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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria

ABSTRACT We have discovered a new cluster of genes that is found exclusively in the Actinobacteria phylum. This locus includes genes for the 2-aminophenol meta -cleavage pathway and the shell proteins of a bacterial microcompartment (BMC) and has been named aromatics (ARO) for its putative role in the breakdown of aromatic compounds. In this study, we provide details about the distribution and composition of the ARO BMC locus and conduct phylogenetic, structural, and functional analyses of the first two enzymes in the catabolic pathway: a unique 2-aminophenol dioxygenase, which is exclusively found alongside BMC shell genes in Actinobacteria, and a semialdehyde dehydrogenase, which works downstream of the dioxygenase. Genomic analysis reveals variations in the complexity of the ARO loci across different orders. Some loci are simple, containing shell proteins and enzymes for the initial steps of the catabolic pathway, while others are extensive, encompassing all the necessary genes for the complete breakdown of 2-aminophenol into pyruvate and acetyl-CoA. Furthermore, our analysis uncovers two subtypes of ARO BMC that likely degrade either 2-aminophenol or catechol, depending on the presence of a pathway-specific gene within the ARO locus. The precise precursor of 2-aminophenol, which serves as the initial substrate and/or inducer for the ARO pathway, remains unknown, as our model organism Micromonospora rosaria cannot utilize 2-aminophenol as its sole energy source. However, using enzymatic assays, we demonstrate the dioxygenase’s ability to cleave both 2-aminophenol and catechol in vitro , in collaboration with the aldehyde dehydrogenase, to facilitate the rapid conversion of these unstable and toxic intermediates. IMPORTANCE Bacterial microcompartments (BMCs) are proteinaceous organelles that are widespread among bacteria and provide a competitive advantage in specific environmental niches. Studies have shown that the genetic information necessary to form functional BMCs is encoded in loci that contain genes encoding shell proteins and the enzymatic core. This allows the bioinformatic discovery of BMCs with novel functions and expands our understanding of the metabolic diversity of BMCs. ARO loci, found only in Actinobacteria, contain genes encoding for phylogenetically remote shell proteins and homologs of the meta -cleavage degradation pathway enzymes that were shown to convert central aromatic intermediates into pyruvate and acetyl-CoA in gamma Proteobacteria. By analyzing the gene composition of ARO BMC loci and characterizing two core enzymes phylogenetically, structurally, and functionally, we provide an initial functional characterization of the ARO BMC, the most unusual BMC identified to date, distinctive among the repertoire of studied BMCs.

2-AP 1,6-dioxygenase↗
DOE OSTI2025

Signal sequences target enzymes and structural proteins to bacterial microcompartments and are critical for microcompartment formation

ABSTRACT Spatial organization of pathway enzymes has emerged as a promising tool to address several challenges in metabolic engineering, such as flux imbalances and off-target product formation. Bacterial microcompartments (MCPs) are a spatial organization strategy used natively by many bacteria to encapsulate metabolic pathways that produce toxic, volatile intermediates. Several recent studies have focused on engineering MCPs to encapsulate heterologous pathways of interest, but how this engineering affects MCP assembly and function is poorly understood. In this study, we investigated the role of signal sequences, short domains that target proteins to the MCP core, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterized two novel Pdu signal sequences on the structural proteins PduM and PduB, which constitute the first report of metabolosome signal sequences on structural proteins rather than enzymes. We then explored the role of enzymatic and structural Pdu signal sequences on MCP assembly by deleting their encoding sequences from the genome alone and in combination. Deleting enzymatic signal sequences decreased the MCP formation, but this defect could be recovered in some cases by overexpressing genes encoding the knocked-out signal sequence fused to a heterologous protein. By contrast, deleting structural signal sequences caused similar defects to knocking out the genes encoding the full-length PduM and PduB proteins. Our results contribute to a growing understanding of how MCPs form and function in bacteria and provide strategies to mitigate assembly disruption when encapsulating heterologous pathways in MCPs. IMPORTANCE Spatially organizing biosynthetic pathway enzymes is a promising strategy to increase pathway throughput and yield. Bacterial microcompartments (MCPs) are proteinaceous organelles that many bacteria natively use as a spatial organization strategy to encapsulate niche metabolic pathways, providing significant metabolic benefits. Encapsulating heterologous pathways of interest in MCPs could confer these benefits to industrially relevant pathways. Here, we investigate the role of signal sequences, short domains that target proteins for encapsulation in MCPs, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterize two novel signal sequences on structural proteins, constituting the first Pdu signal sequences found on structural proteins rather than enzymes, and perform knockout studies to compare the impacts of enzymatic and structural signal sequences on MCP assembly. Our results demonstrate that enzymatic and structural signal sequences play critical but distinct roles in Pdu MCP assembly and provide design rules for engineering MCPs while minimizing disruption to MCP assembly.

Johnson, Elizabeth R. (ORCID:0000000179236881)↗
DOE OSTI2021

Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions

Plant iron (Fe) nutritional status has a significant impact on rhizosphere microbial communities. While this effect has been attributed to alterations in the composition of root exudates, the underlying mechanisms are not known. Here, we investigated the effect of Fe deficiency on the interactions between the grass Brachypodium distachyon and the common soil bacteria Pseudomonas fluorescens SBW25. Increased phytosiderophore production was the most significant response of Brachypodium root exudation to Fe deficiency. We observed upregulated expression of phytosiderophore biosynthesis genes but lower accumulated exudate concentrations in the presence of Pseudomonas, indicating that the bacteria degrade these phytosiderophores. Pseudomonas did not produce endogenous siderophores under the low Fe conditions. Rather, the bacterial transcriptome revealed upregulation of four genes in response to Fe deficiency that contain motifs associated with cellular uptake of small molecules. Collectively, these results suggest that rhizosphere Pseudomonas fluorescens may take up phytosiderophores produced by grasses in response to Fe deficiency, and we propose target genes that may be involved. Our findings provide insight into the molecular basis for the exchange of C, N, and Fe between plants and bacteria under Fe deficient conditions. These interactions may contribute to differences in the rhizosphere microbial community structure across soil pH regimes.

Boiteau, Rene M.↗
DOE OSTI2023

Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

While wetlands are major sources of biogenic methane (CH 4 ), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH 4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site’s methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dancing the Quantum Waltz: Compiling Three-Qubit Gates on Four Level Architectures

Superconducting quantum devices are a leading technology for quantum computation, but they face several challenges. Gate errors, coherence errors and a lack of connectivity all contribute to low fidelity results. In particular, connectivity restrictions enforce a gate set that requires three-qubit gates to be decomposed into one- or two-qubit gates. This substantially increases the number of two-qubit gates that need to be executed. However, many quantum devices have access to higher energy levels. We can expand the qubit abstraction of |0〉 and |1〉 to a ququart which has access to the |2〉 and |3〉 state, but with shorter coherence times. This allows for two qubits to be encoded in one ququart, enabling increased virtual connectivity between physical units from two adjacent qubits to four fully connected qubits. This connectivity scheme allows us to more efficiently execute three-qubit gates natively between two physical devices.We present direct-to-pulse implementations of several three-qubit gates, synthesized via optimal control, for compilation of three-qubit gates onto a superconducting-based architecture with access to four-level devices with the first experimental demonstration of four-level ququart gates designed through optimal control. We demonstrate strategies that temporarily use higher level states to perform Toffoli gates and always use higher level states to improve fidelities for quantum circuits. We find that these methods improve expected fidelities with increases of 2x across circuit sizes using intermediate encoding, and increases of 3x for fully-encoded ququart compilation.

Litteken, Andrew↗
DOE OSTI2026

Scalability Analysis of Quantum Models for Stress and Emotion Detection

Stress and emotion detection from high-dimensional physiological signals is a challenging task, particularly when aiming for accurate classification across diverse behavioral states. Quantum machine learning (QML) is promising for modeling such high-dimensional data, but scalability is limited by qubit resources and the exponential cost of classical statevector simulation. This work studies the scalability of quantum support vector machines (QSVMs) for binary stress detection and three-class emotion recognition (Negative/Neutral/Positive) under varying qubit counts and angle-encoding strategies. We also present a comparison study with one-feature-per-qubit (1:1) and two-features-per-qubit (2:1) mappings. Experiments are executed on HPC infrastructure using NVIDIA CUDA-Q to evaluate performance, variance, and class-dependent separability at higher-qubit setups. Results show that larger Hilbert spaces can improve peak accuracy but may increase instability. At the same time, dense 2:1 encoding yields more consistent stress detection performance. For emotion recognition, scaling improves discrimination for classes like Negative and Positive more than Neutral. We find that effective QML scaling is task-dependent and benefits more from encoding design than simply increasing qubit count.

Onim, Md. Saif Hassan [University of Tennessee, Kn↗
DOE OSTI2024

Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium

Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short- and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition. Overall design: Sampling of Chlamydomonas CC-4532 cells cultivated photoheterotrophically (TAP) under Fe-starvation condition (0 uM Fe-EDTA). Samples were collected at multiple timepoints from biological duplicate cultures after washing in TAP medium lacking Fe. Two time courses were collected. A short time course with t=0 (pre-wash), 0 (post-wash), 5, 10, 15, 30, 60, 120, and 240 min. A long time course with t= 0, 0.5, 1, 2, 4, 8, 12, 24 and 48 hours. Please note that, for long time course, the GSE44611/PRJNA190650 samples were re-used/re-analyzed together with the short time course data: GSM1087792 C.reinhardtii_Fe_Long_0_hours SRX245324 SAMN01924672 GSM1087793 C.reinhardtii_Fe_Long_0.5_hours SRX245325 SAMN01924673 GSM1087794 C.reinhardtii_Fe_Long_1_hours SRX245326 SAMN01924674 GSM1087795 C.reinhardtii_Fe_Long_2_hours SRX245327 SAMN01924675 GSM1087796 C.reinhardtii_Fe_Long_4_hours SRX245328 SAMN01924676 GSM1087797 C.reinhardtii_Fe_Long_8_hours SRX245329 SAMN01924677 GSM1087798 C.reinhardtii_Fe_Long_12_hours SRX245330 SAMN01924678 GSM1087799 C.reinhardtii_Fe_Long_24_hours SRX245331 SAMN01924679 GSM1087800 C.reinhardtii_Fe_Long_48_hours SRX245332 SAMN01924680

Source record↗
DOE OSTI2023

Engineered Escherichia coli platforms for tyrosine-derivative production from phenylalanine using phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system

Aromatic compounds derived from tyrosine are important and diverse chemicals that have industrial and commercial applications. Although these aromatic compounds can be obtained by extraction from natural producers, their growth is slow, and their content is low. To overcome these problems, many of them have been chemically synthesized from petroleum-based feedstocks. However, because of the environmental burden and depleting availability of feedstock, microbial cell factories are attracting much attention as sustainable and environmentally friendly processes. To facilitate development of microbial cell factories for producing tyrosine derivatives, we developed simple and convenient tyrosine-producing Escherichia coli platforms with a bacterial phenylalanine hydroxylase, which converted phenylalanine to tyrosine with tetrahydromonapterin as a cofactor, using a synthetic biology approach. By introducing a tetrahydrobiopterin-regeneration system, the tyrosine titer of the plasmid-based engineered strain was 4.63 g/L in a medium supplemented with 5.00 g/L phenylalanine with a test tube. The strains were successfully used to produce industrially attractive compounds, such as tyrosol with a yield of 1.58 g/L by installing a tyrosol-producing module consisting of genes encoding tyrosine decarboxylase and tyramine oxidase on a plasmid. Gene integration into E. coli chromosomes has an advantage over the use of plasmids because it increases genetic stability without antibiotic feeding to the culture media and enables more flexible pathway engineering by accepting more plasmids with artificial pathway genes. Therefore, we constructed a plasmid-free tyrosine-producing platform by integrating five modules, comprising genes encoding the phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system, into the chromosome. The platform strain could produce 1.04 g/L of 3,4-dihydroxyphenylalanine, a drug medicine, by installing a gene encoding tyrosine hydroxylase and the tetrahydrobiopterin-regeneration system on a plasmid. Moreover, by installing the tyrosol-producing module, tyrosol was produced with a yield of 1.28 g/L. We developed novel E. coli platforms for producing tyrosine from phenylalanine at multi-gram-per-liter levels in test-tube cultivation. The platforms allowed development and evaluation of microbial cell factories installing various designed tyrosine-derivative biosynthetic pathways at multi-grams-per-liter levels in test tubes.

09 BIOMASS FUELS↗
DOE OSTI2022

Dynamic wavelength control of laser pulse profiles at picosecond to nanosecond timescales

We report on a novel combined laser pulse shaping and dynamic wavelength encoding capability based on a simple architecture implementing direct space to time mapping. There are several potential applications that can be enabled by the ability to control the instantaneous intensity or wavelength of an optical waveform on a picosecond-to-nanosecond timescale. To our knowledge, no known methods can access this temporal regime with a practical architecture. Here, we demonstrate an extension of the Space–Time Induced Linearly Encoded Transcription for Temporal Optimization (STILETTO) technique that can generate optical waveforms with a programmable instantaneous wavelength vs. time. We experimentally demonstrate the technique by generating self-gated spectrograms and show that it can encode dynamic wavelength vs time profiles at timescales not achievable by any other known method.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Orthogonal spatial coding with stimulated parametric down-conversion

Orthogonal optical coding is widely used in classical multi-user communication networks. Using the phase conjugation property of stimulated parametric down-conversion, we extend the current time-domain orthogonal optical coding scheme to the spatial domain to encode and decode image information. In this process, the idler beam inherits the complex conjugate of the field information encoded in the seed beam. An encoding phase mask introduced onto the input seed beam blurs the image transferred to the idler. The original image is restored by passing the coded transferred image through a corrective phase mask placed in the momentum space of the idler beam. We expect that this scheme can also inspire new techniques in secure image transmission, aberration cancellation, and frequency conversion imaging.

Xu, Yang↗
DOE OSTI2021

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii

Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4 . The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas , land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery

Arboviruses are a diverse group of insect-transmitted pathogens that pose global public health challenges. Identifying evolutionarily conserved host factors that combat arbovirus replication in disparate eukaryotic hosts is important as they may tip the balance between productive and abortive viral replication, and thus determine virus host range. Here, we exploit naturally abortive arbovirus infections that we identified in lepidopteran cells and use bacterial effector proteins to uncover host factors restricting arbovirus replication. Bacterial effectors are proteins secreted by pathogenic bacteria into eukaryotic hosts cells that can inhibit antimicrobial defenses. Since bacteria and viruses can encounter common host defenses, we hypothesized that some bacterial effectors may inhibit host factors that restrict arbovirus replication in lepidopteran cells. Thus, we used bacterial effectors as molecular tools to identify host factors that restrict four distinct arboviruses in lepidopteran cells. By screening 210 effectors encoded by seven different bacterial pathogens, we identify several effectors that individually rescue the replication of all four arboviruses. We show that these effectors encode diverse enzymatic activities that are required to break arbovirus restriction. We further characterize Shigella flexneri-encoded IpaH4 as an E3 ubiquitin ligase that directly ubiquitinates two evolutionarily conserved proteins, SHOC2 and PSMC1, promoting their degradation in insect and human cells. We show that depletion of either SHOC2 or PSMC1 in insect or human cells promotes arbovirus replication, indicating that these are ancient virus restriction factors conserved across invertebrate and vertebrate hosts. Collectively, our study reveals a novel pathogen-guided approach to identify conserved antimicrobial machinery, new effector functions, and conserved roles for SHOC2 and PSMC1 in virus restriction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fungal community and functional responses to soil warming are greater than for soil nitrogen enrichment

Soil fungi are key regulators of forest carbon cycling and their responses to global change have effects that ripple throughout ecosystems. Global changes are expected to push many fungi beyond their environmental niches, but there are relatively few studies involving multiple, simultaneous global change factors. Here, we studied soil fungal diversity, community composition, co-occurrence patterns, and decomposition gene responses to 10 years of soil warming and nitrogen addition, alone and in combination. We specifically examined whether there were fungal community characteristics that could explain changes in soil carbon storage and organic matter chemistry in chronically warmed and fertilized soil. We found that fungal communities in warmed soils are less diverse and shift in composition. Warming also favored hyperdominance by a few mycorrhizal fungal species and lowered manganese peroxidase but increased hydrolytic enzyme encoding gene potentials. Nitrogen addition did not significantly affect fungal community composition but, like warming, did reduce fungal diversity and favored overdominance by a unique set of mycorrhizal taxa. Warming alone and in combination with nitrogen addition also reduced negative but increased positive fungal co-occurrence probabilities, promoting species coexistence. Negative fungal co-occurrence was positively correlated to soil carbon content, while the proportion of fungal hydrolytic enzyme encoding genes was negatively correlated with soil carbon content. This may reflect fungal life history trade-offs between competition (e.g., reduced negative co-occurrence) and resource acquisition (e.g., higher abundance of hydrolytic enzyme encoding genes) with implications for carbon storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

XMark: Reliable Multi-Bit Watermarking for LLM-Generated Texts

Multi-bit watermarking has emerged as a promising solution for embedding imperceptible binary messages into Large Language Model (LLM)-generated text, enabling reliable attribution and tracing of malicious usage of LLMs. Despite recent progress, existing methods still face key limitations: some become computationally infeasible for large messages, while others suffer from a poor trade-off between text quality and decoding accuracy. Moreover, the decoding accuracy of existing methods drops significantly when the number of tokens in the generated text is limited, a condition that frequently arises in practical usage. To address these challenges, we propose XMark, a novel method for encoding and decoding binary messages in LLM-generated texts. The unique design of XMark’s encoder produces a less distorted logit distribution for watermarked token generation, preserving text quality, and also enables its tailored decoder to reliably recover the encoded message with limited tokens. Extensive experiments across diverse downstream tasks show that XMark significantly improves decoding accuracy while preserving the quality of watermarked text, outperforming prior methods. The code will be made publicly available upon acceptance.

Xu, Jiahao [University of Nevada, Reno]↗
DOE OSTI2023

Moore Machine Motion Controls Refurbishment Statement of Work and Specification

Diamond Turning Machines known as “Moore” machines are used in the production of Potassium diHydrogen Phosphate (KDP) optics required for the National Ignition Facility (NIF). These machines are owned by the Department of Energy, as provided by Lawrence Livermore National Security LLC (LLNS). Moore Machines 1 and 2 are located at the Gooch & Housego (G&H) facility in Highland Heights, OH. The existing Aerotech motion controllers, motor drivers/amplifiers, input/output (I/O) hardware, control computer, software user interface, human machine interface (HMI), cabling, and encoders are beyond service life and require replacement. This Statement of Work (SoW) defines the motion control system refurbishment requirements for the Moore diamond turning machines designated Moore 1 and Moore 2. The motion controls system design shall include a motion control computer, control software, motor drive amplifiers and controllers, linear scale encoders, rotary encoders, HMI, power distribution, emergency stop (E-Stop) and interlocks, cabling, switches, solenoids, transducers, sensors, actuators, ancillary system interfaces, and related components necessary for a complete machine tool control system. The Subcontractor shall include effort to standardize systems between the two machines if reasonably possible.

42 ENGINEERING↗
DOE OSTI2023

ARENA: Adversary-Resistant Evolving Neural Architectures

Neural networks are becoming the cornerstone for national security prediction tasks. However, designing them requires significant research and trial/error, as they have many hyperparameters, including their computation graph (“architecture”). Neural architecture search (NAS) employs secondary optimizers to search for architectures maximizing objectives like accuracy. Evolutionary algorithms (EAs) are the most used class of optimizer for NAS. However, existing Python libraries for writing EAs limit the complexity of experiments a user can design. In this project, we built ARENA, a Python framework that encodes complex, hyper-realistic EAs. ARENA collects detailed information as it runs and is flexible enough to encode non-EA search algorithms. We tested ARENA on 4 toy optimization problems by encoding 3 search algorithms for each—random search, an EA, and simulated annealing. We also designed an EA that performs NAS on the MNIST dataset. Our experiments suggest the potential for immediate mission impact through solving lab-wide optimization problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Hierarchical memories: Simulating quantum LDPC codes with local gates

Constant-rate low-density parity-check (LDPC) codes are promising candidates for constructing efficient fault-tolerant quantum memories. However, if physical gates are subject to geometric-locality constraints, it becomes challenging to realize these codes. In this paper, we construct a new family of [[N,K,D]] codes, referred to as hierarchical codes, that encode a number of logical qubits K=Ω(N/log(N) 2 ). The N th element of this code family is obtained by concatenating a constant-rate quantum LDPC code with a surface code; nearest-neighbor gates in two dimensions are sufficient to implement the corresponding syndrome-extraction circuit and achieve a threshold. Below threshold the logical failure rate vanishes superpolynomially as a function of the distance D(N). We present a bilayer architecture for implementing the syndrome-extraction circuit, and estimate the logical failure rate for this architecture. Under conservative assumptions, we find that the hierarchical code outperforms the basic encoding where all logical qubits are encoded in the surface code.

Pattison, Christopher A. [California Institute of ↗
DOE OSTI2021

The Hyperthermophilic Restriction-Modification Systems of Thermococcus kodakarensis Protect Genome Integrity

Thermococcus kodakarensis (T. kodakarensis), a hyperthermophilic, genetically accessible model archaeon, encodes two putative restriction modification (R-M) defense systems, TkoI and TkoII. TkoI is encoded by TK1460 while TkoII is encoded by TK1158. Bioinformative analysis suggests both R-M enzymes are large, fused methyltransferase (MTase)-endonuclease polypeptides that contain both restriction endonuclease (REase) activity to degrade foreign invading DNA and MTase activity to methylate host genomic DNA at specific recognition sites. In this work, we demonsrate T. kodakarensis strains deleted for either or both R-M enzymes grow more slowly but display significantly increased competency compared to strains with intact R-M systems, suggesting that both TkoI and TkoII assist in maintenance of genomic integrity in vivo and likely protect against viral- or plasmid-based DNA transfers. Pacific Biosciences single molecule real-time (SMRT) sequencing of T. kodakarensis strains containing both, one or neither R-M systems permitted assignment of the recognition sites for TkoI and TkoII and demonstrated that both R-M enzymes are TypeIIL; TkoI and TkoII methylate the N 6 position of adenine on one strand of the recognition sequences GTGAAG and TTCAAG, respectively. Further in vitro biochemical characterization of the REase activities reveal TkoI and TkoII cleave the DNA backbone GTGAAG(N) 20 /(N) 18 and TTCAAG(N) 10 /(N) 8 , respectively, away from the recognition sequences, while in vitro characterization of the MTase activities reveal transfer of tritiated S-adenosyl methionine by TkoI and TkoII to their respective recognition sites. Together these results demonstrate TkoI and TkoII restriction systems are important for protecting T. kodakarensis genome integrity from invading foreign DNA.

59 BASIC BIOLOGICAL SCIENCES↗