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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 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Gate Set Tomography

Gate set tomography (GST) is a protocol for detailed, predictive characterization of logic operations (gates) on quantum computing processors. Early versions of GST emerged around 2012-13, and since then it has been refined, demonstrated, and used in a large number of experiments. This paper presents the foundations of GST in comprehensive detail. The most important feature of GST, compared to older state and process tomography protocols, is that it is calibration-free . GST does not rely on pre-calibrated state preparations and measurements. Instead, it characterizes all the operations in a gate set simultaneously and self-consistently, relative to each other. Long sequence GST can estimate gates with very high precision and efficiency, achieving Heisenberg scaling in regimes of practical interest. In this paper, we cover GST's intellectual history, the techniques and experiments used to achieve its intended purpose, data analysis, gauge freedom and fixing, error bars, and the interpretation of gauge-fixed estimates of gate sets. Our focus is fundamental mathematical aspects of GST, rather than implementation details, but we touch on some of the foundational algorithmic tricks used in the pyGSTi implementation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Adaptive estimation of quantum observables

The accurate estimation of quantum observables is a critical task in science. With progress on the hardware, measuring a quantum system will become increasingly demanding, particularly for variational protocols that require extensive sampling. Here, we introduce a measurement scheme that adaptively modifies the estimator based on previously obtained data. Our algorithm, which we call AEQuO, continuously monitors both the estimated average and the associated error of the considered observable, and determines the next measurement step based on this information. We allow both for overlap and non-bitwise commutation relations in the subsets of Pauli operators that are simultaneously probed, thereby maximizing the amount of gathered information. AEQuO comes in two variants: a greedy bucket-filling algorithm with good performance for small problem instances, and a machine learning-based algorithm with more favorable scaling for larger instances. The measurement configuration determined by these subroutines is further post-processed in order to lower the error on the estimator. We test our protocol on chemistry Hamiltonians, for which AEQuO provides error estimates that improve on all state-of-the-art methods based on various grouping techniques or randomized measurements, thus greatly lowering the toll of measurements in current and future quantum applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Towards Quantum Gravity in the Lab on Quantum Processors

The holographic principle and its realization in the AdS/CFT correspondence led to unexpected connections between general relativity and quantum information. This set the stage for studying aspects of quantum gravity models, which are otherwise difficult to access, in table-top quantum-computational experiments. Recent works have designed a special teleportation protocol that realizes a surprising communication phenomenon most naturally explained by the physics of a traversable wormhole. In this work, we have carried out quantum experiments based on this protocol on state-of-the-art quantum computers. The target quantum processing units (QPUs) included the Quantinuum's trapped-ion System Model H1-1 and five IBM superconducting QPUs of various architectures, with public and premium user access. We report the observed teleportation signals from these QPUs with the best one reaching 80% of theoretical predictions. We outline the experimental challenges we have faced in the course of implementation, as well as the new theoretical insights into quantum dynamics the work has led to. We also developed QGLab – an open-source end-to-end software solution that facilitates conducting the wormhole-inspired teleportation experiments on state-of-the-art and emergent generations of QPUs supported by the Q i s k i t and t k e t SDKs. We consider our study and deliverables as an early practical step towards the realization of more complex experiments for the indirect probing of quantum gravity in the lab.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Can Error Mitigation Improve Trainability of Noisy Variational Quantum Algorithms?

Variational Quantum Algorithms (VQAs) are often viewed as the best hope for near-term quantum advantage. However, recent studies have shown that noise can severely limit the trainability of VQAs, e.g., by exponentially flattening the cost landscape and suppressing the magnitudes of cost gradients. Error Mitigation (EM) shows promise in reducing the impact of noise on near-term devices. Thus, it is natural to ask whether EM can improve the trainability of VQAs. In this work, we first show that, for a broad class of EM strategies, exponential cost concentration cannot be resolved without committing exponential resources elsewhere. This class of strategies includes as special cases Zero Noise Extrapolation, Virtual Distillation, Probabilistic Error Cancellation, and Clifford Data Regression. Second, we perform analytical and numerical analysis of these EM protocols, and we find that some of them (e.g., Virtual Distillation) can make it harder to resolve cost function values compared to running no EM at all. As a positive result, we do find numerical evidence that Clifford Data Regression (CDR) can aid the training process in certain settings where cost concentration is not too severe. Our results show that care should be taken in applying EM protocols as they can either worsen or not improve trainability. On the other hand, our positive results for CDR highlight the possibility of engineering error mitigation methods to improve trainability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Single-shot Quantum Signal Processing Interferometry

Quantum systems of infinite dimension, such as bosonic oscillators, provide vast resources for quantum sensing. Yet, a general theory on how to manipulate such bosonic modes for sensing beyond parameter estimation is unknown. We present a general algorithmic framework, quantum signal processing interferometry (QSPI), for quantum sensing at the fundamental limits of quantum mechanics by generalizing Ramsey-type interferometry. Our QSPI sensing protocol relies on performing nonlinear polynomial transformations on the oscillator's quadrature operators by generalizing quantum signal processing (QSP) from qubits to hybrid qubit-oscillator systems. We use our QSPI sensing framework to make efficient binary decisions on a displacement channel in the single-shot limit. Theoretical analysis suggests the sensing accuracy, given a single-shot qubit measurement, scales inversely with the sensing time or circuit depth of the algorithm. We further concatenate a series of such binary decisions to perform parameter estimation in a bit-by-bit fashion. Numerical simulations are performed to support these statements. Our QSPI protocol offers a unified framework for quantum sensing using continuous-variable bosonic systems beyond parameter estimation and establishes a promising avenue toward efficient and scalable quantum control and quantum sensing schemes beyond the NISQ era.

Physics↗
DOE OSTI2021

Ripple-Type Control for Enhancing Resilience of Networked Physical Systems

Distributed control agents have been advocated as an effective means for improving the resiliency of our physical infrastructures under unexpected events. Purely local control has been shown to be insufficient, centralized optimal resource allocation approaches can be slow. In this context, we put forth a hybrid low-communication saturation-driven protocol for the coordination of control agents that are distributed over a physical system and are allowed to communicate with peers over a “hotline” communication network. According to this protocol, agents act on local readings unless their control resources have been depleted, in which case they send a beacon for assistance to peer agents. Our ripple-type scheme triggers communication locally only for the agents with saturated resources and it is proved to converge. Moreover, under a monotonicity assumption on the underlying physical law coupling control outputs to inputs, the devised control is proved to converge to a configuration satisfying safe operational constraints. The assumption is shown to hold for voltage control in electric power systems and pressure control in water distribution networks. Numerical tests corroborate the efficacy of the novel scheme.

distributed control↗
DOE OSTI2024

Elemental profiling and genomewide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

Samples were collected from a population of 1,089 black cottonwood genotypes (P. trichocarpa) assembled from native stands to encompass the central portion of the natural range of the species, stretching from 38.8° to 54.3° N Q13 latitude from California, USA, to British Columbia, Canada. Establishment of the common garden, growth conditions, and site maintenance have been described by Muchero et al (2015). In this study, leaf samples for ionomic profiling were collected from 4-year-old trees, during the growing season, in July 2012, from a field located in Clatskanie, Oregon, USA (46°6′11″N 123°12′13″W). The field site was located in a protected alluvial floodplain containing a uniform Wauna-Locoda silt loam soil area characterized by an acidic pH, in Columbia County, Oregon. A subset of 584 out of the 1,089 P. trichocarpa genotypes were represented in this sampling. These genotypes were randomly selected to represent the geographical distribution of the population. A single fully mature (LPI 7-9) leaf on the south side of the tree exposed to full sunlight conditions was removed from the tree within a 6-hour window centering on solar noon and immediately frozen under dry ice before processing. Leaf samples of 584 P. trichocarpa genotypes were finely ground to 40 mm particle size using a mortar and pestle, and ionomic composition was analyzed using ICP-MS. In total, 20 elements were profiled, including aluminum (Al27), arsenic (As75), boron (B11), cadmium (Cd111), calcium (Ca43), cobalt (Co), copper (Cu), iron (Fe57), magnesium (Mg25), manganese (Mn55), molybdenum (Mo), nickel (Ni60), phosphorus (P31), potassium (K39), rubidium (Rb85), selenium (Se82), sodium (Na23), strontium (Sr88), sulfur (S34), and zinc (Zn66), following a protocol established by Ziegler et al. (2013). For each sample, 75mg of powder was digested overnight in 2.5 mL HNO3 containing 20 parts per billion (ppb) indium as an internal standard, following the protocol described in Ziegler et al. (2013). Following a dilution, concentration of the 20 elements was measured using an Elan 6000 DRC-e mass spectrometer (Perkin-Elmer SCIEX) connected to a PFA microflow nebulizer (Elemental Scientific) and Apex HF desolvator (Elemental Scientific). One measurement per sample per genotype was done. For subsequent analyses, the quantifications were converted to total element concentration.

CBI ionomics, GWAS, plasma-mass spectrometry, neut↗
DOE OSTI2026

Simulation-Based Validation of An Open-Source, Scalable Framework for Building Energy Management in Small and Medium-Sized Commercial Buildings

Abstract: Small and medium-sized commercial buildings (SMCBs) represent 94% of U.S. commercial buildings but encounter substantial obstacles in adopting Building Energy Management (BEM) systems. Current approaches exhibit fundamental limitations: vendor-specific API platforms restrict interoperability through proprietary ecosystems; commercial automation software demands extensive technical expertise and licensing costs; open-source IoT solutions lack native support for building automation protocols and semantic models. This paper introduces a configuration-driven web interface framework addressing the gap between smart device advancements and accessible BEM software infrastructure for SMCBs. The framework leverages VOLTTRON middleware integrated with an automated converter that processes unified YAML configurations into heterogeneous system files, reducing required configuration artifacts from six separate files to a single unified specification. The system architecture enables vendor-agnostic operation through BACnet and Modbus protocols while supporting semantic building model integration via automated Brick Schema parsing. Configuration-driven interfaces automatically adapt to diverse HVAC types without custom development. Simulation-based validation using BOPTEST demonstrates automatic interface generation between fan coil and hydronic systems, with the automated converter successfully generating all platform-specific outputs from the single YAML input. The result demonstrates the framework's capability to streamline BEM system deployment through reduced configuration complexity. This work bridges simulation capabilities with operational deployment, demonstrating how virtual testbeds validate generalizable software frameworks for real-world building automation.

Chung, Jihoon [ORNL] (ORCID:0000000184880815)↗
DOE OSTI2024

Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum

Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Measurement of Resistance, Porosity, and Water Contact Angle of Porous Transport Layers for Low-Temperature Electrolysis Technologies

The porous transport layer is an important component of low-temperature electrolysis devices, such as proton exchange membrane water electrolyzers or anion exchange membrane water electrolyzers. PTLs have significant influence on the cell performance as their bulk resistance can impact the ohmic resistance, their contact resistance can impact electrode performance, and their structure can impact the liquid flow to the cell, which could cause mass-transport losses. In order to improve cell performance, optimization of the PTL is critical. Standardized protocols should be utilized to adequately compare PTLs being developed from different institutions. This method will detail a standardized protocol for measuring the resistance of the PTL using a four-wire setup and will also detail a process for measuring the porosity and water contact angle of the PTL using capillary flow porometry.

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

Multiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid Sugarcane

Genome editing with sequence-specific nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), is revolutionizing crop improvement. Developing efficient genome-editing protocols for highly polyploid crops, including sugarcane ( x = 10–13), remains challenging due to the high level of genetic redundancy in these plants. Here, we report the efficient multiallelic editing of magnesium chelatase subunit I ( MgCh ) in sugarcane. Magnesium chelatase is a key enzyme for chlorophyll biosynthesis. CRISPR/Cas9-mediated targeted co-mutagenesis of 49 copies/alleles of magnesium chelatase was confirmed via Sanger sequencing of cloned PCR amplicons. This resulted in severely reduced chlorophyll contents, which was scorable at the time of plant regeneration in the tissue culture. Heat treatment following the delivery of genome editing reagents elevated the editing frequency 2-fold and drastically promoted co-editing of multiple alleles, which proved necessary to create a phenotype that was visibly distinguishable from the wild type. Despite their yellow leaf color, the edited plants were established well in the soil and did not show noticeable growth retardation. This approach will facilitate the establishment of genome editing protocols for recalcitrant crops and support further optimization, including the evaluation of alternative RNA-guided nucleases to overcome the limitations of the protospacer adjacent motif (PAM) site or to develop novel delivery strategies for genome editing reagents.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9

Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required. We presented here new and improved methodologies for introducing CRISPRCas9 to the model diatom Phaeodactylum tricornutum cells and a streamlined protocol for genotyping mutant cell lines with previously unknown phenotypes. First, bacterialconjugation was optimized for the delivery of Cas9 by transcriptionally fusing Cas9 to a selectable marker by the 2A peptide. An episome cloning strategy using both negative and positive selection was developed to streamline CRISPR-episome assembly. Next, cell line picking and genotyping strategies, that utilize manual sequencing curation, TIDE sequencing analysis, and a T7 endonuclease assay, were developed to shorten the time required to generate mutants. Following this new experimental pipeline, both singlegene and two-gene knockout cell lines were generated at mutagenesis efficiencies of 48% and 25%, respectively. Lastly, a protocol for precise gene insertions via CRISPRCas9 targeting was developed using particle-bombardment transformation methods. Overall, the novel Cas9 episome design and improved genotyping methods presented here allow for quick and easy genotyping and isolation of Phaeodactylum mutant cell lines (less than 3 weeks) without relying on a known phenotype to screen for mutants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Swimming and the human microbiome at the intersection of sports, clinical, and environmental sciences: A scoping review of the literature

The human microbiota is comprised of more than 10–100 trillion microbial taxa and symbiotic cells. Two major human sites that are host to microbial communities are the gut and the skin. Physical exercise has favorable effects on the structure of human microbiota and metabolite production in sedentary subjects. Recently, the concept of “athletic microbiome” has been introduced. To the best of our knowledge, there exists no review specifically addressing the potential role of microbiomics for swimmers, since each sports discipline requires a specific set of techniques, training protocols, and interactions with the athletic infrastructure/facility. Therefore, to fill in this gap, the present scoping review was undertaken. Four studies were included, three focusing on the gut microbiome, and one addressing the skin microbiome. It was found that several exercise-related variables, such as training volume/intensity, impact the athlete’s microbiome, and specifically the non-core/peripheral microbiome, in terms of its architecture/composition, richness, and diversity. Swimming-related power-/sprint- and endurance-oriented activities, acute bouts and chronic exercise, anaerobic/aerobic energy systems have a differential impact on the athlete’s microbiome. Therefore, their microbiome can be utilized for different purposes, including talent identification, monitoring the effects of training methodologies, and devising ad hoc conditioning protocols, including dietary supplementation. Microbiomics can be exploited also for clinical purposes, assessing the effects of exposure to swimming pools and developing potential pharmacological strategies to counteract the insurgence of skin infections/inflammation, including acne. In conclusion, microbiomics appears to be a promising tool, even though current research is still limited, warranting, as such, further studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies

Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.

Mathematics and Computing↗
DOE OSTI2022

An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue

Human disease states are biomolecularly multifaceted and can span across phenotypic states, therefore it is important to understand diseases on all levels, across cell types, and within and across microanatomical tissue compartments. To obtain an accurate and representative view of the molecular landscape within human lungs, this fragile tissue must be inflated and embedded to maintain spatial fidelity of the location of molecules and minimize molecular degradation for molecular imaging experiments. Here, we evaluated agarose inflation and carboxymethyl cellulose embedding media and determined effective tissue preparation protocols for performing bulk and spatial mass spectrometry-based omics measurements. Mass spectrometry imaging methods were optimized to boost the number of annotatable molecules in agarose inflated lung samples. This optimized protocol permitted the observation of unique lipid distributions within several airway regions in the lung tissue block. Laser capture microdissection of these airway regions followed by high-resolution proteomic analysis allowed us to begin linking the lipidome with the proteome in a spatially resolved manner, where we observed proteins with high abundance specifically localized to the airway regions. We also compared our mass spectrometry results to lung tissue samples preserved using two other inflation/embedding media, but we identified several pitfalls with the sample preparation steps using this preservation method. Overall, we demonstrated the versatility of the inflation method, and we can start to reveal how the metabolome, lipidome, and proteome are connected spatially in human lungs and across disease states through a variety of different experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Building MCP-native hierarchical AI scientist ecosystems: a perspective on scaling multi-agent scientific discovery

Large language models (LLMs) are evolving from chatbots with limited tool-using capabilities to agentic AI systems that can perform deep research, assist in proposing hypotheses, help design experiments, automate data analysis, and draft scientific reports. However, there are currently two bottlenecks limiting LLMs' real-world impact on the broader scientific research community beyond academic demonstrations: lack of interoperability (repetitive manual tool-integration is required across scenarios) and the need for scalable coordination (unstructured communication and memory become brittle as the number of agents grows). In this Perspective, we argue that the next phase of agentic scientific discovery requires the development of an ecosystem of protocol-native agents and tools organized through hierarchies inspired by human society, beyond the current paradigm of a single monolithic “AI scientist”. We use Model Context Protocol (MCP) as a concrete example of an emerging interoperability layer for scientific tool and context exchange, and we propose three complementary pathways to increase the scaling capabilities of an MCP-native scientific ecosystem by addressing the composability issues: (1) MCP servers for high-value scientific tools maintained by domain experts, (2) automated transformation of existing code repositories into MCP services, and (3) autonomous invention and evolution of new agents and workflows. Finally, we provide a practical roadmap for scaling AI-driven scientific discovery by expanding tool supply and coordination in MCP-native scientific ecosystems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Quantifying Antibiotic Distribution in Solid and Liquid Fractions of Manure Using a Two-Step, Multi-Residue Antibiotic Extraction

Antibiotic distribution and analysis within liquid and solid fractions of manure are highly variable due to each compound’s respective physiochemical properties. This study developed and evaluated a uniform method extracting 10 antibiotics from 4 antibiotic classes (tetracycline, sulfonamides, macrolides, and β-lactam) from unprocessed manure, solid–liquid separated manure, and composted solids. Through systematic manipulation of previously published liquid chromatography tandem mass spectrometry methods; this study developed an extraction protocol with optimized recovery efficiencies for varied manure substrates. The method includes a two-step, liquid-solid extraction using 10 mL of 0.1 M EDTA-McIlviane buffer followed by 10 mL of methanol. Antibiotics recoveries from unprocessed manure, separated liquids, separated solids, and heat-treated solids using the two-step extraction method had relative standard deviations < 30% for all but ceftiofur. Total antibiotic recoveries were 67–131% for tetracyclines, 56% for sulfonamide, 49–53% for macrolides, and 1.3–66% for β-lactams. This is the first study to use one protocol to assess four classes of antibiotics in liquid and solid manure fractions. This study allowed for more precise risk assessment of antibiotic transport in manure waste stream applied to fields as a liquid or solid compost.

59 BASIC BIOLOGICAL SCIENCES↗