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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,675 records · Page 93
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Quantum mixed state compiling

The task of learning a quantum circuit to prepare a given mixed state is a fundamental quantum subroutine. We present a variational quantum algorithm (VQA) to learn mixed states which is suitable for near-term hardware. Our algorithm represents a generalization of previous VQAs that aimed at learning preparation circuits for pure states. We consider two different ansätze for compiling the target state; the first is based on learning a purification of the state and the second on representing it as a convex combination of pure states. In both cases, the resources required to store and manipulate the compiled state grow with the rank of the approximation. Thus, by learning a lower rank approximation of the target state, our algorithm provides a means of compressing a state for more efficient processing. As a byproduct of our algorithm, one effectively learns the principal components of the target state, and hence our algorithm further provides a new method for principal component analysis. We investigate the efficacy of our algorithm through extensive numerical implementations, showing that typical random states and thermal states of many body systems may be learnt this way. Additionally, we demonstrate on quantum hardware how our algorithm can be used to study hardware noise-induced states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Hybrid biophysical systems for atmospheric CO 2 capture

Negative emissions technologies will be essential for limiting anthropogenic global temperature increases to 2 °C in the later years of the 21st century. Carbonic anhydrase (CA) metalloenzymes catalyze the otherwise slow conversion of CO 2 into carbonic acid (H 2 CO 3 ), suggesting their utility in the rapid hydration and downstream capture of dissolved CO 2 in aqueous media for a variety of CO 2 capture methods, such as thermal and pH swings and mineralization. The possibility of driving the rapid capture of CO 2 by catalyzing the CO 2 hydration bottleneck carries real potential for realizing efficient direct air capture (DAC) and direct ocean capture (DOC) systems. However, scaled application of CAs will be dependent on some way of economically sourcing the enzymes at volumes relevant to scaled DAC/DOC operations. In this perspective, we consider the prospect of catalyzing CO 2 hydration using a CA that is bound to the outer membrane of a cyanobacterial host, engineered constructs we call CyCAMs. Coupling extracellular CA expression to a marine, photosynthetic cyanobacterial host results in a CO 2 hydration catalyst that is continuously refreshed during the bacterial growth cycle, without the need for enzyme purification or harvesting steps. In the case of marine cyanobacteria, sunlight and the solutes native to seawater provide the respective energy, nutrients and sources of inorganic carbon essential to maintaining the bacterial population. We consider the potential impact of CA-mediated CO 2 hydration on a variety of DAC processes, with CO 2 mineralization explored as a primary use case.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Chromosome-Level Genome Assembly of Mentha longifolia L. Reveals Gene Organization Underlying Disease Resistance and Essential Oil Traits

Mentha longifolia (L.) Huds., a wild, diploid mint species, has been developed as a model for mint genetic and genomic research to aid breeding efforts that target Verticillium wilt disease resistance and essential oil monoterpene composition. Here, we present a near-complete, chromosome-scale mint genome assembly for M. longifolia USDA accession CMEN 585. This new assembly is an update of a previously published genome draft, with dramatic improvements. A total of 42,107 protein-coding genes were annotated and placed on 12 chromosomal scaffolds. One hundred fifty-three genes contained conserved sequence domains consistent with nucleotide binding site-leucine-rich-repeat (NBS-LRR) plant disease resistance genes. Homologs of genes implicated in Verticillium wilt resistance in other plant species were also identified. Multiple paralogs of genes putatively involved in p-menthane monoterpenoid biosynthesis were identified and several cases of gene clustering documented. Heterologous expression of candidate genes, purification of recombinant target proteins, and subsequent enzyme assays allowed us to identify the genes underlying the pathway that leads to the most abundant monoterpenoid volatiles. Here, the bioinformatic and functional analyses presented here are laying the groundwork for using marker-assisted selection in improving disease resistance and essential oil traits in mints.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning

Abstract The Structural Classification of Proteins—extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit

Using affinity purification and mass spectrometry, we identified the subunits of Arabidopsis thaliana multisubunit RNA Polymerases I and III (abbreviated as Pol I and Pol III), providing the first description of their physical compositions in plants. AC40 and AC19 subunits are typically common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes whose mutation, in humans, is a cause of the craniofacial disorder, Treacher-Collins Syndrome. Surprisingly, A. thaliana, and related species, express two distinct AC40 paralogs, one of which assembles into Pol I and the other of which assembles into Pol III. Changes at eight amino acid positions correlate with this functional divergence of Pol I and Pol III-specific AC40 paralogs. Two genes encode homologs of the yeast C53 subunit, and either variant can assemble into Pol III. By contrast, only one of two potential C17 variants, and one of two potential C31 variants were detected in Pol III. We introduce a new nomenclature system for plant Pol I and Pol III subunits in which the twelve subunits that are structurally and functionally homologous among Pols I through V are assigned equivalent numbers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structural and functional characterization of the PNKP–XRCC4–LigIV DNA repair complex

Non-homologous end joining (NHEJ) repairs DNA double strand breaks in non-cycling eukaryotic cells. NHEJ relies on polynucleotide kinase/phosphatase (PNKP), which generates 5'-phosphate/3'-hydroxyl DNA termini that are critical for ligation by the NHEJ DNA ligase, LigIV. PNKP and LigIV require the NHEJ scaffolding protein, XRCC4. The PNKP FHA domain binds to the CK2-phosphorylated XRCC4 C-terminal tail, while LigIV uses its tandem BRCT repeats to bind the XRCC4 coiled-coil. Yet, the assembled PNKP-XRCC4-LigIV complex remains uncharacterized. Here, we report purification and characterization of a recombinant PNKP-XRCC4-LigIV complex. We show that the stable binding of PNKP in this complex requires XRCC4 phosphorylation and that only one PNKP protomer binds per XRCC4 dimer. Small angle X-ray scattering (SAXS) reveals a flexiblemultistate complex that suggests that both the PNKP FHA and catalytic domains contact the XRCC4 coiled-coil and LigIV BRCT repeats. Hydrogen-deuterium exchange indicates protection of a surface on the PNKP phosphatase domain that may contact XRCC4-LigIV. Amutation on this surface (E326K) causes the hereditary neuro-developmental disorder, MCSZ. This mutation impairs PNKP recruitment to damaged DNA in human cells and provides a possible disease mechanism. Together, this work unveils multipoint contacts between PNKP and XRCC4-LigIV that regulate PNKP recruitment and activity within NHEJ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Knocksideways in plants: an inducible system for in planta visualization of protein interactions

Understanding protein-protein interactions (PPIs) is key to unlocking the secrets of various cellular processes. While many tools have been developed to detect PPIs, such as the yeast two-hybrid assay, bimolecular fluorescence complementation, and affinity purification, there is great demand for additional methods to complement existing ones. As all approaches have limitations, evidence from at least two independent assays is required to validate PPIs. In a Breakthrough Report, Joanna Winkler and colleagues present here a promising method, named “knocksideways in plants” (KSP), for inducible visualization of PPIs in planta.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modeling temporal and hormonal regulation of plant transcriptional response to wounding

Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Conformations of macromolecules and their complexes from heterogeneous datasets

We explain a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Single quantum emitters with spin ground states based on Cl bound excitons in ZnSe

Defects in wide-band-gap semiconductors are promising qubit candidates for quantum communication and computation. Epitaxially grown II-VI semiconductors are particularly promising host materials due to their direct band gap and potential for isotopic purification to a spin-zero nuclear background. Here, we show an alternative type of single photon emitter with potential electron spin qubits based on Cl impurities in ZnSe. We utilize a quantum well to increase the binding energies of donor emission and confirm single photon emission with short radiative lifetimes of 192 ps. Furthermore, we verify that the ground state of the Cl donor complex contains a single electron by observing two-electron-satellite emission, leaving the electron in higher orbital states. We also characterize the Zeeman splitting of the exciton transition by performing polarization-resolved magnetic spectroscopy on single emitters. Our results suggest single Cl impurities are suitable as a single photon source with a potential photonic interface.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2010

Information conservation and entropy change in quantum measurements

The information transfer in the system-apparatus-environment trio is of fundamental importance for both the theory and practice of quantum information. Based on a canonical joint purification which encodes the system, apparatus, and environment as well as their interplay, we establish several basic relations involving various entropies arising from the most general quantum measurements. Some celebrated results concerning entropy change and information-disturbance tradeoff are recaptured as particular cases in a unified framework of information conservation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2010

Decorrelating capabilities of operations with application to decoherence

Decoherence, interpreted broadly, is essentially the leakage of system information into the environment and is often accompanied by dissipation. The basic questions arise: how to quantify decoherence induced by an operation and how to quantitatively compare decoherence induced by different operations. In this paper, based on a joint ancilla-system-environment tripartite purification for the initial system state and the operation, and by exploiting the intrinsic relations between the loss of correlations in the ancilla-system and the correlations established in the system-environment, we characterize and quantify decoherence from a decorrelating perspective. For this purpose, we first address the issue of separating and quantifying the classical and quantum parts of decorrelation. By use of the canonical isomorphism between operations and bipartite states, we propose two intrinsic decorrelation measures: One is the classical decorrelation based on the loss of classical correlations, and the other is the quantum decorrelation based on the loss of quantum correlations. With the help of quantum decorrelation, we introduce an intuitive measure of (quantum) decoherence. We further employ these informational quantities to analyze some widely used channels such as the complete decoherent channel, the depolarizing channel, the bit-flip channel, the transpose depolarizing channel, the amplitude damping channel, and the phase damping channel. Our analysis illustrates the intriguing interplay between classical and quantum decorrelations and sheds some light on the informational nature of decoherence.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

One-step error correction for multipartite polarization entanglement

We present two economical one-step error-correction protocols for multipartite polarization-entangled systems in a Greenberger-Horne-Zeilinger state. One uses spatial entanglement to correct errors in the polarization entanglement of an N-photon system, resorting to linear optical elements. The other uses frequency entanglement to correct errors in the polarization entanglement of an N-photon system. The parties in quantum communication can obtain a maximally entangled state from each N-photon system transmitted with one step in these two protocols, and both of their success probabilities are 100%, in principle. That is, they both work in a deterministic way, and they do not largely consume the less-entangled photon systems, which is far different from conventional multipartite entanglement purification schemes. These features may make these two protocols more useful for practical applications in long-distance quantum communication.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Informational derivation of quantum theory

We derive quantum theory from purely informational principles. Five elementary axioms - causality, perfect distinguishability, ideal compression, local distinguishability, and pure conditioning - define a broad class of theories of information processing that can be regarded as standard. One postulate - purification - singles out quantum theory within this class.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Operator-sum representation for bosonic Gaussian channels

Operator-sum or Kraus representations for single-mode bosonic Gaussian channels are developed, and several of their consequences explored. The fact that the two-mode metaplectic operators acting as unitary purification of these channels do not, in their canonical form, mix the position and momentum variables is exploited to present a procedure which applies uniformly to all families in the Holevo classification. In this procedure the Kraus operators of every quantum-limited Gaussian channel can be simply read off from the matrix elements of a corresponding metaplectic operator. Kraus operators are employed to bring out, in the Fock basis, the manner in which the antilinear, unphysical matrix transposition map when accompanied by injection of a threshold classical noise becomes a physical channel, denoted D({kappa}) in the Holevo classification. The matrix transposition channels D({kappa}), D({kappa}{sup -1}) turn out to be a dual pair in the sense that their Kraus operators are related by the adjoint operation. The amplifier channel with amplification factor {kappa} and the beam-splitter channel with attenuation factor {kappa}{sup -1} turn out to be mutually dual in the same sense. The action of the quantum-limited attenuator and amplifier channels as simply scaling maps on suitable quasiprobabilities in phase space is examined in the Kraus picture. Consideration of cumulants is used to examine the issue of fixed points. The semigroup property of the amplifier and attenuator families leads in both cases to a Zeno-like effect arising as a consequence of interrupted evolution. In the cases of entanglement-breaking channels a description in terms of rank 1 Kraus operators is shown to emerge quite simply. In contradistinction, it is shown that there is not even one finite rank operator in the entire linear span of Kraus operators of the quantum-limited amplifier or attenuator families, an assertion far stronger than the statement that these are not entanglement breaking channels. A characterization of extremality in terms of Kraus operators, originally due to Choi, is employed to show that all quantum-limited Gaussian channels are extremal. The fact that almost every noisy Gaussian channel can be realized as a product of a pair of quantum-limited channels is used to construct a discrete set of linearly independent Kraus operators for these noisy Gaussian channels, including the classical noise channel, and these Kraus operators have a particularly simple structure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Theory of the phase transition in random unitary circuits with measurements

Here, we present a theory of the entanglement transition tuned by measurement strength in qudit chains evolved by random unitary circuits and subject to either weak or random projective measurements. The transition can be understood as a nonanalytic change in the amount of information extracted by the measurements about the initial state of the system, quantified by the Fisher information. To compute the von Neumann entanglement entropy $\textit{S}$ and the Fisher information $\mathcal{F}$, we apply a replica method based on a sequence of quantities $\tilde{S}^{(n)}$ and $\mathcal{F}^{(n)}$ that depend on the $\textit{n}$th moments of density matrices and reduce to $\textit{S}$ and $\mathcal{F}$ in the limit $\textit{n}$ → 1. These quantities with $\textit{n}$ ≥ 2 are mapped to free energies of a classical spin model with $\textit{n}$! internal states in two dimensions with specific boundary conditions. In particular, $\tilde{S}^{(n)}$ is the excess free energy of a domain wall terminating on the top boundary, and $\mathcal{F}^{(n)}$ is related to the magnetization on the bottom boundary. Phase transitions occur as the spin models undergo ordering transitions in the bulk. Taking the limit of large local Hilbert space dimension $\textit{q}$ followed by the replica limit $\textit{n}$ → 1, we obtain the critical measurement probability $p_c$ = 1/2 and identify the transition as a bond percolation in the 2D square lattice in this limit. Finally, we show there is no phase transition if the measurements are allowed in an arbitrary nonlocal basis, thereby highlighting the relation between the phase transition and information scrambling. We establish an explicit connection between the entanglement phase transition and the purification dynamics of a mixed state evolution and discuss implications of our results to experimental observations of the transition and simulability of quantum dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Topological order and entanglement dynamics in the measurement-only XZZX quantum code

We examine the dynamics of a ( 1 + 1 ) -dimensional measurement-only circuit defined by the stabilizers of the [[5,1,3]] quantum error correcting code interrupted by single-qubit Pauli measurements. The code corrects arbitrary single-qubit errors and it stabilizes an area law entangled state with a D 2 = Z 2 × Z 2 symmetry protected topological (SPT) order, as well as a symmetry breaking (SB) order from a twofold bulk degeneracy. The Pauli measurements break the topological order and induce a phase transition into a trivial area law phase. Allowing more than one type of Pauli measurement increases the measurement-induced frustration and the SPT and SB order can be broken either simultaneously or separately at nonzero measurement rate. This yields a rich phase diagram and unanticipated critical behavior at the phase transitions. Although the correlation length exponent ν = 4 3 and the dynamical critical exponent z = 1 are consistent with bond percolation, the prefactor of the logarithmic entanglement growth may take noninteger multiples of the percolation value. Remarkably, we identify a robust transient scaling regime for the purification dynamics of L qubits. It reveals a modified dynamical critical exponent z * ≠ z , which is observable up to times t ~ L z * and is reminiscent of the relaxation of critical systems into a prethermal state.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Topology, criticality, and dynamically generated qubits in a stochastic measurement-only Kitaev model

Here we consider a paradigmatic solvable model of topological order in two dimensions, Kitaev's honeycomb Hamiltonian, and turn it into a measurement-only dynamics consisting of stochastic measurements of two-qubit bond operators. We find an entanglement phase diagram that resembles that of the Hamiltonian problem in some ways, while being qualitatively different in others. When one type of bond is dominantly measured, we find area-law entangled phases that protect two topological qubits (on a torus) for a time exponential in system size. This generalizes the recently proposed idea of Floquet codes, where logical qubits are dynamically generated by a time-periodic measurement schedule, to a stochastic setting. When all types of bonds are measured with comparable frequency, we find a critical phase with a logarithmic violation of the area law, which sharply distinguishes it from its Hamiltonian counterpart. The critical phase has the same set of topological qubits, as diagnosed by the tripartite mutual information, but protects them only for a time polynomial in system size. Furthermore, we observe an unusual behavior for the dynamical purification of mixed states, characterized at late times by the dynamical exponent z = $\frac{1}{2}$ a superballistic dynamics made possible by measurements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗