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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies

Here, we report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded “heavy” and “light” GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the “heavy” and “light” peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2018

Vaccination with a DNA vaccine encoding CD317-targeting HBs antigen elicits enhanced immunity in mice

Highlights: • DNA vaccine encoding CD317-targeting HBsAg induces more potent humoral immunity. • DNA vaccine encoding CD317-targeting HBsAg elicits more robust T cell response. • DNA vaccine encoding CD317-targeting HBsAg is a promising candidate for preventing HBV infection. Conventional hepatitis B virus (HBV) vaccines fail to induce protective antibody titers in 5–10% of immune-competent vaccines. Therefore, safe and effective HBV vaccines are still clinically needed.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Ecology of methyl-coenzyme M reductase encoding Thermoproteota

The recent demonstration that members of at least three classes of archaea affiliated with the Thermoproteota superphylum are involved in the production of the climate-active gas methane has sparked discussions about how well we understand the diversity of methanogens. Here, in this work, we show that members of all three of these lineages, as well as several other, yet uncultured and physiologically uncharacterized groups within the Thermoproteota that encode the key enzyme of anaerobic methane cycling, methyl-coenzyme M reductase (MCR), are widely distributed in anoxic ecosystems. We postulate that the taxonomic, metabolic, and ecological diversity of methanogenic and MCR-encoding Thermoproteota are poorly understood, and that the contribution of methylotrophic and thermoproteotal methanogenesis to methane production is largely unknown. We hypothesize that thermoproteotal methanogens could contribute, potentially substantially, to methane emissions in many anoxic environments that harbor methylated precursors, including wetlands, sediments, peat, rice paddies, wastewater sludge, and geothermal systems. We highlight the necessity to experimentally test the (eco)physiology of these widely distributed archaea using both culture-dependent ( in vitro ) and culture-independent ( in situ ) approaches to assess their potential contribution to methane emissions. Last, we stress the importance of remaining agnostic about the physiology of MCR-encoding Thermoproteota in the absence of experimental data because most of these archaea also carry the genetic potential to grow non-methanogenically.

MCR↗
DOE OSTI2017

Transcranial direct current stimulation of dorsolateral prefrontal cortex during encoding improves recall but not recognition memory

Prior work demonstrates that application of transcranial direct current stimulation (tDCS) improves memory. In this study, we investigated tDCS effects on face-name associative memory using both recall and recognition tests. Participants encoded face-name pairs under either active (1.5 mA) or sham (.1 mA) stimulation applied to the scalp adjacent to the left dorsolateral prefrontal cortex (dlPFC), an area known to support associative memory. Participants’ memory was then tested after study (day one) and then again after a 24-h delay (day two), to assess both immediate and delayed stimulation effects on memory. Results indicated that active relative to sham stimulation led to substantially improved recall (more than 50%) at both day one and day two. Recognition memory performance did not differ between stimulation groups at either time point. These results suggest that stimulation at encoding improves memory performance by enhancing memory for details that enable a rich recollective experience, but that these improvements are evident only under some testing conditions, especially those that rely on recollection. Altogether, stimulation of the dlPFC could have led to recall improvement through enhanced encoding from stimulation or from carryover effects of stimulation that influenced retrieval processes, or both.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Safety profile, efficacy, and biodistribution of a bicistronic high-capacity adenovirus vector encoding a combined immunostimulation and cytotoxic gene therapy as a prelude to a phase I clinical trial for glioblastoma

Adenoviral vectors (Ads) are promising gene delivery vehicles due to their high transduction efficiency; however, their clinical usefulness has been hampered by their immunogenicity and the presence of anti-Ad immunity in humans. We reported the efficacy of a gene therapy approach for glioma consisting of intratumoral injection of Ads encoding conditionally cytotoxic herpes simplex type 1 thymidine kinase (Ad-TK) and the immunostimulatory cytokine fms-like tyrosine kinase ligand 3 (Ad-Flt3L). Herein, we report the biodistribution, efficacy, and neurological and systemic effects of a bicistronic high-capacity Ad, i.e., HC-Ad-TK/TetOn-Flt3L. HC-Ads elicit sustained transgene expression, even in the presence of anti-Ad immunity, and can encode large therapeutic cassettes, including regulatory elements to enable turning gene expression “on” or “off” according to clinical need. The inclusion of two therapeutic transgenes within a single vector enables a reduction of the total vector load without adversely impacting efficacy. Because clinically the vectors will be delivered into the surgical cavity, normal regions of the brain parenchyma are likely to be transduced. Thus, we assessed any potential toxicities elicited by escalating doses of HC-Ad-TK/TetOn-Flt3L (1 × 10{sup 8}, 1 × 10{sup 9}, or 1 × 10{sup 10} viral particles [vp]) delivered into the rat brain parenchyma. We assessed neuropathology, biodistribution, transgene expression, systemic toxicity, and behavioral impact at acute and chronic time points. The results indicate that doses up to 1 × 10{sup 9} vp of HC-Ad-TK/TetOn-Flt3L can be safely delivered into the normal rat brain and underpin further developments for its implementation in a phase I clinical trial for glioma. - Highlights: ► High capacity Ad vectors elicit sustained therapeutic gene expression in the brain. ► HC-Ad-TK/TetOn-Flt3L encodes two therapeutic genes and a transcriptional switch. ► We performed a dose escalation study at acute and chronic time points. ► Doses up to 1 × 10{sup 9} vp of HC-Ad-TK/TetOn-Flt3L can be safely delivered in the brain. ► Efficacy and safety of HC-Ad-TK/TetOn-Flt3L merits its use in a GBM Phase I trial.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Encoding of linear kinetic plasma problems in quantum circuits via data compression

We propose an algorithm for encoding linear kinetic plasma problems in quantum circuits. The focus is on modelling electrostatic linear waves in a one-dimensional Maxwellian electron plasma. The waves are described by the linearized Vlasov–Ampère system with a spatially localized external current that drives plasma oscillations. This system is formulated as a boundary-value problem and cast in the form of a linear vector equation Aψ = b to be solved by using the quantum signal processing algorithm. The latter requires encoding of matrix A in a quantum circuit as a sub-block of a unitary matrix. We propose how to encode A in a circuit in a compressed form and discuss how the resulting circuit scales with the problem size and the desired precision.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

DNA-Mediated Size-Selective Nanoparticle Assembly for Multiplexed Surface Encoding

Multiplexed surface encoding is achieved by positioning two different sizes of gold nanocubes on gold surfaces with precisely defined locations for each particle via template-confined, DNA-mediated nanoparticle assembly. As a proof-of-concept demonstration, cubes with 86 and 63 nm edge lengths are assembled into arrangements that physically and spectrally encrypt two sets of patterns in the same location. These patterns can be decrypted by mapping the absorption intensity of the substrate at $λ$ = 773 and 687 nm, respectively. This multiplexed encoding platform dramatically increases the sophistication and density of codes that can be written using colloidal nanoparticles, which may enable high-security, high-resolution encoding applications.

36 MATERIALS SCIENCE↗
DOE OSTI2018

DNA-Encoded Protein Janus Nanoparticles

Asymmetric functionality and directional interactions, which are characteristic of noncentrosymmetric particles, such as Janus particles, present an opportunity to encode particles with properties, but also a great synthetic challenge. Here, we exploit the chemical anisotropy of proteins, and the versatile chemistry of DNA to synthesize a protein-based Janus nanoparticle comprised of two proteins encoded with sequence-specific nucleic acid domains, tethered together by an interprotein “DNA bond”. We use these novel nanoparticles to realize a new class of three-dimensional superlattice, only possible when two sides of the particle are modified with orthogonal oligonucleotide sequences. The low symmetry, intrinsic to Janus particles, enables the realization of unprecedented multicomponent nanoparticle superlattices with unique, hexagonal layered architectures. In addition, the interprotein “DNA bond” can be modulated to selectively expand the lattice in a single direction. The results presented herein not only emphasize the power of rationally designing nanoscale building blocks to create highly engineered colloidal crystals, but also establish a precedent for applications of multidomain DNA-encoded nanoparticles, especially in the field of colloidal crystallization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative

Methicillin-resistant Staphylococcus aureus (MRSA) is a public-health threat worldwide. Although the mobile genomic island responsible for this phenotype, staphylococcal cassette chromosome (SCC), has been thought to be nonreplicative, we predicted DNA-replication-related functions for some of the conserved proteins encoded by SCC. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3'-to-5' helicase and that the adjacent ORF encodes a single-stranded DNA–binding protein. Our 2.9-Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch, like the archaeal and eukaryotic MCM-family replicative helicases, belongs to the pre–sensor II insert clade of AAA+ ATPases. Additionally, we found that SCC elements are part of a broader family of mobile elements, all of which encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs)

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirk) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis

During symbiosis, organisms use a range of metabolic and protein-based signals to communicate. Of these protein signals, one class is defined as ‘effectors’, i.e., small secreted proteins (SSPs) that cause phenotypical and physiological changes in another organism. To date, protein-based effectors have been described in aphids, nematodes, fungi and bacteria. Using RNA sequencing of Populus trichocarpa roots in mutualistic symbiosis with the ectomycorrhizal fungus Laccaria bicolor , we sought to determine if host plants also contain genes encoding effector-like proteins. We identified 417 plant-encoded putative SSPs that were significantly regulated during this interaction, including 161 SSPs specific to P. trichocarpa and 15 SSPs exhibiting expansion in Populus and closely related lineages. We demonstrate that a subset of these SSPs can enter L. bicolor hyphae, localize to the nucleus and affect hyphal growth and morphology. Finally, we conclude that plants encode proteins that appear to function as effector proteins that may regulate symbiotic associations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length

Sorghum is an important C4 grass crop grown for grain, forage, sugar, and bioenergy production. While tall, late flowering landraces are commonly grown in Africa, short early flowering varieties were selected in US grain sorghum breeding programs to reduce lodging and to facilitate machine harvesting. Four loci have been identified that affect stem length (Dw1-Dw4). Subsequent research showed that Dw3 encodes an ABCB1 auxin transporter and Dw1 encodes a highly conserved protein involved in the regulation of cell proliferation. In this study, Dw2 was identified by fine-mapping and further confirmed by sequencing the Dw2 alleles in Dwarf Yellow Milo and Double Dwarf Yellow Milo, the progenitor genotypes where the recessive allele of dw2 originated. Furthermore, the Dw2 locus was determined to correspond to Sobic.006G067700, a gene that encodes a protein kinase that is homologous to KIPK, a member of the AGCVIII subgroup of the AGC protein kinase family in Arabidopsis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Quantum-parallel vectorized data encodings and computations on trapped-ion and transmon QPUs

Compact data representations in quantum systems are crucial for the development of quantum algorithms for data analysis. In this study, we present two innovative data encoding techniques, known as QCrank and QBArt, which exhibit significant quantum parallelism via uniformly controlled rotation gates. The QCrank method encodes a series of real-valued data as rotations on data qubits, resulting in increased storage capacity. On the other hand, QBArt directly incorporates a binary representation of the data within the computational basis, requiring fewer quantum measurements and enabling well-established arithmetic operations on binary data. We showcase various applications of the proposed encoding methods for various data types. Notably, we demonstrate quantum algorithms for tasks such as DNA pattern matching, Hamming weight computation, complex value conjugation, and the retrieval of a binary image with 384 pixels, all executed on the Quantinuum trapped-ion QPU. Furthermore, we employ several cloud-accessible QPUs, including those from IBMQ and IonQ, to conduct supplementary benchmarking experiments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Multiresponsive polymeric microstructures with encoded predetermined and self-regulated deformability

Dynamic functions of biological organisms often rely on arrays of actively deformable microstructures undergoing a nearly unlimited repertoire of predetermined and self-regulated reconfigurations and motions, most of which are difficult or not yet possible to achieve in synthetic systems. Here, we introduce stimuli-responsive microstructures based on liquid-crystalline elastomers (LCEs) that display a broad range of hierarchical, even mechanically unfavored deformation behaviors. By polymerizing molded prepolymer in patterned magnetic fields, we encode any desired uniform mesogen orientation into the resulting LCE microstructures, which is then read out upon heating above the nematic–isotropic transition temperature (T N–I ) as a specific prescribed deformation, such as twisting, in- and out-of-plane tilting, stretching, or contraction. By further introducing light-responsive moieties, we demonstrate unique multifunctionality of the LCEs capable of three actuation modes: self-regulated bending toward the light source at T < T N–I , magnetic-field–encoded predetermined deformation at T > T N–I , and direction-dependent self-regulated motion toward the light at T > T N–I . We develop approaches to create patterned arrays of microstructures with encoded multiple area-specific deformation modes and show their functions in responsive release of cargo, image concealment, and light-controlled reflectivity. We foresee that this platform can be widely applied in switchable adhesion, information encryption, autonomous antennae, energy harvesting, soft robotics, and smart buildings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Three-Qubit Encoding in Ytterbium-171 Atoms for Simulating 1+1D Quantum Chromodynamics

Simulating nuclear matter described by quantum chromodynamics using quantum computers is notoriously inefficient because of the assortment of quark degrees of freedom such as matter/antimatter, flavor, color, and spin. Here, we propose to address this resource efficiency challenge by encoding three qubits within individual ytterbium-171 atoms of a neutral atom quantum processor. The three qubits are encoded in three distinct sectors: an electronic “clock” transition, the spin-1/2 nucleus, and the lowest two motional states in one radial direction of the harmonic trapping potential. We develop a family of composite sideband pulses and demonstrate a universal gate set and readout protocol for this three-qubit system. We then apply it to single-flavor quantum chromodynamics in 1+1D axial gauge for which the three qubits directly represent the occupancy of quarks in the three colors. We show that two atoms are sufficient to simulate both vacuum persistence oscillations and a screened hadron-number transition. We consider resource requirements and connections to error detection/correction. Our work is a step toward resource-efficient digital simulation of nuclear matter and opens new opportunities for versatile qubit encoding in neutral atom quantum processors.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Approximate quantum circuit synthesis using block encodings

One of the challenges in quantum computing is the synthesis of unitary operators into quantum circuits with polylogarithmic gate complexity. Exact synthesis of generic unitaries requires an exponential number of gates in general. We propose a novel approximate quantum circuit synthesis technique by relaxing the unitary constraints and interchanging them for ancilla qubits via block encodings. This approach combines smaller block encodings, which are easier to synthesize, into quantum circuits for larger operators. Due to the use of block encodings, our technique is not limited to unitary operators and can be applied for the synthesis of arbitrary operators. Overall, we show that operators which can be approximated by a canonical polyadic expression with a polylogarithmic number of terms can be synthesized with polylogarithmic gate complexity with respect to the matrix dimension.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Fast and Accurate Greenberger-Horne-Zeilinger Encoding Using All-to-All Interactions

The 𝑁-qubit Greenberger-Horne-Zeilinger (GHZ) state is an important resource for quantum technologies. Here, we consider the task of GHZ encoding using all-to-all interactions, which prepares the GHZ state in a special case, and is furthermore useful for quantum error correction, interaction-rate enhancement, and transmitting information using power-law interactions. The naive protocol based on parallelizing CNOT gates takes O(1)-time of Hamiltonian evolution. In this work, we propose a fast protocol that achieves GHZ encoding with high accuracy. The evolution time O⁡(log 2 ⁡𝑁/𝑁) almost saturates the theoretical limit Ω⁡(log⁡𝑁/𝑁). Moreover, the final state is close to the ideal encoded one with high fidelity >1–10 −3 , up to large system sizes 𝑁 ≲ 2000. The protocol only requires a few stages of time-independent Hamiltonian evolution; the key idea is to use the data qubit as control, and to use fast spin-squeezing dynamics generated by e.g., two-axis twisting.

quantum computation↗