Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Encoding”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53

AstroCLIP: a cross-modal foundation model for galaxies

ABSTRACT We present AstroCLIP, a single, versatile model that can embed both galaxy images and spectra into a shared, physically meaningful latent space. These embeddings can then be used – without any model fine-tuning – for a variety of downstream tasks including (1) accurate in-modality and cross-modality semantic similarity search, (2) photometric redshift estimation, (3) galaxy property estimation from both images and spectra, and (4) morphology classification. Our approach to implementing AstroCLIP consists of two parts. First, we embed galaxy images and spectra separately by pre-training separate transformer-based image and spectrum encoders in self-supervised settings. We then align the encoders using a contrastive loss. We apply our method to spectra from the Dark Energy Spectroscopic Instrument and images from its corresponding Legacy Imaging Survey. Overall, we find remarkable performance on all downstream tasks, even relative to supervised baselines. For example, for a task like photometric redshift prediction, we find similar performance to a specifically trained ResNet18, and for additional tasks like physical property estimation (stellar mass, age, metallicity, and specific-star-formation rate), we beat this supervised baseline by 19 per cent in terms of R2. We also compare our results with a state-of-the-art self-supervised single-modal model for galaxy images, and find that our approach outperforms this benchmark by roughly a factor of two on photometric redshift estimation and physical property prediction in terms of R2, while remaining roughly in-line in terms of morphology classification. Ultimately, our approach represents the first cross-modal self-supervised model for galaxies, and the first self-supervised transformer-based architectures for galaxy images and spectra.

Parker, Liam (ORCID:0009000749521674)↗

7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system

Abstract The modified nucleosides 2′-deoxy-7-cyano- and 2′-deoxy-7-amido-7-deazaguanosine (dPreQ0 and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction–modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD–dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray crystal structure of DpdA supported by small-angle X-ray scattering analysis of DpdA and DpdB, the former bound to DNA. While the homology of DpdA with the tRNA-dependent tRNA-guanine transglycosylase enzymes (TGT) in the queuosine pathway suggested a similar transglycosylase activity responsible for the exchange of a guanine base in the DNA for 7-cyano-7-deazaguanine (preQ0), we demonstrate an unexpected ATPase activity in DpdB necessary for insertion of preQ0 into DNA, and identify several catalytically essential active site residues in DpdA involved in the transglycosylation reaction. Further, we identify a modification site for DpdA activity and demonstrate that DpdC functions independently of DpdA/B in converting preQ0-modified DNA to ADG-modified DNA.

59 BASIC BIOLOGICAL SCIENCES↗

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Abstract Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.

59 BASIC BIOLOGICAL SCIENCES↗

Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures

Abstract Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial chromosome has been extensively studied, the pathway targeting DNA replication structures remains poorly understood. We have used an integrative structural biology approach to elucidate how the Tn7-encoded protein TnsE recognizes replication sites. Using native mass spectrometry, we found that TnsE forms 1:1 and 2:1 (TnsE:DNA) complexes on 3′-recessed DNA, with gain-of-function TnsE variants favoring the formation of 2:1 complexes. Structural characterization confirms that two TnsE molecules bind to DNA with the C-terminal domain of the protein recognizing duplex DNA, leaving the N-terminal domain to impose DNA substrate specificity and recruit the core transposition machinery. Collectively, our work is consistent with a model where TnsE-mediated target-site selection relies on the formation of an asymmetric TnsE:DNA complex to recruit the Tn7 transposase to DNA replication structures.

Biochemistry & Molecular Biology↗

Helper-embedded satellites from an integrase clade that repeatedly targets prophage late genes

Abstract Satellites such as phage-induced chromosomal islands (PICIs) are mobile genetic elements relying on helper phages for their mobilization, through trans-regulatory interactions. We discovered a PICI with a more intimate cis-regulatory configuration, integrated within a late gene of its helper prophage. This helper-embedded PICI (HE-PICI) configuration delays expression of the interrupted helper late gene until the satellite excises and provides passive helper-driven components to both HE-PICI replication and late transcription. Upon induction of a helper-satellite composite, precise excision of the entire composite was observed, followed by composite replication, then satellite excision. We mapped 491 additional HE-PICIs to one of 14 sites in cognates of phage lambda late genes. Associated integrases form a single phylogenetic clade with subclades respecting the 14 site groups, exhibiting repeated tropism for prophage late genes as new integration sites evolve. Four ordered zones in a general gram-negative PICI genome organization are: an integration zone encoding integrase and AlpA, a dynamic zone encoding members of the Bro-N network of domain-swapping DNA-interactive proteins and immunity repressor RNAs, a replication zone, and a dynamic late zone in which clusters as large as 17 consecutive helper prophage late genes have been captured. Helper-embedded satellites present new dimensions in satellite/helper relationships.

Tommasini, Dario↗

Bacterium-enabled transient gene activation by artificial transcription factors for resolving gene regulation in maize

Abstract Understanding gene regulatory networks is essential to elucidate developmental processes and environmental responses. Here, we studied regulation of a maize (Zea mays) transcription factor gene using designer transcription activator-like effectors (dTALes), which are synthetic Type III TALes of the bacterial genus Xanthomonas and serve as inducers of disease susceptibility gene transcription in host cells. The maize pathogen Xanthomonas vasicola pv. vasculorum was used to introduce 2 independent dTALes into maize cells to induced expression of the gene glossy3 (gl3), which encodes a MYB transcription factor involved in biosynthesis of cuticular wax. RNA-seq analysis of leaf samples identified, in addition to gl3, 146 genes altered in expression by the 2 dTALes. Nine of the 10 genes known to be involved in cuticular wax biosynthesis were upregulated by at least 1 of the 2 dTALes. A gene previously unknown to be associated with gl3, Zm00001d017418, which encodes aldehyde dehydrogenase, was also expressed in a dTALe-dependent manner. A chemically induced mutant and a CRISPR-Cas9 mutant of Zm00001d017418 both exhibited glossy leaf phenotypes, indicating that Zm00001d017418 is involved in biosynthesis of cuticular waxes. Bacterial protein delivery of dTALes proved to be a straightforward and practical approach for the analysis and discovery of pathway-specific genes in maize.

59 BASIC BIOLOGICAL SCIENCES↗

Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization

Abstract A signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, reproduction, immunity, and stress responses in Arabidopsis (Arabidopsis thaliana). Genes encoding these proteins are members of multigene families in most angiosperms and could generate thousands of signaling complex variants. However, the links between expansion of these gene families and the functional diversification of this critical signaling complex as well as the evolutionary factors underlying the maintenance of gene duplicates remain unknown. Here, we investigated LLG gene family evolution by sampling land plant genomes and explored the function and expression of angiosperm LLGs. We found that LLG diversity within major land plant lineages is primarily due to lineage-specific duplication events, and that these duplications occurred both early in the history of these lineages and more recently. Our complementation and expression analyses showed that expression divergence (i.e. regulatory subfunctionalization), rather than functional divergence, explains the retention of LLG paralogs. Interestingly, all but one monocot and all eudicot species examined had an LLG copy with preferential expression in male reproductive tissues, while the other duplicate copies showed highest levels of expression in female or vegetative tissues. The single LLG copy in Amborella trichopoda is expressed vastly higher in male compared to in female reproductive or vegetative tissues. We propose that expression divergence plays an important role in retention of LLG duplicates in angiosperms.

Plant Sciences↗

Putative rhamnogalacturonan-II glycosyltransferase identified through callus gene editing bypasses embryo lethality

Rhamnogalacturonan II (RG-II) is a structurally complex and conserved domain of the pectin present in the primary cell walls of vascular plants. Borate crosslinking of RG-II is required for plants to grow and develop normally. Mutations that alter RG-II structure also affect crosslinking and are lethal or severely impair growth. Thus, few genes involved in RG-II synthesis have been identified. Here we developed a method to generate viable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants in callus tissue via CRISPR/Cas9-mediated gene editing. We combined this with a candidate gene approach to characterize the male gametophyte defective 2 (MPG2) gene that encodes a putative family GT29 glycosyltransferase. Plants homozygous for this mutation do not survive. We showed that in the callus mutant cell walls, RG-II does not crosslink normally because it lacks 3-deoxy-D-manno-octulosonic acid (Kdo) and thus cannot form the α-L-Rhap-(1→5)-α-D-kdop-(1→ sidechain. We suggest that MGP2 encodes an inverting RG-II CMP-β-Kdo transferase (RCKT1). Our discovery provides further insight into the role of sidechains in RG-II dimerization. Our method also provides a viable strategy for further identifying proteins involved in the biosynthesis of RG-II.

59 BASIC BIOLOGICAL SCIENCES↗

The small protein SbtC is a functional component of the CO 2 concentrating mechanism in Synechocystis sp. PCC 6803

Oxygenic phototrophs fix CO 2 via the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which shows relatively low CO 2 affinity and specificity. To circumvent low and fluctuating CO 2 concentrations in aquatic systems, cyanobacteria and algae have evolved sophisticated inorganic carbon (Ci) concentrating mechanisms (CCMs). Bicarbonate transporters such as SbtA play a crucial role in the cyanobacterial CCM and hence display multiple layers of tight regulation. Control of sbtA gene expression and corresponding transporter activity involves the PII-like protein SbtB, whose gene is frequently co-transcribed with sbtA. A previously non-annotated gene located upstream of the sbtAB operon in the model Synechocystis sp. PCC 6803 encodes the small protein SbtC, composed of 80 amino acids. Presence of SbtC was confirmed by immunoblotting of the sbtC-coding sequence fused to a Flag-tag. Similar to sbtAB , transcription of the sbtC locus is induced by low CO 2 availability; however, it is controlled independently. Mutation of the sbtC locus in a wild-type background produced only a mild phenotype, even under low CO 2 , but impaired diurnal growth resembled that of the mutant ΔsbtB . Biochemical analysis indicated a trimeric SbtABC complex in the membrane. Bicarbonate leakage from cells was strongly elevated when either sbtB or sbtC was deleted from recombinant Synechocystis strains harboring only SbtA as single Ci uptake system. Here, our results provide evidence that SbtC contributes to the formation of the SbtAB complex, thereby regulating bicarbonate exchange at the cytoplasmic membrane. Well-conserved SbtC-like proteins encoded in the neighborhood of sbtAB exist in many cyanobacterial genomes, pointing toward an important role in the cyanobacterial CCM.

Walke, Peter [Univ. of Rostock (Germany)] (ORCID:0↗

A Sorghum F-Box Protein Induces an Oxidative Burst in the Defense Against Colletotrichum sublineola

The hemibiotrophic fungal pathogen Colletotrichum sublineola is the causal agent of anthracnose in sorghum ( Sorghum bicolor), resulting in leaf blight, stalk rot, and head blight in susceptible genotypes, with yield losses of up to 50%. The development of anthracnose-resistant cultivars can reduce reliance on fungicides and provide a more sustainable and economical means for disease management. A previous genome-wide association study of the sorghum association panel identified the candidate resistance gene Sobic.005G172300 encoding an F-box protein. To better understand the role of this gene in the defense against C. sublineola, gene expression following infection with C. sublineola was monitored by RNA sequencing in seedlings of sorghum accession SC110, which harbored the resistance allele, and three accessions that harbored a susceptible allele. Only in SC110 did the expression of Sobic.005G172300 increase during the biotrophic phase of infection. Subsequent transcriptome analysis, gene co-expression networks, and gene regulatory networks of inoculated and mock-inoculated seedlings of resistant and susceptible accessions suggest that the increase in expression of Sobic.005G172300 induces an oxidative burst by lowering the concentration of ascorbic acid during the biotrophic phase of infection. Based on gene regulatory network analysis, the protein encoded by Sobic.005G172300 is proposed to target proteins involved in the biosynthesis of ascorbic acid for polyubiquitination through the SCF E3 ubiquitin ligase, causing their degradation via the proteasome.

Plant Sciences↗

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology↗

Randomized Adiabatic Quantum Linear Solver Algorithm with Optimal Complexity Scaling and Detailed Running Costs

Solving linear systems of equations is a fundamental problem with a wide variety of applications across many fields of science, and there is increasing effort to develop quantum linear solver algorithms. Subaşı et al. [Phys. Rev. Lett. 122, 060504 (2019)] proposed a randomized algorithm inspired by adiabatic quantum computing, based on a sequence of random Hamiltonian simulation steps, with suboptimal scaling in the condition number 𝜅 of the linear system and the target error 𝜖. Here we go beyond these results in several ways. Firstly, using filtering [Lin and Tong, Quantum 4, 361 (2020)] and Poissonization techniques [Cunningham and Roland, ArXiv:2406.03972 (2024)], the algorithm complexity is improved to the optimal scaling 𝑂⁡(𝜅⁢log (1/𝜖))—an exponential improvement in 𝜖, and a shaving of a log 𝜅 scaling factor in 𝜅. Secondly, the algorithm is further modified to achieve constant factor improvements, which are vital as we progress towards hardware implementations on fault-tolerant devices. We introduce a cheaper randomized walk operator method replacing Hamiltonian simulation—which also removes the need for potentially challenging classical precomputations; randomized routines are sampled over optimized random variables; circuit constructions are improved. We obtain a closed formula rigorously upper bounding the expected number of times one needs to apply a block-encoding of the linear system matrix to output a quantum state encoding the solution to the linear system. The upper bound is 837⁢𝜅 at 𝜖 = 10 −10 for Hermitian matrices.

97 MATHEMATICS AND COMPUTING↗

Two-mode bosonic quoctit for high energy physics

In this work, we study a two-mode bosonic encoding of a quoctit inside a non-Abelian group-structured constellation of coherent states. This work is motivated by the importance of non-Abelian symmetry in particle physics and the desire to have transversal non-Abelian logical gates. We use the previously developed 2 T constellation of states used to encode a so-called 2 T qutrit. The fidelity of the 2 T quoctit is benchmarked against other bosonic qudits for different noise models and find it compare favorably when power constraints are considered. This paves the way for the construction of higher-dimensional qudits (e.g., a quicosotetrit with 2 T group structure) in bosonic systems with practical applications in quantum simulations of particle physics.

Kürkçüoglu, Doga Murat [Fermilab] (ORCID:000000031↗

Learning nuclear cross sections across the chart of nuclides with graph neural networks

We explore the use of deep learning techniques to learn how nuclear cross sections change as we add or remove protons and neutrons. As a proof of principle, we focus on the neutron-induced reactions in the fast energy regime. Our approach follows a two-stage learning framework. First, we apply representation learning to encode cross section data into a latent space using either variational autoencoders (VAEs) or implicit neural representations (INRs). Then, we train graph neural networks (GNNs) on the resulting embeddings to predict missing values across the nuclear chart by leveraging the topological structure of neighboring isotopes. We demonstrate accurate cross section predictions within a 9 × 9 block of missing nuclei. We also find that the optimal GNN training strategy depends on the type of latent representation used, with VAE embeddings performing best under end-to-end optimization in the original space, while INR embeddings achieve better results when the GNN is trained only in the latent space. Furthermore, using clustering algorithms, we map groups of latent vectors into regions of the nuclear chart and show that VAEs and INRs can discover some of the neutron magic numbers. These findings suggest that deep-learning models based on the representation encoding of cross sections combined with graph neural networks hold significant potential in augmenting nuclear theory models, e.g., by providing reliable estimates of covariances of cross sections, including cross-material covariances.

Machine learning↗

Profusion of symmetry-protected qubits from stable ergodicity breaking

We show how combining a discrete symmetry with topological Hilbert space fragmentation can give rise to exponentially many topologically stable qubits protected by a single discrete symmetry. We illustrate this explicitly with the example of the CZ𝑝 model, where the encoded qubits are prethermally stable to arbitrary symmetry-respecting perturbations for parametrically long times, substantially enhancing the robustness of a recently proposed construction based on nontopological fragmentation. In this model, the encoded qubits naturally come in pairs for which a universal set of transversal logical gates can be performed, ruling out (by the Eastin-Knill theorem) the possibility of using them for quantum error correction. We also comment on the combination of symmetry enrichment and topological fragmentation more generally, and the implications for use of systems exhibiting Hilbert space fragmentation as quantum memories.

kinetically constrained models↗

Advancing quantum simulations of the nuclear shell model with Gray-code–based resource-efficient protocols

Background: Some of the computational limitations in solving the nuclear many-body problem could be overcome by utilizing quantum computers. The nuclear shell-model calculations providing deeper insights into the properties of atomic nuclei are one such case with high demand for resources, as the size of the Hilbert space grows exponentially with the number of particles involved. Quantum algorithms are being developed to overcome these challenges and advance such calculations. Purpose: To develop quantum circuits for the nuclear shell-model, leveraging the capabilities of noisy intermediate-scale quantum (NISQ) devices. Here, we aim to minimize resource requirements (specifically in terms of qubits and gates) and strive to reduce the impact of noise by employing relevant mitigation techniques. Methods: We achieve noise resilience by designing an optimized Ansatz for the variational quantum eigensolver (VQE) based on Givens rotations and incorporating qubit-ADAPT-VQE in combination with variational quantum deflation (VQD) to compute ground and excited states, incorporating the zero-noise extrapolation mitigation technique. Furthermore, the qubit requirements are significantly reduced by mapping the basis states to qubits using Gray-code encoding and generalizing transformations of fermionic operators to efficiently represent many-body states. Results: By employing the resource-efficient protocols, we achieve the ground and excited state energy levels of 38 Ar and 6 Li with better accuracy. These energy levels are presented for noiseless simulations, noisy conditions, and after applying noise mitigation techniques. Results are compared for Jordan-Wigner and Gray-code encoding using VQE, qubit-ADAPT-VQE, and VQD. Conclusions: Our work highlights the potential of resource-efficient protocols to leverage the full potential of NISQ devices in scaling the nuclear shell model calculations, offering a pathway toward more complex quantum simulations in nuclear physics. This approach establishes a framework for studying other nuclear systems with improved quantum resource efficiency, marking a significant advancement in applying quantum computing to realistic nuclear physics applications.

Physics - Nuclear physics and radiation physics↗

Spectral Properties and Coding Transitions of Haar-Random Quantum Codes

A quantum error-correcting code with a nonzero error threshold undergoes a mixed-state phase transition when the error rate reaches that threshold. We explore this phase transition for Haar-random quantum codes, in which the logical information is encoded in a random subspace of the physical Hilbert space. We focus on the spectrum of the encoded system density matrix as a function of the rate of uncorrelated, single-qudit errors. For low error rates, this spectrum consists of well-separated bands, representing errors of different weights. As the error rate increases, the bands for high-weight errors merge. The evolution of these bands with increasing error rate is well described by a simple analytic ansatz. Using this ansatz, as well as an explicit calculation, we show that the threshold for Haar-random quantum codes saturates the hashing bound, and thus coincides with that for random stabilizer codes. For error rates that exceed the hashing bound, typical errors are uncorrectable, but postselected error correction remains possible until a much higher detection threshold. Postselection can in principle be implemented by projecting onto subspaces corresponding to low-weight errors, which remain correctable past the hashing bound.

decoherence↗

Optimal Control for the Quantum Simulation of Nuclear Dynamics

We propose a method for enacting the unitary time propagation of two interacting neutrons at leading order of chiral effective-field theory by efficiently encoding the nuclear dynamics into a single multilevel quantum device. The emulated output of the quantum simulation shows that, by applying a single gate that draws on the underlying characteristics of the device, it is possible to observe multiple cycles of the nuclear dynamics before the onset of decoherence. Owing to the signal's longevity, we can then extract spectroscopic properties of the simulated nuclear system. This allows us to validate the encoding of the nuclear Hamiltonian and the robustness of the simulation in the presence of quantum-hardware noise by comparing the extracted spectroscopic information to exact calculations. This work paves the way for transformative calculations of the dynamical properties of nuclei on near-term quantum devices.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗