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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

An emerging multi-omic understanding of the genetics of opioid addiction

Opioid misuse, addiction, and associated overdose deaths remain global public health crises. Despite the tremendous need for pharmacological treatments, current options are limited in number, use, and effectiveness. Fundamental leaps forward in our understanding of the biology driving opioid addiction are needed to guide development of more effective medication-assisted therapies. This Review focuses on the omics-identified biological features associated with opioid addiction. Recent GWAS have begun to identify robust genetic associations, including variants in OPRM1, FURIN, and the gene cluster SCAI/PPP6C/RABEPK. An increasing number of omics studies of postmortem human brain tissue examining biological features (e.g., histone modification and gene expression) across different brain regions have identified broad gene dysregulation associated with overdose death among opioid misusers. Drawn together by meta-analysis and multi-omic systems biology, and informed by model organism studies, key biological pathways enriched for opioid addiction–associated genes are emerging, which include specific receptors (e.g., GABAB receptors, GPCR, and Trk) linked to signaling pathways (e.g., Trk, ERK/MAPK, orexin) that are associated with synaptic plasticity and neuronal signaling. Studies leveraging the agnostic discovery power of omics and placing it within the context of functional neurobiology will propel us toward much-needed, field-changing breakthroughs, including identification of actionable targets for drug development to treat this devastating brain disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis

Abstract Background Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions. Results To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13 C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13 C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts. Conclusions Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Analytic Binary Alloy Volume–Concentration Relations and the Deviation from Zen’s Law

Alloys expand or contract as concentrations change, and the resulting relationship between atomic volume and alloy content is an important property of the solid. While a well-known approximation posits that the atomic volume varies linearly with concentration (Zen’s law), the actual variation is more complicated. Here we use the apparent size of the solute (solvent) atom and the elasticity to derive explicit analytical expressions for the atomic volume of binary solid alloys. Two approximations, continuum and terminal, are proposed. Deviations from Zen’s law are studied for 22 binary alloy systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

U–Pb Geochronology and Stable Isotope Geochemistry of Terrestrial Carbonates, Lower Cretaceous Cedar Mountain Formation, Utah: Implications for Synchronicity of Terrestrial and Marine Carbon Isotope Excursions

The terrestrial Lower Cretaceous Cedar Mountain Formation, Utah, is a critical archive of paleoclimate, tectonics, and vertebrate ecology and evolution. Early Cretaceous carbon cycle perturbations associated with ocean anoxia have been interpreted from this succession, as expressed in stable carbon isotopes. However, refining the timing of the observed stable isotope excursions remains a key challenge in understanding how marine anoxia affects the Earth system, and is ultimately recorded in the terrestrial realm. The geochronology and geochemistry of a terrestrial carbonate near the base of this succession, which potentially records the Ap7 global carbon isotope excursion, is studied here. Petrographic and geochemical analyses are used to test plausible mechanisms for U incorporation into the calcite lattice in this sample. Using these methods, the hypothesis that the incorporation of U was at or close to the timing of carbonate precipitation is evaluated. U–Pb geochronology of calcite indicates a plausible Early Cretaceous age. However, comparison of the new U–Pb ages of calcite with detrital zircon maximum depositional ages immediately beneath the studied sample indicates a disparity in the apparent sedimentation rates if both types of geochronologic information are interpreted as reflecting the timing of sediment deposition. The totality of data supports an early, and high-temperature, diagenetic timing of U incorporation, with potential for minor leaching of U in subsequent fluid–rock interaction. The most likely mechanism for U transport and immobilization in these samples is hydrothermal fluid–rock interaction. Therefore, the radiometric ages, and corresponding stable isotope composition of U-bearing carbonate domains in this sample, indicate early subsurface fluid–rock interactions and not a record of atmosphere–soil geochemical reactions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

CRISPR-COPIES: Web Tool

CRISPR/Cas system has emerged as a powerful genome-editing tool for metabolic engineering and human gene therapy. However, the conundrum of where to integrate heterologous genes on the chromosome using the CRISPR/Cas system remains an open question. Selecting a site for gene integration requires incorporation of complex criteria such as factors involved in CRISPR/Cas-mediated integration, genetic stability, and gene expression and therefore, usually requires strenuous characterization of sites on particular or different chromosomal locations. To address these issues, we developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. The tool applies ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. This submission contains the code we developed to create a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate CRISPR-COPIES will serve as a useful tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.

Bioinformatics↗
DOE OSTI2024

Distinct universality classes of diffusive transport from full counting statistics

The hydrodynamic transport of local conserved densities furnishes an effective coarse-grained description of the dynamics of a many-body quantum system. However, the full quantum dynamics contains much more structure beyond the simplified hydrodynamic description. Here we show that systems with the same hydrodynamics can nevertheless belong to distinct dynamical universality classes, as revealed by new classes of experimental observables accessible in synthetic quantum systems, which can, for instance, measure simultaneous site-resolved snapshots of all of the particles in a system. Specifically, we study the full counting statistics of spin transport, whose first moment is related to linear-response transport, but the higher moments go beyond. We present an analytic theory of the full counting statistics of spin transport in various integrable and nonintegrable anisotropic one-dimensional spin models, including the XXZ spin chain. We find that spin transport, while diffusive on average, is governed by a distinct non-Gaussian dynamical universality class in the models considered. We consider a setup in which the left and right half of the chain are initially created at different magnetization densities, and consider the probability distribution of the magnetization transferred between the two half-chains. We derive a closed-form expression for the probability distribution of the magnetization transfer, in terms of random walks on the half-line. We show that this distribution strongly violates the large-deviation form expected for diffusive chaotic systems, and explain the physical origin of this violation. Here, we discuss the crossovers that occur as the initial state is brought closer to global equilibrium. Our predictions can directly be tested in experiments using quantum gas microscopes or superconducting qubit arrays.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Sex Differences in Vagus Nerve Stimulation Effects on Rat Cardiovascular and Immune Systems

Background: Investigations into the benefits of vagus nerve stimulation (VNS) through pre-clinical and clinical research have led to promising findings for treating several disorders. Despite proven effectiveness of VNS on conditions such as epilepsy and depression, understanding of off-target effects and contributing factors such as sex differences can be beneficial to optimize therapy design. New Methods: In this article, we assessed longitudinal effects of VNS on cardiovascular and immune systems, and studied potential sex differences using a rat model of longterm VNS. Rats were implanted with cuff electrodes around the left cervical vagus nerve for VNS, and wireless physiological monitoring devices for continuous monitoring of cardiovascular system using electrocardiogram (ECG) signals. ECG morphology and heart rate variability (HRV) features were extracted to assess cardiovascular changes resulting from VNS in short-term and long-term timescales. We also assessed VNS effects on expression of inflammatory cytokines in blood during the course of the experiment. Statistical analysis was performed to compare results between Treatment and Sham groups, and between male and female animals from Treatment and Sham groups. Results: Considerable differences between male and female rats in cardiovascular effects of VNS were observed in multiple cardiovascular features. However, the effects seemed to be transient with approximately 1-h recovery after VNS. While short-term cardiovascular effects were mainly observed in male rats, females in general showed more significant long-term effects even after VNS stopped. We did not observe notable changes or sex differences in systemic cytokine levels resulting from VNS. Comparison With Existing Methods: Compared to existing methods, our study design incorporated wireless physiological monitoring and systemic blood cytokine level analysis, along with long-term VNS experiments in unanesthetized rats to study sex differences. Conclusion: The contribution of sex differences for long-term VNS off-target effects on cardiovascular and immune systems was assessed using awake behaving rats. Although VNS did not change the concentration of inflammatory biomarkers in systemic circulation for male and female rats, we observed significant differences in cardiovascular effects of VNS characterized using ECG morphology and HRV analyses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Extending C++ for Heterogeneous Quantum-Classical Computing

In this report we present qcor - a language extension to C++ and compiler implementation that enables heterogeneous quantum-classical programming, compilation, and execution in a single-source context. Our work provides a first-of-its-kind C++ compiler enabling high-level quantum kernel (function) expression in a quantum-language agnostic manner, as well as a hardware-agnostic, retargetable compiler workflow targeting a number of physical and virtual quantum computing backends. qcor leverages novel Clang plugin interfaces and builds upon the XACC system-level quantum programming framework to provide a state-of-the-art integration mechanism for quantum-classical compilation that leverages the best from the community at-large. qcor translates quantum kernels ultimately to the XACC intermediate representation, and provides user-extensible hooks for quantum compilation routines like circuit optimization, analysis, and placement. This work details the overall architecture and compiler workflow for qcor, and provides a number of illuminating programming examples demonstrating its utility for near-term variational tasks, quantum algorithm expression, and feed-forward error correction schemes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Automated Generation of Integrated Digital and Spiking Neuromorphic Machine Learning Accelerators

The growing numbers of application areas for artificial intelligence (AI) methods have led to an explosion of domain-specific accelerators that could support every new machine learning (ML) algorithm advancement, clearly highlighting the need for a capability to quickly and automatically transition from algorithm definition to hardware implementation and explore design space along a variety of SWaP (size, weight and Power). The software defined architectures (SODA) synthesizer implements a compiler-based modular infrastructure for the end-to-end generation of machine learning accelerators from high-level frameworks to hardware description language. At the same time, neuromorphic computing, by mimicking how the brain operates, promises to perform artificial intelligence tasks at efficiencies orders of magnitude higher than the current conventional tensor-processing based accelerators, as demonstrated by a variety of specialized designs leveraging Spiking Neural Networks (SNNs). Nevertheless, the mapping of an artificial neural network (ANN) to solutions supporting SNNs is still a non-trivial and very device-specific task, and completely lack the possibility to design hybrid systems that integrate conventional and spiking neural models. In this paper we discuss the support for such an integrated generation leveraging the SODA Synthesizer framework and its modular structure. In particular, we present a new MLIR dialect (part of the SODA frontend) that allows expressing spiking neural network features (e.g., available resources, spiking sequences, analog signal reading, etc.) and illustrate how it enables mapping to Spiking Neurons and deployment to the related specialized hardware (which, in the digital domain, could be generated through the other existing layers of the SODA Synthesizer). We then discuss the opportunities for even deeper integration afforded by the hardware compilation infrastructure, providing a path towards the generation of complex heterogeneous artificial intelligence systems.

Curzel, Serena↗
DOE OSTI2025

Interplay between hydrogen, temperature, and character angle on dissociated dislocation energies in Fe–Ni–Cr austenitic stainless steels

Dislocation energy has an important role in the mechanical performance of structural metals. While dislocation energies cannot be fully obtained from continuum theories due to the contribution of the dislocation core, they have been calculated via atomistic simulations in elemental metals. However, constraints on the local atomic environments have prevented the use of such approaches in systems that incorporate alloying or interstitial solutes. In this work, we develop robust molecular dynamics methods to resolve these issues through a geometric construction of dislocation dipoles and the calculation of time-averaged energies. Furthermore, we apply these methods to calculate dislocation energies (including core energies) in an Fe 70 Ni 11 Cr 19 austenitic steel at a variety of character angles, hydrogen concentrations, temperatures, and dipole spacings. The resulting highly converged energies show an excellent agreement with continuum expressions. Overall, hydrogen concentrations up to 1.0 % do not have a significant effect on the elastic parameters and dislocation energy. The methods and insights derived in this work have the potential to facilitate the calculation of dislocation energies in a wide range of systems, and to guide our understanding of hydrogen embrittlement.

Alloyed systems↗
DOE OSTI2024

The three-pion K -matrix at NLO in ChPT

The three-particle K-matrix, Κ df,3 , is a scheme-dependent quantity that parametrizes short-range three-particle interactions in the relativistic-field-theory three-particle finite-volume formalism. In this work, we compute its value for systems of three pions in all isospin channels through next-to-leading order in Chiral Perturbation Theory, generalizing previous work done at maximum isospin. We obtain analytic expressions through quadratic order (or cubic order, in the case of zero isospin) in the expansion about the three-pion threshold.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Modeling gas release from a Bingham plastic slurry and deconvoluting measured data

Physics-based models for predicting the off-gassing characteristics of agitated slurries are presented. This approach decomposes the system into two separate but coupled slurry and headspace models. The physics driving bubble transport through the slurry and gas mixing within the headspace are discussed. An analytical expression for predicting the time evolution of the headspace concentration using first principles theory is also presented. Predictions from the numerical models, as well as expectations from the analytical solution, both agree with measured off gassing data for two different experimental operating conditions. After benchmarking the numerical model predictions against experimental data, the model was used to make predictions for gas release from a full-scale vessel and to perform sensitivity analyses to examine the sensitivity of gas release to parameters such as yield stress, consistency index, slurry density, bubble size, bubble concentration, and impeller speed.

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

DPM: A deep learning PDE augmentation method with application to large-eddy simulation

A framework is introduced that leverages known physics to reduce overfitting in machine learning for scientific applications. The partial differential equation (PDE) that expresses the physics is augmented with a neural network that uses available data to learn a description of the corresponding unknown or unrepresented physics. Training within this combined system corrects for missing, unknown, or erroneously represented physics, including discretization errors associated with the PDE's numerical solution. For optimization of the network within the PDE, an adjoint PDE is solved to provide high-dimensional gradients, and a stochastic adjoint method (SAM) further accelerates training. Additionally, the approach is demonstrated for large-eddy simulation (LES) of turbulence. High-fidelity direct numerical simulations (DNS) of decaying isotropic turbulence provide the training data used to learn sub-filter-scale closures for the filtered Navier–Stokes equations. Out-of-sample comparisons show that the deep learning PDE method outperforms widely-used models, even for filter sizes so large that they become qualitatively incorrect. It also significantly outperforms the same neural network when a priori trained based on simple data mismatch, not accounting for the full PDE. Measures of discretization errors, which are well-known to be consequential in LES, point to the importance of the unified training formulation's design, which without modification corrects for them. For comparable accuracy, simulation runtime is significantly reduced. A relaxation of the typical discrete enforcement of the divergence-free constraint in the solver is also successful, instead allowing the DPM to approximately enforce incompressibility physics. Since the training loss function is not restricted to correspond directly to the closure to be learned, training can incorporate diverse data, including experimental data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Simple and General Unitarity Conserving Numerical Real-Time Propagators of the Time-Dependent Schrödinger Equation Based on Magnus Expansion

Magnus expansion (ME) provides a general way to expand the real-time propagator of a time-dependent Hamiltonian within the exponential such that the unitarity is satisfied at any order. Here, we use this property and explicit integration of Lagrange interpolation formulas for the time-dependent Hamiltonian within each time interval and derive approximations that preserve unitarity for the differential time evolution operators of general time-dependent Hamiltonians. The resulting second-order approximation is the same as using the average of Hamiltonians for two end points of time. We identify three fourth-order approximations involving commutators of Hamiltonians at different times and also derive a sixth-order expression. A test of these approximations along with other available expressions for a two-state time-dependent Hamiltonian with sinusoidal time dependences provides information on the relative performance of these approximations and suggests that the derived expressions can serve as useful numerical tools for time evolution in time-resolved spectroscopy, quantum control, quantum sensing, real-time ab initio quantum dynamics, and open system quantum dynamics.

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

Deriving the Landauer Principle From the Quantum Shannon Entropy

We derive an expression to determine the equilibrium probability distribution of a quantum state in contact with a noisy thermal environment that formally separates contributions from quantum and classical forms of probabilistic uncertainty. A statistical mechanical interpretation of this probability distribution enables us to derive an expression for the minimum free energy costs for arbitrary (reversible or irreversible) quantum state changes. In conclusion, based on this derivation, we demonstrate that–in contrast to classical systems–the free energy required to erase or reset a qubit depends sensitively on both the fidelity of the target state and on the physical properties of the environment, such as the number of quantum bath states, due primarily to the entropic effects of system-bath entanglement.

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

Rational Modulation of Plant Root Development Using Engineered Cytokinin Regulators

Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.

Cell signaling↗
DOE OSTI2023

Extensive cellular multi-tasking within Bacillus subtilis biofilms

Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells “multi-task,” simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula, in response to rhizobial signals that trigger the formation of root nodules. We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis-regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.

59 BASIC BIOLOGICAL SCIENCES↗