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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites

Abstract Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

BioTransformer 3.0 – A Web Server for Accurately Predicting Metabolic Transformation Products

BioTransformer 3.0 is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively viewable/sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes a few seconds. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0, uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human and/or environmental biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40-50% more accurate, much less prone to combinatorial “explosions” and far more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Hydroxycinnamaldehyde-derived benzofuran components in lignins

Abstract Lignin is an abundant polymer in plant secondary cell walls. Prototypical lignins derive from the polymerization of monolignols (hydroxycinnamyl alcohols), mainly coniferyl and sinapyl alcohol, via combinatorial radical coupling reactions and primarily via the endwise coupling of a monomer with the phenolic end of the growing polymer. Hydroxycinnamaldehyde units have long been recognized as minor components of lignins. In plants deficient in cinnamyl alcohol dehydrogenase, the last enzyme in the monolignol biosynthesis pathway that reduces hydroxycinnamaldehydes to monolignols, chain-incorporated aldehyde unit levels are elevated. The nature and relative levels of aldehyde components in lignins can be determined from their distinct and dispersed correlations in 2D 1H–13C-correlated nuclear magnetic resonance (NMR) spectra. We recently became aware of aldehyde NMR peaks, well resolved from others, that had been overlooked. NMR of isolated low-molecular-weight oligomers from biomimetic radical coupling reactions involving coniferaldehyde revealed that the correlation peaks belonged to hydroxycinnamaldehyde-derived benzofuran moieties. Coniferaldehyde 8-5-coupling initially produces the expected phenylcoumaran structures, but the derived phenolic radicals undergo preferential disproportionation rather than radical coupling to extend the growing polymer. As a result, the hydroxycinnamaldehyde-derived phenylcoumaran units are difficult to detect in lignins, but the benzofurans are now readily observed by their distinct and dispersed correlations in the aldehyde region of NMR spectra from any lignin or monolignol dehydrogenation polymer. Hydroxycinnamaldehydes that are coupled to coniferaldehyde can be distinguished from those coupled with a generic guaiacyl end-unit. These benzofuran peaks may now be annotated and reported and their structural ramifications further studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

An evolutionary algorithm for designing microbial communities via environmental modification

Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

End-to-end protocol for high-quality quantum approximate optimization algorithm parameters with few shots

The quantum approximate optimization algorithm (QAOA) is a quantum heuristic for combinatorial optimization that has been demonstrated to scale better than state-of-the-art classical solvers for some problems. For a given problem instance, QAOA performance depends crucially on the choice of the parameters. While average-case optimal parameters are available in many cases, meaningful performance gains can be obtained by fine-tuning these parameters for a given instance. This task is especially challenging, however, when the number of circuit executions (shots) is limited. In this work, we develop an end-to-end protocol that combines multiple parameter settings and fine-tuning techniques. We use large-scale numerical experiments to optimize the protocol for the shot-limited setting and observe that optimizers with the simplest internal model (linear) perform best. We implement the optimized pipeline on a trapped-ion processor using up to 32 qubits and 5 QAOA layers, and we demonstrate that the pipeline is robust to small amounts of hardware noise. To the best of our knowledge, these are the largest demonstrations of QAOA parameter fine-tuning on a trapped-ion processor in terms of two-qubit gate count.

quantum algorithms & computation↗
DOE OSTI2025

Magneto-optical spectroscopy based on pump-probe strobe light

Here, we demonstrate a pump-probe strobe light spectroscopy for sensitive detection of magneto-optical dynamics in the context of hybrid magnonics. The technique uses a combinatorial microwave-optical pump-probe scheme, leveraging both the high-energy resolution of microwaves and high-efficiency detection using optical photons. In contrast with conventional stroboscopy using continuous-wave light, we apply microwave and optical pulses with varying pulse widths, and demonstrate magneto-optical detection of magnetization dynamics in Y 3 Fe 5 O 12 films. The detected magneto-optical signals depend strongly on the characteristics of both the microwave and the optical pulses, as well as their relative time delays. We show that good magneto-optical sensitivity and coherent stroboscopic character are maintained, even at a microwave pump pulse of 1.5 ns and an optical probe pulse of 80 ps, under a 7 MHz clock rate, corresponding to a pump-probe footprint of approximately 1% in one detection cycle. Our results show that time-dependent strobe light measurement of magnetization dynamics can be achieved in the gigahertz frequency range under a pump-probe detection scheme.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Kinematic Flow and the Emergence of Time

Perhaps the most basic question we can ask about cosmological correlations is how their strength changes as we smoothly vary kinematic parameters. The answer is encoded in differential equations that govern this evolution in kinematic space. In this Letter, we introduce a new perspective on these differential equations. We show that, in the simplified setting of conformally coupled scalars in power-law Friedmann-Robertson-Walker spacetimes, the equations for arbitrary tree-level processes can be obtained from a small number of simple combinatorial rules. While this “kinematic flow” is defined purely in terms of boundary data, it reflects the physics of bulk time evolution. The unexpected regularity of the equations suggests the existence of an autonomously defined mathematical structure from which cosmological correlations and the time evolution of the associated spacetime emerge.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Fixed-angle conjectures for the quantum approximate optimization algorithm on regular MaxCut graphs

The quantum approximate optimization algorithm (QAOA) is a near-term combinatorial optimization algorithm suitable for noisy quantum devices. However, little is known about performance guarantees for p > 2. A recent work computing MaxCut performance guarantees for 3-regular graphs conjectures that any d-regular graph evaluated at particular fixed angles has an approximation ratio greater than some worst-case guarantee. In this work, we provide numerical evidence for this fixed angle conjecture for p < 12. We compute and provide these angles via numerical optimization and tensor networks. These fixed angles serve for an optimization-free version of QAOA and have universally good performance on any 3-regular graph. Heuristic evidence is presented for the fixed angle conjecture on graph ensembles, which suggests that these fixed angles are "close" to global optimum. Under the fixed angle conjecture, QAOA has a larger performance guarantee than the Goemans Williamson algorithm on 3-regular graphs for p >= 11.

Wurtz, Jonathan↗
DOE OSTI2024

4-Clique network minor embedding for quantum annealers

Quantum annealing is a quantum algorithm for computing solutions to combinatorial optimization problems. This study proposes a method for minor embedding optimization problems onto sparse quantum annealing hardware graphs called 4-clique network minor embedding. This method is in contrast to the standard minor embedding technique of using a path of linearly connected qubits in order to represent a logical variable state. The 4-clique minor embedding is possible on Pegasus graph connectivity, which is the native hardware graph for some of the current D-Wave quantum annealers. The Pegasus hardware graph contains many cliques of size 4, making it possible to form a graph composed entirely of paths of connected 4-cliques on which a problem can be minor-embedded. The 4-clique chains come at the cost of additional qubit usage on the hardware graph, but they allow for stronger coupling within each chain, thereby increasing chain integrity, reducing chain breaks, and allow for greater usage of the available energy scale for programming logical problem coefficients on current quantum annealers. The 4-clique minor embedding technique is compared with the standard linear path minor embedding with experiments on two D-Wave quantum annealing processors with Pegasus hardware graphs. We show proof-of-concept experiments where the 4-clique minor embeddings can use weak chain strengths while successfully carrying out the computation of minimizing random all-to-all spin glass problem instances. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Semiclassical shell-structure micro-macroscopic approach for the level density

Level density ρ(E,A) is derived for a one-component nucleon system with a given energy E and particle number A within the mean-field semiclassical periodic-orbit theory beyond the saddle-point method of the Fermi gas model. We obtain ρ∝I ν (S)/S ν , with I ν (S) being the modified Bessel function of the entropy S. Within the micro-macro-canonical approximation (MMA), for a small thermal excitation energy U, with respect to rotational excitations E rot , one obtains ν = 3/2 for ρ(E,A). In the case of excitation energy U larger than E rot but smaller than the neutron separation energy, one finds a larger value of ν = 5/2. A role of the fixed spin variables for rotating nuclei is discussed. The MMA level density ρ reaches the well-known grand-canonical ensemble limit (Fermi gas asymptote) for large S related to large excitation energies, and also reaches the finite micro-canonical limit for small combinatorial entropy S at low excitation energies (the constant “temperature” model). Fitting the ρ(E,A) of the MMA to the experimental data for low excitation energies, taking into account shell and, qualitatively, pairing effects, one obtains for the inverse level density parameter K a value which differs essentially from that parameter derived from data on neutron resonances.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Anatomy of $tthh$ physics at the HL-LHC

The t t h h production at colliders contains rich information on the nature of the Higgs boson. In this article, we systematically studied its physics at the high-luminosity Large Hadron Collider (HL-LHC), using exclusive channels with multiple ( ≥ 5 ) b -jets and one lepton ( 5 b 1 ℓ ), multiple ( ≥ 5 ) b -jets and opposite-sign dilepton ( 5 b 2 ℓ ), same-sign dilepton ( SS 2 ℓ ), multiple leptons (multi- ℓ ), and ditau resonance ( τ τ ). The scenarios analyzed include: (1) the t t h h production in Standard Model; (2) the t t h h production mediated by anomalous cubic Higgs self-coupling and t t h h contact interaction; (3) heavy Higgs ( H ) production with t t H → t t h h ; and (4) pair production of fermionic top partners ( T ) with T T → t t h h . To address the complication of event topologies and the mess of combinatorial backgrounds, a tool of boosted-decision-tree was applied in the analyses. The 5 b 1 ℓ and SS 2 ℓ analyses define the two most promising channels. For the nonresonant t t h h production, a combination of these exclusive analyses allows for its measurement in the SM with a statistical significance ~ 0.9 σ (with S / B > 1 % ), and may partially break the sensitivity degeneracy with respect to a varying cubic Higgs self-coupling, a difficulty usually thought to exist in gluon fusion di-Higgs analysis at HL-LHC. These sensitivities were also projected to future hadron colliders at 27 TeV and 100 TeV. For the resonant t t h h productions, the heavy Higgs boson in type II two-Higgs-doublet-model could be efficiently searched for between the mass thresholds 2 m h < m H < 2 m t and even beyond that, for relatively small tan β (vacuum alignment), while the fermionic top partners in composite Higgs models could be probed up to ~ 1.5 TeV and ~ 1.7 TeV , for Br ( T → t h ) = 25 % and 50%, respectively.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Generic two-phase coexistence in a type-2 Schloegl model for autocatalysis on a square lattice: Analysis via heterogeneous master equations

Schloegl's second model (also known as the quadratic contact process) on a square lattice involves spontaneous annihilation of particles at lattice sites at rate p, and their autocatalytic creation at unoccupied sites with n ≥ 2 occupied neighbors at rate k n . Here, kinetic Monte Carlo (KMC) simulation reveals that these models exhibit a nonequilibrium discontinuous phase transition with generic two-phase coexistence: the p value for equistability of coexisting populated and vacuum states, p eq (S), depends on the orientation or slope, S, of a planar interface separating those phases. The vacuum state displaces the populated state for p > eq (S), and the opposite applies for p < p eq (S) for 0 < S < ∞. The special “combinatorial” rate choice k n = n(n–1)/12 facilitates an appealing simplification of the exact master equations for the evolution of spatially heterogeneous states in the model, which aids analytic investigation of these equations via hierarchical truncation approximations. Truncation produces coupled sets of lattice differential equations which can describe orientation-dependent interface propagation and equistability. The pair approximation predicts that p eq (max) = p eq (S = 1) = 0.09645 and p eq (min) = p eq (S → ∞) = 0.08827, values deviating less than 15% from KMC predictions. In the pair approximation, a perfect vertical interface is stationary for all p < p eq (S = ∞) = 0.08907, a value exceeding p eq (S → ∞). One can regard an interface for large S → ∞ as a vertical interface decorated with isolated kinks. For p < p eq (S = ∞), the kink can move in either direction along this otherwise stationary interface depending upon p, but for p = p eq (min) the kink is also stationary.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Reversible, irreversible, and mixed regimes for periodically driven disks in random obstacle arrays

We examine an assembly of repulsive disks interacting with a random obstacle array under a periodic drive and find a transition from reversible to irreversible dynamics as a function of drive amplitude or disk density. At low densities and drives, the system rapidly forms a reversible state where the disks return to their exact positions at the end of each cycle. In contrast, at high amplitudes or high densities, the system enters an irreversible state where the disks exhibit normal diffusion. Between these two regimes, there can be an intermediate irreversible state where most of the system is reversible, but localized irreversible regions are present that are prevented from spreading through the system due to a screening effect from the obstacles. Here, we also find states that we term “combinatorial reversible states” in which the disks return to their original positions after multiple driving cycles. In these states, individual disks exchange positions but form the same configurations during the subcycles of the larger reversible cycle.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Biased degenerate ground-state sampling of small Ising models with converged quantum approximate optimization algorithm

The quantum alternating operator ansatz, a generalization of the quantum approximate optimization algorithm (QAOA), is a quantum algorithm used for approximately solving combinatorial optimization problems. QAOA typically uses the transverse field mixer as the driving Hamiltonian. One of the interesting properties of the transverse field driving Hamiltonian is that it results in nonuniform sampling of degenerate ground states of optimization problems. In this study, we numerically examine the fair sampling properties of the transverse field mixer QAOA, and Grover mixer QAOA (GM-QAOA), which provides theoretical guarantees of fair sampling of degenerate optimal solutions, up to a large enough p such that the mean expectation value converges to an optimal approximation ratio of 1. This comparison is performed with high-quality heuristically computed, but not necessarily optimal, QAOA angles, which give strictly monotonically improving solution quality as p increases. These angles are computed using the Julia based numerical simulation software JuliQAOA. Fair sampling of degenerate ground states is quantified using the Shannon entropy of the ground-state amplitudes distribution. The fair sampling properties are reported on several quantum signature Hamiltonians from previous quantum annealing fair sampling studies. Small random fully connected spin glasses are shown, which exhibit exponential suppression of some degenerate ground states with transverse field mixer QAOA. The transverse field mixer QAOA simulations show that some problem instances clearly saturate the Shannon entropy of 0 with a maximally biased distribution that occurs when the learning converges to an approximation ratio of 1 while other problem instances never deviate from a maximum Shannon entropy (uniform distribution) at any p step. Published by the American Physical Society 2025

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Computational design of high-entropy rare earth aluminum garnets for advanced thermal and environmental barrier coatings

To enhance the protection of Ni-based superalloys in gas turbine engines’ high-temperature environments, it’s crucial to develop advanced thermal/environmental barrier coating (T/EBC) materials with a balanced combination of thermal and mechanical properties. This optimization is essential to safeguard against chemical and thermal challenges. Here, in this study, we harness the power of density functional theory (DFT) in conjunction with combinatorial chemistry methodologies to engineer high-performance high-entropy rare earth disilicates of the RE 3 Al 5 O 12 family (where RE denotes Y, Gd, Er, and Yb). These materials are meticulously designed to exhibit superior phase stability, a targeted coefficient of thermal expansion (CTE), low lattice thermal conductivity, and robust mechanical properties. The determination of CTE values is accomplished through phonon calculations at various volume settings within the quasi-harmonic approximation, while lattice thermal conductivities are rigorously assessed employing the Debye-Callaway model, accounting for three distinct phonon processes. Our findings highlight the remarkable attributes of the solid solution (Y 1/4 Gd 1/4 Er 1/4 Yb 1/4 ) 3 Al 5 O 12 , which displays a reduction in lattice thermal conductivity compared to its individual constituents while maintaining a favorable range of CTE values. The novel T/EBC material, distinguished by their multifaceted functionalities, are poised to use in substantial enhancements in the performance of engines.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Resolving local structural motifs across the phase evolution of zinc titanates with computational x-ray absorption spectroscopy

Resolving the local structure motifs that characterize phase evolution as a function of composition is a key challenge in structure characterization of complex materials. Here, in this study, we combine first-principles simulations and x-ray absorption near-edge structures (XANES) analysis to gain insights into the structure evolution revealed by measurements across a combinatorial zinc titanate thin film, which was grown with smoothly varying composition over a wide range of the Ti:Zn ratio. Specifically, we propose a cluster blind-signal-separation (cBSS) method for XANES spectral analysis based on a library of the structures and spectra of representative local motifs. In addition to motifs from zinc titanate crystals, two types of Ti-defect models constructed in this study are key to the understanding of the structure characteristics in the Zn-rich region. The cBSS method makes use of both spectral clustering of the simulated site-XANES spectra library and the BSS procedure to construct high-fidelity spectral basis functions from an experimental spectral sequence. The method provides a rigorous measure of the spectral sensitivity and basis completeness. The results of the XANES analysis are corroborated with other experimental modalities, including x-ray diffraction and spectroscopic ellipsometry, to validate the cBSS method. The calculated motif weights resulting from fitting the XANES spectra with the cBSS basis probe the atomic structure characteristics of both crystalline and amorphous phases as a function of the Ti/Zn composition. The insights of the local structure motif evolution are pivotal to the understanding of the nonmonotonic trend in the optical gap, which may lead to potential applications through tuning the optical properties of zinc titanate. The workflow of the XANES spectral analysis developed in this work can be generalized to construct the structure-property relationship in a broad material space.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Modeling Intercalation Chemistry with Multiredox Reactions by Sparse Lattice Models in Disordered Rocksalt Cathodes

Modern battery materials can contain many elements with substantial site disorder, and their configurational state has been shown to be critical for their performance. The intercalation voltage profile is a critical parameter to evaluate the performance of energy storage. The application of commonly used cluster expansion techniques to model the intercalation thermodynamics of such systems ab initio is challenged by the combinatorial increase in configurational degrees of freedom as the number of species grows. Such challenges necessitate the efficient generation of lattice models without overfitting and proper sampling of the configurational space under the requirement of charge balance in ionic systems. In this work, we introduce a combined approach that addresses these challenges by (1) constructing a robust cluster expansion Hamiltonian using the sparse regression technique, including -norm regularization and structural hierarchy; and (2) implementing semigrand-canonical Monte Carlo to sample charge-balanced ionic configurations using the table-exchange method and an ensemble average approach. These techniques are applied to a disordered rocksalt oxyfluoride (LMNOF) that is part of a family of promising earth-abundant cathode materials. The simulated voltage profile is found to be in good agreement with experimental data and particularly provides a clear demonstration of the and oxygen contributions to the redox potential as a function of content.

25 ENERGY STORAGE↗
DOE OSTI2022

Qubit Assignment Using Time Reversal

As quantum computers with large numbers of qubits become increasingly available, experiments executed on a given device may not utilize all available qubits. In this case, the outcome of executing a quantum program will depend on the ability to efficiently select a subset of high-performing physical qubits. For any given quantum program and device there are many ways to assign physical qubits for execution of the program, and assignments will differ in performance due to the variability in quality across qubits and entangling operations on a single device. Evaluating the performance of each assignment using fidelity estimation introduces significant experimental overhead and will be infeasible for many applications, while relying on standard device benchmarks provides incomplete information about the performance of any specific program. Furthermore, the number of possible assignments grows combinatorially in the number of qubits on the device and in the program, motivating the use of heuristic optimization techniques. We demonstrate a practical solution to the problem of qubit assignment by using simulated annealing with a cost function based on the Loschmidt echo, a diagnostic that measures the reversibility of a quantum process. We provide theoretical justification for this choice of cost function by demonstrating that the optimal qubit assignment coincides with the optimal qubit assignment based on state fidelity in the weak error limit, and we provide experimental justification using diagnostics performed on Google’s superconducting qubit devices. We then establish the performance of simulated annealing for qubit assignment using classical simulations of noisy devices as well as optimization experiments performed on a quantum processor. Our results demonstrate that the use of Loschmidt echoes and simulated annealing provides a scalable and flexible approach to optimizing qubit assignment on near-term hardware.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗