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DOE OSTI2026

Fidelity Comparison of Time-Bin and Fock State Encoding in Hybrid Quantum Systems Under Channel and Transduction Effects

Future quantum networks are expected to integrate a heterogeneous combination of quantum systems, owing to the diverse advantages offered by different physical platforms in terms of scalability, coherence times, and interfacing capabilities. Within the context of this emerging quantum communication paradigm, this paper presents an analytical comparison of two photonic encoding schemes—time-bin and Fock state (single rail)—in hybrid quantum systems where flying qubits are entangled with stationary matter qubits. We evaluate their resilience against fiber channel and quantum transduction effects by calculating the fidelity of the final states relative to their ideal forms. Employing the characteristic function approach, we derive analytical fidelity expressions and investigate their dependence on parameters such as transmissivity, noise levels, fiber length, and source generation success probability. Additionally, we simulate the scenario with a dedicated QuTiP software implementation to verify the validity of the theoretical models. Our findings reveal that due to its inherent single-mode structure, the Fock state encoding consistently outperforms time-bin encoding in fidelity, as this structure significantly minimizes susceptibility to losses compared to the two-mode nature of the time-bin scheme. This analysis offers valuable insights for future hybrid quantum communication and information processing applications.

Fiorini, Francesco [Pisa U.]↗

DOE OSTI2018

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio , Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments: Hydrogenovibrio, Thiomicrorhabdus, Thiomicrospira

Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1–3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb 3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba 3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO 2 concentrating mechanisms. Finally, these adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Galactomannan utilization by Cellvibrio japonicus relies on a single essential α‐galactosidase encoded by the aga27A gene

Plant mannans are a component of lignocellulose that can have diverse compositions in terms of its backbone and side-chain substitutions. Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides that can include mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has 10 predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential mannan-degrading components in this bacterium. The transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode carbohydrate active enzymes (CAZymes) when mannan was actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme-encoding genes in the context of mannan utilization. Growth analysis of the mutant strains found that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α-galactosidase, and mannosidase, respectively, were important for the deconstruction of galactomannan, with Aga27A being essential. Our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the complete degradation of this hemicellulose.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack [plus supplemental information]

A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc 2 155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems. IMPORTANCE: Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli . Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome’s capacity to take up environmental DNA enables rapid adaptation to environmental stresses. Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Results from laboratory tests of the two-dimensional Time-Encoded Imaging System.

A series of laboratory experiments were undertaken to demonstrate the feasibility of two dimensional time-encoded imaging. A prototype two-dimensional time encoded imaging system was designed and constructed. Results from imaging measurements of single and multiple point sources as well as extended source distributions are presented. Time encoded imaging has proven to be a simple method for achieving high resolution two-dimensional imaging with potential to be used in future arms control and treaty verification applications.

Marleau, Peter↗

DOE OSTI2021

LUNA Condition-Based Monitoring Update: Auto-encoders on Actuator Data [Slides]

An auto-encoder is a neural network trained to output a reconstruction of its input. There is a ‘bottleneck’ layer whose dimension is typically lower than that of the input. Because the input passes through the bottleneck, the auto-encoder must learn to compress (encode) the input into this low-dimensional form, and to decompress (decode) the compressed data into a close approximation of its original form.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Efficient Hamiltonian encoding algorithms for extracting quantum control mechanism as interfering pathway amplitudes in the Dyson series

Hamiltonian encoding is a methodology for revealing the mechanism behind the dynamics governing controlled quantum systems. In this paper, following Mitra and Rabitz \cite{abhra_1}, we define mechanism via pathways of eigenstates that describe the evolution of the system, where each pathway is associated with a complex-valued amplitude corresponding to a term in the Dyson series. The evolution of the system is determined by the constructive and destructive interference of these pathway amplitudes. Pathways with similar attributes can be grouped together into pathway classes. The amplitudes of pathway classes are computed by modulating the Hamiltonian matrix elements and decoding the subsequent evolution of the system rather than by direct computation of the individual terms in the Dyson series. The original implementation of Hamiltonian encoding was computationally intensive and became prohibitively expensive in large quantum systems. This paper presents two new encoding algorithms that calculate the amplitudes of pathway classes by using techniques from graph theory and algebraic topology to exploit patterns in the set of allowed transitions, greatly reducing the number of matrix elements that need to be modulated. These new algorithms provide an exponential decrease in both computation time and memory utilization with respect to the Hilbert space dimension of the system. To demonstrate the use of these techniques, they are applied to two illustrative state-to-state transition problems.

Abrams, Erez [Princeton University, Massachusetts ↗

DOE OSTI2013

Detailed analysis of putative genes encoding small proteins in legume genomes

Diverse plant genome sequencing projects coupled with powerful bioinformatics tools have facilitated massive data analysis to construct specialized databases classified according to cellular function. However, there are still a considerable number of genes encoding proteins whose function has not yet been characterized. Included in this category are small proteins (SPs, 30–150 amino acids) encoded by short open reading frames (sORFs). SPs play important roles in plant physiology, growth, and development. Unfortunately, protocols focused on the genome-wide identification and characterization of sORFs are scarce or remain poorly implemented. As a result, these genes are underrepresented in many genome annotations. In this work, we exploited publicly available genome sequences of Phaseolus vulgaris, Medicago truncatula, Glycine max, and Lotus japonicus to analyze the abundance of annotated SPs in plant legumes. Our strategy to uncover bona fide sORFs at the genome level was centered in bioinformatics analysis of characteristics such as evidence of expression (transcription), presence of known protein regions or domains, and identification of orthologous genes in the genomes explored. We collected 6170, 10,461, 30,521, and 23,599 putative sORFs from P. vulgaris, G. max, M. truncatula, and L. japonicus genomes, respectively. Expressed sequence tags (ESTs) available in the DFCI Gene Index database provided evidence that ~one-third of the predicted legume sORFs are expressed. Most potential SPs have a counterpart in a different plant species and counterpart regions or domains in larger proteins. Potential functional sORFs were also classified according to a reduced set of GO categories, and the expression of 13 of them during P. vulgaris nodule ontogeny was confirmed by qPCR. This analysis provides a collection of sORFs that potentially encode for meaningful SPs, and offers the possibility of their further functional evaluation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2010

Nucleic acids encoding antifungal polypeptides and uses thereof

Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

Altier, Daniel J↗

DOE OSTI2014

Reader set encoding for directory of shared cache memory in multiprocessor system

In a parallel processing system with speculative execution, conflict checking occurs in a directory lookup of a cache memory that is shared by all processors. In each case, the same physical memory address will map to the same set of that cache, no matter which processor originated that access. The directory includes a dynamic reader set encoding, indicating what speculative threads have read a particular line. This reader set encoding is used in conflict checking. A bitset encoding is used to specify particular threads that have read the line.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Cache directory lookup reader set encoding for partial cache line speculation support

In a multiprocessor system, with conflict checking implemented in a directory lookup of a shared cache memory, a reader set encoding permits dynamic recordation of read accesses. The reader set encoding includes an indication of a portion of a line read, for instance by indicating boundaries of read accesses. Different encodings may apply to different types of speculative execution.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Entropy agnostic data encoding and decoding

Entropy agnostic data encoding includes: receiving, by an encoder, input data including a bit string; generating a plurality of candidate codewords, including encoding the input data bit string with a plurality of binary vectors, wherein the plurality of binary vectors includes a set of deterministic biased binary vectors and a set of random binary vectors; selecting, in dependence upon a predefined criteria, one of the plurality of candidate codewords; and transmitting the selected candidate codeword to a decoder.

Seyedzadehdelcheh, Seyedmohammad↗

DOE OSTI2022

Entropy agnostic data encoding and decoding

SeyedzadehDelcheh, SeyedMohammad↗

DOE OSTI2022

Temporal link encoding

Temporal link encoding, including: identifying a data type of a data value to be transmitted; determining that the data type is included in one or more data types for temporal encoding; and transmitting the data value using temporal encoding.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Quantum block encoding for one-pair semiseparable matrices

Quantum block encoding (QBE) is a crucial step in the development of most quantum algorithms, as it provides an embedding of a given matrix into a suitable larger unitary matrix. Historically, the development of efficient techniques for QBE has mostly focused on sparse matrices; less effort has been devoted to data-sparse (e.g., rank-structured) matrices. In this work we examine a particular case of rank structure, namely, one-pair semiseparable matrices. We present a new block encoding approach that relies on a suitable factorization of the given matrix as the product of triangular and diagonal factors. To encode the matrix, the algorithm needs $2\log(N)+7$ ancillary qubits. Assuming that the data input oracles can be implemented with polylogarithmic depth, or that a QRAM input model is available, our proposed method requires $\mathcal{O}({\rm polylog} (N))$ time and has an error of $\mathcal{O}(N^2)$, where $N$ is the matrix size.

Antonioli, Giacomo [Pisa U.; CERN] (ORCID:00090000↗

DOE OSTI2023

TDD LoRa and Delta Encoding in Low-Power Networks of Environmental Sensor Arrays for Temperature and Deformation Monitoring

Abstract Densely distributed sensor networks can revolutionize environmental observations by providing real-time data with an unprecedented spatiotemporal resolution. However, field deployments often pose unique challenges in terms of power provisions and wireless connectivity. We present a framework for wirelessly connected distributed sensor arrays for near-surface temperature and/or deformation monitoring. Our research focuses on a novel time division duplex implementation of the LoRa protocol, enabling battery powered base stations and avoiding collisions within the network. In order to minimize transmissions and improve battery life throughout the network, we propose a dedicated delta encoding algorithm that utilizes the spatial and temporal similarity in the acquired data sets. We implemented the developed technologies in a AA battery powered hardware platform that can be used as a wireless data logger or base station, and we conducted an assessment of the power consumption. Without data compression, the projected battery life for a data logger is 4.74 years, and a wireless base stations can last several weeks or months depending on the amount of network traffic. The delta encoding algorithm can further improve this battery life with a factor of up to 3.50. Our results demonstrate the viability of the proposed methods for low-power environmental wireless sensor networks.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Bi-fidelity variational auto-encoder for uncertainty quantification

Quantifying the uncertainty of quantities of interest (QoIs) from physical systems is a primary objective in model validation. However, achieving this goal entails balancing the need for computational efficiency with the requirement for numerical accuracy. To address this trade-off, we propose a novel bi-fidelity formulation of variational auto-encoders (BF-VAE) designed to estimate the uncertainty associated with a QoI from low-fidelity (LF) and high-fidelity (HF) samples of the QoI. Here, this model allows for the approximation of the statistics of the HF QoI by leveraging information derived from its LF counterpart. Specifically, we design a bi-fidelity auto-regressive model in the latent space which is integrated within the VAE’s probabilistic encoder–decoder structure. An effective algorithm is proposed to maximize the variational lower bound of the HF log-likelihood in the presence of limited HF data, resulting in the synthesis of HF realizations with a reduced computational cost. Additionally, we introduce the concept of the bi-fidelity information bottleneck (BF-IB) to provide an information-theoretic interpretation of the proposed BF-VAE model. Our numerical results demonstrate that the BF-VAE leads to considerably improved accuracy, as compared to a VAE trained using only HF data, when limited HF data is available.

42 ENGINEERING↗