TEM data sets, and to use nanomorphology to link synthesis and processing conditions to properties. We develop an automated, descriptor-free analysis workflow for TEM data that utilizes convolutional neural networks and unsupervised learning to quantify and classify nanomorphology, and thereby reveal synthesis–nanomorphology relationships in three different systems. While TEM records nanomorphology readily in two-dimensional (2D) images or three-dimensional (3D) tomograms, we advance the analysis of these images by identifying and applying a universal shape fingerprint function to characterize nanomorphology. After dimensionality reduction through principal component analysis, this function then serves as the input for morphology grouping through unsupervised learning. We demonstrate the wide applicability of our workflow to both 2D and 3D TEM data sets, and to both inorganic and organic nanomaterials, including tetrahedral gold nanoparticles mixed with irregularly shaped impurities, hybrid polymer-patched gold nanoprisms, and polyamide membranes with irregular and heterogeneous 3D crumple structures. In each of these systems, unsupervised nanomorphology grouping identifies both the diversity and the similarity of the nanomaterial across different synthesis conditions, revealing how synthetic parameters guide nanomorphology development. Our work opens possibilities for enhancing synthesis of nanomaterials through artificial intelligence and for understanding and controlling complex nanomorphology, both for 2D systems and in the far less explored case of 3D structures, such as those with embedded voids or hidden interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Vacancy-Dependent Diffusion Mechanism in Oxygen-Defective SrFeO 3 Perovskite Materials: First-Principles Density Functional Theory and Experimental Approach

Understanding oxygen diffusion at the atomic scale in SrFeO 3−δ perovskites is crucial for developing oxygen storage materials with optimal performance. Such materials are required to have high stability, corrosion resistance, and acceptable oxygen storage capacity at moderate operating temperatures and pressures. Here, in this study, we used first-principles density functional theory and thermogravimetric analysis to study the vacancy-dependent oxygen diffusion in oxygen-deficient SrFeO 3−δ (δ = 0, 0.065, 0.125, 0.25, 0.5) perovskites. The electronic structures, including the partial- and spin-resolved density of states, for different SrFeO 3−δ phases were calculated and compared with available experimental and theoretical results. By mapping the migration pathways, we investigated diffusion mechanisms and calculated the energy barriers for oxygen diffusion in cubic, orthorhombic, and brownmillerite phases of SrFeO 3−δ perovskites. Using the calculated energy barriers, we deduced the diffusion time scales and diffusion coefficients within SrFeO 3−δ . A diffusion coefficient on the order of 10 –8 m 2 /s was obtained for SrFeO 2.875 . We experimentally investigated the roles of temperature and oxygen partial pressures on the redox kinetics and deduced the kinetics rate and diffusion density, which agreed well with the calculated values for the density of diffusing oxygen vacancy in the lattice. Our results showed that the energy barrier tends to reduce at higher oxygen concentrations. Our results serve as an important guideline for designing oxygen storage materials with optimal redox kinetics.

chemical looping with oxygen uncoupling (CLOU)↗
DOE OSTI2023

Ultrafast Jahn‐Teller Photoswitching in Cobalt Single‐Ion Magnets

Abstract Single‐ion magnets (SIMs) constitute the ultimate size limit in the quest for miniaturizing magnetic materials. Several bottlenecks currently hindering breakthroughs in quantum information and communication technologies could be alleviated by new generations of SIMs displaying multifunctionality. Here, ultrafast optical absorption spectroscopy and X‐ray emission spectroscopy are employed to track the photoinduced spin‐state switching of the prototypical complex [Co(terpy) 2 ] 2+ (terpy = 2,2′:6′,2″‐terpyridine) in solution phase. The combined measurements and their analysis supported by density functional theory (DFT), time‐dependent‐DFT (TD‐DFT) and multireference quantum chemistry calculations reveal that the complex undergoes a spin‐state transition from a tetragonally elongated doublet state to a tetragonally compressed quartet state on the femtosecond timescale, i.e., it sustains ultrafast Jahn‐Teller (JT) photoswitching between two different spin multiplicities. Adding new Co‐based complexes as possible contenders in the search for JT photoswitching SIMs will greatly widen the possibilities for implementing magnetic multifunctionality and eventually controlling ultrafast magnetization with optical photons.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Alternate Synthesis Method for High-Performance Manganese Rich Cation Disordered Rocksalt Cathodes

Cation-disordered rocksalt (DRX) cathodes have recently emerged as a promising class of cobalt-free, high-capacity cathodes for lithium-ion batteries. To facilitate their commercialization, the development of scalable synthesis techniques providing control over composition and morphology is critical. To this end, a sol-gel synthesis route to prepare Mn-rich DRX cathodes with high capacities is presented here. Several compositions with varied Mn content and nominal F doping are successfully prepared using this technique. In-situ X-ray diffraction measurements demonstrate that DRX formation proceeds at moderate temperature (800 °C) through the sol-gel route, which enables intimate mixing among reactive intermediate phases that form at lower temperatures. All synthesized compositions possess cation short-range order, as evidenced by neutron pair distribution function and electron diffraction analysis. These DRX materials demonstrate promising electrochemical performance with reversible capacities up to 275 mAh g. Compared to the baseline oxide (Li 1.2 Mn 0.4 Ti 0.4 O 2 ), the Mn-rich compositions exhibit improved cycling stability, with some showing an increase in capacity upon cycling. Finally, this study demonstrates the feasibility of preparing high-capacity DRX cathodes through a sol-gel based synthesis route, which may be further optimized to provide better control over the product morphology compared to traditional synthesis methods.

25 ENERGY STORAGE↗
DOE OSTI2021

Thermal Unequilibrium of PdSn Intermetallic Nanocatalysts: From In Situ Tailored Synthesis to Unexpected Hydrogenation Selectivity

Abstract Effective control on chemoselectivity in the catalytic hydrogenation of C=O over C=C bonds is uncommon with Pd‐based catalysts because of the favored adsorption of C=C bonds on Pd surface. Here we report a unique orthorhombic PdSn intermetallic phase with unprecedented chemoselectivity toward C=O hydrogenation. We observed the formation and metastability of this PdSn phase in situ. During a natural cooling process, the PdSn nanoparticles readily revert to the favored Pd 3 Sn 2 phase. Instead, using a thermal quenching method, we prepared a pure‐phase PdSn nanocatalyst. PdSn shows an >96 % selectivity toward hydrogenating C=O bonds of various α,β‐unsaturated aldehydes, highest in reported Pd‐based catalysts. Further study suggests that efficient quenching prevents the reversion from PdSn‐ to Pd 3 Sn 2 ‐structured surface, the key to the desired catalytic performance. Density functional theory calculations and analysis of reaction kinetics provide an explanation for the observed high selectivity.

Chen, Minda↗
DOE OSTI2021

Thermal Unequilibrium of PdSn Intermetallic Nanocatalysts: From In Situ Tailored Synthesis to Unexpected Hydrogenation Selectivity

Effective control on chemoselectivity in the catalytic hydrogenation of C=O over C=C bonds is uncommon with Pd-based catalysts because of the favored adsorption of C=C bonds on Pd surface. Here we report a unique orthorhombic PdSn intermetallic phase with unprecedented chemoselectivity toward C=O hydrogenation. We observed the formation and metastability of this PdSn phase in situ. During a natural cooling process, the PdSn nanoparticles readily revert to the favored Pd 3 Sn 2 phase. Instead, using a thermal quenching method, we prepared a pure-phase PdSn nanocatalyst. Furthermore, PdSn shows an >96% selectivity toward hydrogenating C=O bonds of various α,β-unsaturated aldehydes, highest in reported Pd-based catalysts. Further study suggests that efficient quenching prevents the reversion from PdSn- to Pd 3 Sn 2 -structured surface, the key to the desired catalytic performance. Density functional theory calculations and analysis of reaction kinetics provide an explanation for the observed high selectivity.

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

Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature

Objectives/Hypothesis: To establish comprehensive transcriptomic profiles of cholesteatoma perimatrix tissue and granulation tissue from chronic otitis media (COM) that did not develop cholesteatoma, which can indicate molecular pathways involved in the cholesteatoma perimatrix pathology and invasiveness. Study Design: Retrospective Case Series. Methods: Transcriptome data were obtained from cholesteatoma perimatrix tissue and COM granulation tissue by an Illumina iScan microarray. Differentially expressed genes (DEGs) were subsequently analyzed using both bioinformatical functional annotation and network analysis. Expression of candidate genes (MMP9 and LCN2) was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on a larger group of samples. Results: Analysis of the transcriptome led to the identification of 169 differentially expressed genes between investigated tissues. Bioinformatic analysis suggested that most significant biological processes involving DEGs were previously described in cholesteatoma pathology. Network analysis identified ERBB2, TFAP2A, and TP63 as major hubs of the DEGs molecular network. Furthermore, it was observed that the cellular component most significantly enriched in DEGs was extracellular space containing 47 DEGs. Using qRT-PCR, it was confirmed that mRNA levels of the major extracellular hub (MMP9) are increased, whereas its interacting molecule (LCN2) mRNA levels were decreased in cholesteatoma perimatrix tissue compared to COM granulation tissue. Conclusions: The current study approach offers an overall look at molecular mechanisms that describe the cholesteatoma entity by focusing exclusively on the perimatrix processes in comparison to COM granulation tissue. The observed differences in gene expression between cholesteatoma perimatrix and COM granulation tissue could suggest novel markers potentially influenced by the perimatrix–matrix molecular interplay, which is not present in COM without cholesteatoma. Level of Evidence: NA. Laryngoscope, 130:E220–E227, 2020. © 2019 The American Laryngological, Rhinological and Otological Society, Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗
DOE OSTI2020

Spectral emittance measurements of micro/nanostructures in energy conversion: a review

Micro/nanostructures play a key role in tuning the radiative properties of materials and have been applied to the high-temperature energy conversion systems for improved performance. Among the various radiative properties, spectral emittance is of integral importance for the design and analysis of materials that function as radiative absorbers or emitters. This article presents an overview of the spectral emittance measurement techniques using both the direct and indirect methods. Several micro/nanostructures are also introduced, and a special emphasis is placed on the emissometers developed for characterizing engineered micro/nanostructures in high-temperature applications (e.g., solar energy conversion and thermophotovoltaic devices). Both experimental facilities and measured results for different materials are summarized. Future prospects in developing instrumentation and micro/nanostructured surfaces for practical applications are also outlined. This study provides a comprehensive source of information for the application of micro/nanostructures in high-temperature energy conversion engineering.

14 SOLAR ENERGY↗
DOE OSTI2021

Gauge invariance and Ward identities in nonlinear response theory

We present a formal analysis of nonlinear response functions in terms of correlation functions in real- and imaginary-time domains. In particular, we show that causal nonlinear response functions, expressed in terms of nested commutators in real time, can be obtained from the analytic continuation of time-ordered response functions, which are more easily amenable to diagrammatic calculation. This generalizes the well-known result of linear response theory. We then use gauge invariance arguments to derive exact relations between second-order response functions in density and current channels. These identities, which are non-perturbative in the strength of inter-particle interactions, allow us to establish exact connections between nonlinear optics calculations done in different electromagnetic gauges.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

PYSIMFRAC: A Python library for synthetic fracture generation and analysis

In this paper, we introduce PYSIMFRAC, an open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. PYSIMFRAC allows the user to specify one of three fracture generation techniques (Box, Gaussian, or Spectral) and perform statistical analysis including the autocorrelation, moments, and probability density functions of the fracture surfaces and aperture. This analysis and accessibility of a python library allows the user to create realistic fracture realizations and vary properties of interest. In addition, PYSIMFRAC includes integration examples to two different pore-scale simulators and the discrete fracture network simulator, dfnWorks. The capabilities developed in this work provides opportunity for quick and smooth adoption and implementation by the wider scientific community for accurate characterization of fluid transport in geologic media. We present PYSIMFRAC along with integration examples and discuss the ability to extend PYSIMFRAC from a single complex fracture to complex fracture networks.

58 GEOSCIENCES↗
DOE OSTI2020

Inverse design of two-dimensional graphene/h-BN hybrids by a regressional and conditional GAN

Design of materials with desired properties is currently laborious and heavily relies on intuition of researchers through a trial-and-error process. To tackle this challenge, in this work we propose a novel regressional and conditional generative adversarial network (RCGAN) for inverse design of representative two-dimensional materials, the graphene and boron-nitride (BN) hybrids. RCGAN incorporates a supervised regressor network, thus overcoming the common technical barrier in the traditional unsupervised GANs, which cannot generate data when fed with continuous and quantitative labels. RCGAN can autonomously generate graphene/BN hybrids given any target bandgap values. These structures are distinguished from the ones used for training and exhibit high diversity for a given bandgap. Moreover, they exhibit high fidelity, yielding bandgaps within ~10% MAE F of the desired bandgaps as validated by density functional theory (DFT) calculations. Analysis by the principle component analysis (PCA) and modified locally linear embedding (MLLE) reveals that the generator has successfully generated structures following the statistical distribution of the real structures. It implies the possibility of the RCGAN in recognizing physical rules hidden in the high-dimensional data. The novel strategy for designing regressional GAN architecture together with the successful application to inverse design of materials would inspire further exploration in research fields beyond materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Multimodal Bayesian registration of noisy functions using Hamiltonian Monte Carlo

Functional data registration is a necessary processing step for many applications. The observed data can be inherently noisy, often due to measurement error or natural process uncertainty; which most functional alignment methods cannot handle. A pair of functions can also have multiple optimal alignment solutions, which is not addressed in current literature. In this paper, a flexible Bayesian approach to functional alignment is presented, which appropriately accounts for noise in the data without any pre-smoothing required. Additionally, by running parallel MCMC chains, the method can account for multiple optimal alignments via the multi-modal posterior distribution of the warping functions. To most efficiently sample the warping functions, the approach relies on a modification of the standard Hamiltonian Monte Carlo to be well-defined on the infinite-dimensional Hilbert space. In this work, this flexible Bayesian alignment method is applied to both simulated data and real data sets to show its efficiency in handling noisy functions and successfully accounting for multiple optimal alignments in the posterior; characterizing the uncertainty surrounding the warping functions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Magnetic ordering in Eu 2 In and Eu 2 Sn

Eu 2 In and Eu 2 Sn crystallize in the orthorhombic Co 2 Si-type structure (oP12, Pnma, No. 62) with In and Sn atoms occupying one 4c site and the Eu atoms filling two other 4c sites. Eu 2 In has a nearly ideal first-order magnetostructural transition (FOMT) at 55 K with a hysteresis of less than 0.1 K, a large entropy change and an adiabatic temperature change of 5.0 K in a field of 2 T. The anhysteretic nature of the FOMT is likely due to there being no change in cell symmetry and relatively small changes in the lattice parameters. There is no magnetostructural transition in Eu2Sn. In this work we present the results of powder neutron diffraction, magnetization, and Eu Mössbauer spectroscopy aimed to investigate the nature of magnetic order for both Eu 2 In and Eu 2 Sn. The Eu Mössbauer spectrum of Eu 2 In at 5 K shows two equal area components, consistent with Eu occupying two equal multiplicity crystallographic sites. However, the different hyperfine fields (B) of 27 T and 17 T suggest that the magnetic environments of the Eu moments on the two 4c sites are different. Neutron diffraction data at 2.5 K show that in Eu 2 In the order is ferromagnetic, with Eu moments on both Eu sites oriented parallel to the a-axis; moment values of 6.8 μB and 6.5 μB were found. For Eu 2 Sn measurements find two antiferromagnetic transitions, which are corroborated by neutron diffraction. Analysis of density-functional theory calculations shows negligible energy difference between differing magnetic configurations, indirectly supporting stability of multiple magnetic structures observed experimentally. While the transition at T N1 = 30 K corresponds to the formation of a simple k 1 = 0 antiferromagnetic structure with Eu-moments pointing along the b-axis, at T N2 = 13 K a coexisting second magnetic order with k 2 = [0, ½, ½] appears.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Goal-oriented a-posteriori estimation of model error as an aid to parameter estimation

In this work, a Bayesian model calibration framework is presented that utilizes goal-oriented a-posterior error estimates in quantities of interest (QoIs) for classes of high-fidelity models characterized by PDEs. It is shown that for a large class of computational models, it is possible to develop a computationally inexpensive procedure for calibrating parameters of high-fidelity models of physical events when the parameters of low-fidelity (surrogate) models are known with acceptable accuracy. The main ingredients in the proposed model calibration scheme are goal-oriented a-posteriori estimates of error in QoIs computed using a so-called lower fidelity model compared to those of an uncalibrated higher fidelity model. The estimates of error in QoIs are used to define likelihood functions in Bayesian inversion analysis. A standard Bayesian approach is employed to compute the posterior distribution of model parameters of high-fidelity models. As applications, parameters in a quasi-linear second-order elliptic boundary-value problem (BVP) are calibrated using a second-order linear elliptic BVP. In a second application, parameters of a tumor growth model involving nonlinear time-dependent PDEs are calibrated using a lower fidelity linear tumor growth model with known parameter values.

A-posterior estimates↗
DOE OSTI2022

Estimation of process steady state with autoregressive models and Bayesian inference

To improve efficiency, separations engineers will typically design process circuits containing recirculating streams, which mix one or more of the process outputs with the feed material. Doing so can improve efficiency, but will cause a delay in the system reaching steady state conditions until the recirculating load mass flows stabilize. In testing separation circuits, engineers will often test a variety of factors and complete an analysis from sample results. Knowledge of if a process is at steady state, as well as the steady state conditions of a process, is essential for a valid techno-economic analysis. However, the definition of process steady state is often poorly defined, or does not include uncertainty quantification. If the performance of a process operating under two different sets of conditions are compared, an engineer who does not test for steady state or quantify steady state conditions risks producing a faulty analysis. In this work, a Bayesian statistical method for testing if all streams are at steady state is further motivated and then derived. Then after testing for steady state, the same model is used with a prior distribution that enforces a steady state assumption to estimate steady state conditions. Further, these methods were validated in a solvent extraction pilot plant where steady state conditions for all outflows were inferred with uncertainty quantification. Analysis is completed with functions available to the reader as part of the BayesMassBal (V 1.1.0) software package written in R.

01 COAL, LIGNITE, AND PEAT↗