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At least 109 records · Page 6

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Abstract There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

54 ENVIRONMENTAL SCIENCES↗

AmeriFlux US-MZA Hidden Marsh, Montezuma NWR

This is the AmeriFlux version of the carbon flux data for the site US-MZA Hidden Marsh, Montezuma NWR. Site Description - This is a restored (from Ag) emergent marsh system located in the Montezuma National Wildlife Refuge. It is dominated by cattail most of the time, but experiences periodic, managed drying that produces other drier wetland vegetation types. In 2024, it was inundated and had abundant Typha and Phragmites.

Morin, Tim [SUNY ESF]↗

Hidden orders and phase transitions for the fully packed quantum loop model on the triangular lattice

Abstract Quantum loop and dimer models are prototypical correlated systems with local constraints, which are not only intimately connected to lattice gauge theories and topological orders but are also widely applicable to the broad research areas of quantum materials and quantum simulation. Employing our sweeping cluster quantum Monte Carlo algorithm, we reveal the complete phase diagram of the triangular-lattice fully packed quantum loop model. Apart from the known lattice nematic (LN) solid and the even$${{\mathbb{Z}}}_{2}$$ Z 2 quantum spin liquid (QSL) phases, we discover a hidden vison plaquette (VP) phase, which had been overlooked and misinterpreted as a QSL for more than a decade. Moreover, the VP-to-QSL continuous transition belongs to the (2 + 1)D cubic * universality class, which offers a lattice realization of the (fractionalized) cubic fixed point that had long been considered as irrelevant towards the O(3) symmetry until corrected recently by conformal bootstrap calculations. Our results are therefore of relevance to recent developments in both experiments and theory, and facilitate further investigations of hidden phases and transitions.

Physics↗

A Deep Generative Model for Non-Intrusive Identification of EV Charging Profiles

The proliferation of electric vehicles (EVs) brings environmental benefits and technical challenges to power grids. An identification algorithm which can accurately extract individual EV charging profiles out of widely available smart meter measurements has attracted great interests. This paper proposes a non-intrusive identification framework for EV charging profile extraction, which is driven by deep generative models (DGM). First, the proposed DGM is designed as a representation layer embedded into the Markov process and used to model the joint probability distribution of available time-series data. A novel contribution is to approximate posterior distributions by neural networks whose parameters are obtained by variational inference and supervised learning. Second, the EV charging status is inferred from the DGM via dynamic programming. Lastly, the desired EV charging profile can be reconstructed by the rated power of EV models and inferred status. Compared with the benchmark Hidden Markov Models, the proposed framework can better handle noise in data with less computational complexity and better overall accuracy performances with smaller recall. The proposed framework is validated by numerical experiments on the Pecan Street dataset.

33 ADVANCED PROPULSION SYSTEMS↗

Discovering Hidden Geothermal Signatures using Unsupervised Machine Learning

Discovering hidden geothermal resources is a very challenging task. It requires the mining of large datasets, including various diverse data attributes representing subsurface hydrogeological and geothermal conditions. The commonly used Play Fairway Analysis (PFA) typically relies on subject-matter expertise to analyze site or regional data to estimate geothermal conditions and prospectivity. Here, we demonstrate an alternative approach based on machine learning (ML) to process a geothermal dataset of Southwest New Mexico (SWNM). The study region includes low- and medium-temperature hydrothermal systems. However, most of these systems are poorly characterized because of insufficient existing data and limited past explorative studies. This study aims to discover hidden patterns and relationships in the SWNM geothermal dataset to better understand regional hydrothermal conditions. This is achieved by applying an unsupervised machine learning algorithm based on non-negative matrix factorization coupled with customized k-means clustering (NMFk). NMFk can automatically identify (1) hidden (latent) signatures characterizing datasets, (2) the optimal number of these signatures, (3) dominant data attributes associated with each signature, and (4) spatial distribution of the extracted signatures. Here, NMFk is applied to analyze 18 geological, geophysical, hydrogeological, geothermal attributes at 44 locations in SWNM. NMFk successfully finds data patterns and identifies the spatial associations of hydrothermal signatures with the four physiographic provinces in SWNM (Colorado Plateau, Volcanic Field, Basin and Range, and the Rio Grande rift). The algorithm identified up to 5 hydrothermal signatures in the SWNM datasets that differentiate between low- and medium-temperature hydrothermal systems in different provinces. Also, the algorithm identifies two medium-temperature hydrothermal systems in SWNM that require further exploration for geothermal resource development. Based on our analyses, 12 of the attributes are important to identify medium-temperature hydrothermal systems, and the remaining six attributes are critical to characterize low-temperature hydrothermal systems. Based on the obtained results, we identify potential physiographic provinces for further exploration to characterize them as geothermal resources. The resulting NMFk model can be applied to predict geothermal conditions and their uncertainties at new SWNM locations based on limited data from unexplored areas.

58 GEOSCIENCES↗

Machine learning of hidden variables in multiscale fluid simulation

Solving fluid dynamics equations often requires the use of closure relations that account for missing microphysics. For example, when solving equations related to fluid dynamics for systems with a large Reynolds number, sub-grid effects become important and a turbulence closure is required, and in systems with a large Knudsen number, kinetic effects become important and a kinetic closure is required. By adding an equation governing the growth and transport of the quantity requiring the closure relation, it becomes possible to capture microphysics through the introduction of ‘hidden variables’ that are non-local in space and time. The behavior of the ‘hidden variables’ in response to the fluid conditions can be learned from a higher fidelity or ab-initio model that contains all the microphysics. In our study, a partial differential equation simulator that is end-to-end differentiable is used to train judiciously placed neural networks against ground-truth simulations. We show that this method enables an Euler equation based approach to reproduce non-linear, large Knudsen number plasma physics that can otherwise only be modeled using Boltzmann-like equation simulators such as Vlasov or particle-in-cell modeling.

42 ENGINEERING↗

Reinforcement learning for adaptive maintenance policy optimization under imperfect knowledge of the system degradation model and partial observability of system states

Maintenance policy optimization usually is faced with challenges that arise from an imperfect knowledge of system degradation models and from the partial observability of system degradation states. Here, this paper proposes a reinforcement learning method to address these two challenges for a class of maintenance problems with Markov degradation processes. The reinforcement learning approach consists of a learning component and a planning component. Using sequentially collected observations, at each step of decision-making the learning component improves the knowledge of system degradation in terms of the probability distributions of the transition rates based on sequential Bayesian inference. Using the updated transition rates, at each step of decision-making the maintenance policy optimization problem is then formulated as a partially observable Markov decision problem, and the planning component computes the optimal maintenance policy that maximizes the expected cumulative reward. The proposed method is illustrated using a numerical example with repair and inspection maintenance actions. The result shows that as more observations are collected, the learning component progressively learns the true system degradation process, and the planning component adjusts the optimal maintenance policy accordingly as well, which leads to increased reward.

42 ENGINEERING↗

Hidden magnetism uncovered in a charge ordered bilayer kagome material ScV 6 Sn 6

Charge ordered kagome lattices have been demonstrated to be intriguing platforms for studying the intertwining of topology, correlation, and magnetism. The recently discovered charge ordered kagome material ScV 6 Sn 6 does not feature a magnetic groundstate or excitations, thus it is often regarded as a conventional paramagnet. Here, using advanced muon-spin rotation spectroscopy, we uncover an unexpected hidden magnetism of the charge order. We observe an enhancement of the internal field width sensed by the muon ensemble, which takes place within the charge ordered state. More importantly, the muon spin relaxation rate below the charge ordering temperature is substantially enhanced by applying an external magnetic field. Taken together with the hidden magnetism found in AV 3 Sb 5 (A = K, Rb, Cs) and FeGe kagome systems, our results suggest ubiqitous time-reversal symmetry-breaking in charge ordered kagome lattices.

36 MATERIALS SCIENCE↗

Far-field speckle correlations as a function of object position for microscopically distinguishing objects hidden in a randomly scattering medium

Super-resolution optical sensing is of critical importance in science and technology and has required prior information about an imaging system or obtrusive near-field probing. Additionally, coherent imaging and sensing in heavily scattering media such as biological tissue has been challenging, and practical approaches have either been restricted to measuring the field transmission of a single point source, or to where the medium is thin. We present the concept of far-subwavelength spatial sensing with relative object motion in speckle as a means to coherently sense through heavy scatter. Experimental results demonstrate the ability to distinguish nominally identical objects with nanometer-scale translation while hidden in randomly scattering media, without the need for precise or known location and with imprecise replacement. The theory and supportive illustrations presented provide the basis for super-resolution sensing and the possibility of virtually unlimited spatial resolution, including through thick, heavily scattering media with relative motion of an object in a structured field. This work provides enabling opportunities for material inspection, security, and biological sensing.

Hastings, Ryan L. (ORCID:0009000095977807)↗

System for controller area network payload decoding

A system for decoding an unknown automotive controller area network (“CAN”) message definitions. CAN data vehicle signal mappings are typically held in secret and varied by automotive model and year. Without knowledge of the mappings, the wealth of real-time vehicle data hidden in the automotive CAN packets is uninterpretable—impeding research, after-market tuning, efficiency and performance monitoring, fault diagnosis, and privacy-related technologies. This system can ascertain the CAN signals' boundaries (start bit and length), endianness (byte ordering), signedness (binary-to-integer encoding) from raw CAN data. This allows conversion of CAN data to time series. Interpreting the translated CAN data's physical meaning and finding a linear mapping to standard units (e.g., knowing the signal is speed and scaling values to represent units of miles per hour) can be achieved for many signals by leveraging diagnostic standards to obtain real-time measurements of in-vehicle systems. The system can be integrated into lightweight hardware enabling an OBD-II plugin for real-time in-vehicle CAN decoding or run on standard computers. The system can output a standard DBC file with the signal definition information.

Verma, Kiren E.↗

Interpretable Data-Driven Probabilistic Power System Load Margin Assessment with Uncertain Renewable Energy and Loads

The increasing uncertainties caused by the high-penetration of stochastic renewable generation resources poses a significant threat to the power system voltage stability. To address this issue, this paper proposes a probabilistic deep kernel learning enabled surrogate model to extract the hidden relationship between uncertain sources, i.e., wind power and loads, and load margin for probabilistic load margin assessment (PLMA). Unlike other deep learning approaches, a kernel SHAP provides the sensitivity analysis as well as interpretability of the inputs to outputs influences. This allows identifying the critical factors that affect load margin so that corrective control can be initiated for stability enhancement. Numerical results carried out on the IEEE 118-bus power system demonstrate the accuracy and efficiency of the proposed data-driven PLMA scheme.

deep kernel learning↗

Search for resonant production of strongly coupled dark matter in proton-proton collisions at 13 TeV

The first collider search for dark matter arising from a strongly coupled hidden sector is presented and uses a data sample corresponding to 138 fb$^{-1}$, collected with the CMS detector at the CERN LHC, at $ \sqrt{s} $ = 13 TeV. The hidden sector is hypothesized to couple to the standard model (SM) via a heavy leptophobic Z' mediator produced as a resonance in proton-proton collisions. The mediator decay results in two “semivisible” jets, containing both visible matter and invisible dark matter. The final state therefore includes moderate missing energy aligned with one of the jets, a signature ignored by most dark matter searches. No structure in the dijet transverse mass spectra compatible with the signal is observed. Assuming the Z' boson has a universal coupling of 0.25 to the SM quarks, an inclusive search, relevant to any model that exhibits this kinematic behavior, excludes mediator masses of 1.5–4.0 TeV at 95% confidence level, depending on the other signal model parameters. To enhance the sensitivity of the search for this particular class of hidden sector models, a boosted decision tree (BDT) is trained using jet substructure variables to distinguish between semivisible jets and SM jets from background processes. When the BDT is employed to identify each jet in the dijet system as semivisible, the mediator mass exclusion increases to 5.1 TeV, for wider ranges of the other signal model parameters. These limits exclude a wide range of strongly coupled hidden sector models for the first time.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NISQ+: Boosting quantum computing power by approximating quantum error correction

Quantum computers are growing in size, and design decisions are being made now that attempt to squeeze more computation out of these machines. In this spirit, we design a method to boost the computational power of near-term quantum computers by adapting protocols used in quantum error correction to implement "Approximate Quantum Error Correction (AQEC)." By approximating fully-fledged error correction mechanisms, we can increase the compute volume (qubits × gates, or "Simple Quantum Volume (SQV)") of near-term machines. The crux of our design is a fast hardware decoder that can approximately decode detected error syndromes rapidly. Specifically, we demonstrate a proof-of-concept that approximate error decoding can be accomplished online in near-term quantum systems by designing and implementing a novel algorithm in Single-Flux Quantum (SFQ) superconducting logic technology. This avoids a critical decoding backlog, hidden in all offline decoding schemes, that leads to idle time exponential in the number of T gates in a program. Our design utilizes one SFQ processing module per physical qubit. Employing state-of-the-art SFQ synthesis tools, we show that the circuit area, power, and latency are within the constraints of contemporary quantum system designs. Under pure dephasing error models, the proposed accelerator and AQEC solution is able to expand SQV by factors between 3,402 and 11,163 on expected near-term machines. The decoder achieves a 5% accuracy-threshold and pseudo-thresholds of ~ 5%,4.75%,4.5%, and 3.5% physical error-rates for code distances 3,5,7, and 9. Decoding solutions are achieved in a maximum of ~20 nanoseconds on the largest code distances studied. By avoiding the exponential idle time in offline decoders, we achieve a 10x reduction in required code distances to achieve the same logical performance as alternative designs.

97 MATHEMATICS AND COMPUTING↗

Uncovering Hidden Entanglement in Twin Beams

Proper characterization of quantum correlations in multimode optical quantum states is critical for applications in quantum information science. However, standard entanglement measurements can lead to incomplete state reconstruction and characterization. Here, we implement a resonator-based detection system that reveals entanglement between sideband modes of twin beams, achieving full tomography and retrieving often ignored quantum correlations. Unlike standard spectral measurements such as homodyne detection, resonator detection can independently address the sidebands of each beam, thereby accessing these hidden correlations. Additionally, we show how phase shifts between the carrier and the sideband modes of the involved fields redistribute information and modify the observation of entanglement for different witnesses. The ability of the resonant detection to independently address sideband modes of entangled states can contribute to enhancing the capacity for secure communication and quantum networking protocols.

Rincon Celis, Raul [University of Sao Paulo, Brazi↗

Unlocking hidden information in sparse small-angle neutron scattering measurements

Hypothesis Small-Angle Neutron Scattering (SANS) is a powerful technique for studying soft matter systems such as colloids, polymers, and lyotropic phases, providing nanoscale structural insights. However, its effectiveness is limited by low neutron flux, leading to long acquisition times and noisy data. Here, we hypothesize that Bayesian statistical inference using Gaussian Process Regression (GPR) can reconstruct high-fidelity scattering data from sparse measurements by leveraging intensity smoothness and continuity. Experiments and Simulations The method was benchmarked computationally and validated through SANS experiments on various soft matter systems, including wormlike micelles, colloidal suspensions, polymeric structures, and lyotropic phases. GPR-based inference was applied to both experimental and synthetic data to evaluate its effectiveness in noise reduction and intensity reconstruction. Findings GPR significantly enhances SANS data quality and therefore reducing measurement times by up to two orders of magnitude. This cost-effective approach maximizes experimental efficiency, enabling high-throughput studies and real-time monitoring of dynamic systems. It is particularly beneficial for weakly scattering and time-sensitive studies. Beyond SANS, this framework applies to other low-SNR techniques, including laboratory-based small-angle X-ray scattering and various dynamical scattering methods. Furthermore, it offers transformative potential for compact neutron sources, enhancing their viability for structural analysis in resource-limited settings.

Small angle neutron scattering↗

Detecting hidden layers from spreading dynamics on complex networks

When dealing with spreading processes on networks it can be of the utmost importance to test the reliability of data and identify potential unobserved spreading paths. In this paper we address these problems and propose methods for hidden layer identification and reconstruction. We also explore the interplay between difficulty of the task and the structure of the multilayer network describing the whole system where the spreading process occurs. Our methods stem from an exact expression for the likelihood of a cascade in the susceptible-infected model on an arbitrary graph. We then show that by imploring statistical properties of unimodal distributions and simple heuristics describing joint likelihood of a series of cascades one can obtain an estimate of both existence of a hidden layer and its content with success rates far exceeding those of a null model. Furthermore, we conduct our analyses on both synthetic and real-world networks providing evidence for the viability of the approach presented.

97 MATHEMATICS AND COMPUTING↗

Peridynamic neural operators: A data-driven nonlocal constitutive model for complex material responses

Neural operators, which can act as implicit solution operators of hidden governing equations, have recently become popular tools for learning the responses of complex real-world physical systems. Nevertheless, most neural operator applications have thus far been data-driven and neglect the intrinsic preservation of fundamental physical laws in data. Here, in this work, we introduce a novel integral neural operator architecture called the Peridynamic Neural Operator (PNO) that learns a nonlocal constitutive law from data. This neural operator provides a forward model in the form of state-based peridynamics, with objectivity and momentum balance laws automatically guaranteed. As applications, we demonstrate the expressivity and efficacy of our model in learning complex material behaviors from both synthetic and experimental data sets. We also compare the performances with baseline models that use predefined constitutive laws. We show that, owing to its ability to capture complex responses, our learned neural operator achieves improved accuracy and efficiency. Moreover, by preserving the essential physical laws within the neural network architecture, the PNO is robust in treating noisy data. The method shows generalizability to different domain configurations, external loadings, and discretizations.

42 ENGINEERING↗

Seeking regularity from irregularity: unveiling the synthesis–nanomorphology relationships of heterogeneous nanomaterials using unsupervised machine learning

Nanoscale morphology of functional materials determines their chemical and physical properties. However, despite increasing use of transmission electron microscopy (TEM) to directly image nanomorphology, it remains challenging to quantify the information embedded in TEM data sets, and to use nanomorphology to link synthesis and processing conditions to properties. We develop an automated, descriptor-free analysis workflow for TEM data that utilizes convolutional neural networks and unsupervised learning to quantify and classify nanomorphology, and thereby reveal synthesis–nanomorphology relationships in three different systems. While TEM records nanomorphology readily in two-dimensional (2D) images or three-dimensional (3D) tomograms, we advance the analysis of these images by identifying and applying a universal shape fingerprint function to characterize nanomorphology. After dimensionality reduction through principal component analysis, this function then serves as the input for morphology grouping through unsupervised learning. We demonstrate the wide applicability of our workflow to both 2D and 3D TEM data sets, and to both inorganic and organic nanomaterials, including tetrahedral gold nanoparticles mixed with irregularly shaped impurities, hybrid polymer-patched gold nanoprisms, and polyamide membranes with irregular and heterogeneous 3D crumple structures. In each of these systems, unsupervised nanomorphology grouping identifies both the diversity and the similarity of the nanomaterial across different synthesis conditions, revealing how synthetic parameters guide nanomorphology development. Our work opens possibilities for enhancing synthesis of nanomaterials through artificial intelligence and for understanding and controlling complex nanomorphology, both for 2D systems and in the far less explored case of 3D structures, such as those with embedded voids or hidden interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗