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At least 433 records · Page 24

ASYMMETRIC FUNDAMENTAL BAND CO LINES AS A SIGN OF AN EMBEDDED GIANT PLANET

We investigate the formation of double-peaked asymmetric line profiles of CO in the fundamental band spectra emitted by young (1-5 Myr) protoplanetary disks hosted by a 0.5-2 M {sub ☉} star. Distortions of the line profiles can be caused by the gravitational perturbation of an embedded giant planet with q = 4.7 × 10{sup –3} stellar-to-planet mass ratio. Locally isothermal, two-dimensional hydrodynamic simulations show that the disk becomes globally eccentric inside the planetary orbit with stationary ∼0.2-0.25 average eccentricity after ∼2000 orbital periods. For orbital distances 1-10 AU, the disk eccentricity is peaked inside the region where the fundamental band of CO is thermally excited. Hence, these lines become sensitive indicators of the embedded planet via their asymmetries (both in flux and wavelength). We find that the line shape distortions (e.g., distance, central dip, asymmetry, and positions of peaks) of a given transition depend on the excitation energy (i.e., on the rotational quantum number J). The magnitude of line asymmetry is increasing/decreasing with J if the planet orbits inside/outside the CO excitation zone (R {sub CO} ≤ 3, 5, and 7 AU for a 0.5, 1, and 2 M {sub ☉} star, respectively), thus one can constrain the orbital distance of a giant planet by determining the slope of the peak asymmetry-J profile. We conclude that the presented spectroscopic phenomenon can be used to test the predictions of planet formation theories by pushing the age limits for detecting the youngest planetary systems.

79 ASTRONOMY AND ASTROPHYSICS↗

DEEPLY EMBEDDED PROTOSTELLAR POPULATION IN THE 20 km s{sup −1} CLOUD OF THE CENTRAL MOLECULAR ZONE

We report the discovery of a population of deeply embedded protostellar candidates in the 20 km s{sup −1} cloud, one of the massive molecular clouds in the Central Molecular Zone (CMZ) of the Milky Way, using interferometric submillimeter continuum and H{sub 2}O maser observations. The submillimeter continuum emission shows five 1 pc scale clumps, each of which further fragments into several 0.1 pc scale cores. We identify 17 dense cores, among which 12 are gravitationally bound. Among the 18 H{sub 2}O masers detected, 13 coincide with the cores and probably trace outflows emanating from the protostars. There are also 5 gravitationally bound dense cores without H{sub 2}O maser detection. In total, the 13 masers and 5 cores may represent 18 protostars with spectral types later than B1 or potentially growing more massive stars at earlier evolutionary stages, given the non-detection in the centimeter radio continuum. In combination with previous studies of CH{sub 3}OH masers, we conclude that the star formation in this cloud is at an early evolutionary phase, before the presence of any significant ionizing or heating sources. Our findings indicate that star formation in this cloud may be triggered by a tidal compression as it approaches pericenter, similar to the case of G0.253+0.016 but with a higher star formation rate, and demonstrate that high angular resolution, high-sensitivity maser, and submillimeter observations are promising techniques to unveil deeply embedded star formation in the CMZ.

79 ASTRONOMY AND ASTROPHYSICS↗

Comparing three generations of D-Wave quantum annealers for minor embedded combinatorial optimization problems

Abstract Quantum annealing (QA) is a novel type of analog computation that aims to use quantum mechanical fluctuations to search for optimal solutions of Ising problems. QA in the transverse Ising model, implemented on D-Wave quantum processing units, are available as cloud computing resources. In this study we report concise benchmarks across three generations of D-Wave quantum annealers, consisting of four different devices, for the NP-hard discrete combinatorial optimization problems unweighted maximum clique and unweighted maximum cut on random graphs. The Ising, or equivalently quadratic unconstrained binary optimization, formulation of these problems do not require auxiliary variables for order reduction, and their overall structure and weights are not highly variable, which makes these problems simple test cases to understand the sampling capability of current D-Wave quantum annealers. All-to-all minor embeddings of size 52, with relatively uniform chain lengths, are used for a direct comparison across the Chimera, Pegasus, and Zephyr device topologies. A grid-search over annealing times and the minor embedding chain strengths is performed in order to determine the level of reasonable performance for each device and problem type. Experiment metrics that are reported are approximation ratios for non-broken chain samples, chain break proportions, and time-to-solution for the maximum clique problem instances. How fairly the quantum annealers sample optimal maximum cliques, for instances which contain multiple maximum cliques, is quantified using entropy of the measured ground state distributions. The newest generation of quantum annealing hardware, which has a Zephyr hardware connectivity, performed the best overall with respect to approximation ratios and chain break frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein–protein interaction network

Abstract Although drug combinations in cancer treatment appear to be a promising therapeutic strategy with respect to monotherapy, it is arduous to discover new synergistic drug combinations due to the combinatorial explosion. Deep learning technology holds immense promise for better prediction of in vitro synergistic drug combinations for certain cell lines. In methods applying such technology, omics data are widely adopted to construct cell line features. However, biological network data are rarely considered yet, which is worthy of in-depth study. In this study, we propose a novel deep learning method, termed PRODeepSyn, for predicting anticancer synergistic drug combinations. By leveraging the Graph Convolutional Network, PRODeepSyn integrates the protein–protein interaction (PPI) network with omics data to construct low-dimensional dense embeddings for cell lines. PRODeepSyn then builds a deep neural network with the Batch Normalization mechanism to predict synergy scores using the cell line embeddings and drug features. PRODeepSyn achieves the lowest root mean square error of 15.08 and the highest Pearson correlation coefficient of 0.75, outperforming two deep learning methods and four machine learning methods. On the classification task, PRODeepSyn achieves an area under the receiver operator characteristics curve of 0.90, an area under the precision–recall curve of 0.63 and a Cohen’s Kappa of 0.53. In the ablation study, we find that using the multi-omics data and the integrated PPI network’s information both can improve the prediction results. Additionally, the case study demonstrates the consistency between PRODeepSyn and previous studies.

Wang, Xiaowen↗

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↗

Domain-specific text embedding model for accelerator physics

Accelerator physics presents unique challenges for natural language processing (NLP) due to its specialized terminology and complex concepts. A key component in overcoming these challenges is the development of robust text embedding models that transform textual data into dense vector representations, facilitating efficient information retrieval and semantic understanding. In this work, we introduce AccPhysBERT, a sentence embedding model fine-tuned specifically for accelerator physics. Our model demonstrates superior performance across a range of downstream NLP tasks, surpassing existing models in capturing the domain-specific nuances of the field. We further showcase its practical applications, including semantic paper-reviewer matching and integration into retrieval-augmented generation systems, highlighting its potential to enhance information retrieval and knowledge discovery in accelerator physics. Published by the American Physical Society 2025

Hellert, Thorsten (ORCID:0000000227970926)↗

Ab initio self-energy embedding for the photoemission spectra of NiO and MnO

The accurate ab initio simulation of periodic solids with strong correlations is one of the grand challenges of condensed matter. While mature methods exist for weakly correlated solids, the ab initio description of strongly correlated systems is an active field of research. In this work, we show results for the single-particle spectral function of the two correlated $\textit{d}$-electron solids NiO and MnO from self-energy embedding theory. Unlike earlier work, the theory does not use any adjustable parameters and is fully ab initio, while being able to treat both the strong correlation and the nonlocal screening physics of these materials. Here, we derive the method, discuss aspects of the embedding and choices of physically important orbitals, and compare our results to x-ray and angle-resolved photoemission spectroscopy as well as bremsstrahlung-isochromat spectroscopy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Embedded boron nitride domains in graphene nanoribbons for transport gap engineering

In this study, we numerically investigate the impact of boron nitride (BN) domains on the transport properties of graphene nanoribbons with lengths ranging from a few to several hundreds of nanometers and lateral size up to 4 nm. By varying the size and morphology of the BN islands embedded in the graphene matrix, a wide transport tunability is obtained from perfect insulating interfaces to asymmetric electron-hole transmission profiles, providing the possibility to engineer mobility gaps to improve device performances. Even in the low-density limit of embedded BN islands, transport properties are found to be highly dependent on both the BN-domain shape and the size with a strong tendency toward an insulating regime when increasing the number of ionic bonds in the ribbon. This versatility of conduction properties offers remarkable opportunities for transport gap engineering for the design of complex device architectures based on a newly synthesized one-atom hybrid layered material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Photonic band gap of a graphene-embedded quarter-wave stack

Here, we present a mechanism for tailoring the photonic band structure of a quarter-wave stack without changing its physical periods by embedding conductive sheets. Graphene is utilized and studied as a realistic, two-dimensional conductive sheet. In a graphene-embedded quarter-wave stack, the synergic actions of Bragg scattering and graphene conductance contributions open photonic gaps at the center of the reduced Brillouin zone that are nonexistent in conventional quarter-wave stacks. Such photonic gaps show giant, loss-independent density of optical states at the fixed lower-gap edges, of even-multiple characteristic frequency of the quarter-wave stack. The conductive sheet-induced photonic gaps provide a platform for the enhancement of light-matter interactions.

36 MATERIALS SCIENCE↗

Baryon spectrum from superconformal quantum mechanics and its light-front holographic embedding

We describe the observed light-baryon spectrum by extending superconformal quantum mechanics to the light front and its embedding in AdS space. This procedure uniquely determines the confinement potential for arbitrary half-integer spin. To this end, we show that fermionic wave equations in AdS space are dual to light-front supersymmetric quantum-mechanical bound-state equations in physical space-time. The specific breaking of conformal invariance explains hadronic properties common to light mesons and baryons, such as the observed mass pattern in the radial and orbital excitations, from the spectrum generating algebra. Lastly, the holographic embedding in AdS also explains distinctive and systematic features, such as the spin-J degeneracy for states with the same orbital angular momentum, observed in the light-baryon spectrum.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

SpeckleNN: a unified embedding for real-time speckle pattern classification in X-ray single-particle imaging with limited labeled examples

With X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structure of noncrystalline nanoscale particles using X-ray single-particle imaging (SPI) techniques at room temperature. Classifying SPI scattering patterns, or `speckles', to extract single-hits that are needed for real-time vetoing and three-dimensional reconstruction poses a challenge for high-data-rate facilities like the European XFEL and LCLS-II-HE. Here, we introduce SpeckleNN, a unified embedding model for real-time speckle pattern classification with limited labeled examples that can scale linearly with dataset size. Trained with twin neural networks, SpeckleNN maps speckle patterns to a unified embedding vector space, where similarity is measured by Euclidean distance. We highlight its few-shot classification capability on new never-seen samples and its robust performance despite having only tens of labels per classification category even in the presence of substantial missing detector areas. Without the need for excessive manual labeling or even a full detector image, our classification method offers a great solution for real-time high-throughput SPI experiments.

47 OTHER INSTRUMENTATION↗

TGE: Machine Learning Based Task Graph Embedding for Large-Scale Topology Mapping

Task mapping is an important problem in parallel and distributed computing. The goal in task mapping is to find an optimal layout of the processes of an application (or a task) onto a given network topology. We target this problem in the context of staging applications. A staging application consists of two or more parallel applications (also referred to as staging tasks) which run concurrently and exchange data over the course of computation. Task mapping becomes a more challenging problem in staging applications, because not only data is exchanged between the staging tasks, but also the processes of a staging task may exchange data with each other. We propose a novel method, called Task Graph Embedding (TGE), that harnesses the observable graph structures of parallel applications and network topologies. TGE employs a machine learning based algorithm to find the best representation of a graph, called an embedding, onto a space in which the task-to-processor mapping problem can be solved. We evaluate and demonstrate the effectiveness of TGE experimentally with the communication patterns extracted from runs of XGC, a large-scale fusion simulation code, on Titan.

Choi, Jong Youl↗

SNNVis: Visualizing Graph Embedding of Evolutionary Optimization for Spiking Neural Networks

While Spiking Neural Networks (SNNs) show a lot of promise, it is difficult to optimize them because applying traditional gradient-based optimization techniques is difficult. Even though evolutionary algorithms (EAs) have been shown to promise to optimize SNNs, understanding the relationship between evolving the characteristics of SNNs and their performance to improve the optimization algorithm is challenging because of the complex characteristics and huge population size. We propose visual analytics with novel graph embedding for evolutionary SNNs to address the challenges. While existing graph embedding techniques have limitations in preserving the specific features of the nodes and edges, our approach maintains them. Also, we develop visual analytics for understanding the relationship between the network performance and the features of nodes and edges and exploring and analyzing the evolving SNNs to build insights into improving the EA.

Chae, Junghoon [ORNL] (ORCID:0000000206016746)↗

Development and Validation of Resistance-Capacitance Model for Phase Change Material Embedded in Porous Media

A simple and effective way to enhance PCM thermal conductivity is by embedding porous materials with high thermal conductivities. In this work, CFD was used to evaluate the melting of PCM embedded in metal foam supplied with constant heat flux. Good agreement between experimental and numerical results has been found with a mean PCM local temperature deviation of 1.62K and 2.97K in two locations. The CFD simulation time was 56 hours for 6.5 hours of flow time. A computationally efficient resistance capacitance-based model (RCM) was developed to improve simulation speed. The proposed RCM exhibited mean local temperature deviations of 1.86K and 2.96K when compared against the experimental data for two thermocouple positions, however, it was approximately 2.5x10 5 times faster than CFD. The charging time deviation was less than 1% compared to CFD, and no significant change in thermal energy stored was observed since the temperature differences were small enough to result in insignificant sensible heat deviation. A simulation cost-effectiveness index (CEI) considering accuracy and computational affordability was introduced; the CEI of the RCM solver is 10 3 times better compared to CFD for the prediction of local PCM temperature.

25 ENERGY STORAGE↗

A Digital Twin Approach to Study Additive Manufacturing Processing Using Embedded Optical Fiber Sensors and Numerical Modeling

One of the major challenges for metal-powder-based additive manufacturing is measuring and mitigating residual strain induced during the manufacturing processes. This article reports distributed fiber optic sensors embedded in Inconel alloy components as experimental means to validate numerical models of additive manufacturing process. Electroplating was used to deposit a metal protective jacket onto standard telecom single-mode fibers for strain measurements, Fiber sensors were embedded in an Inconel alloy substrate using the laser engineered net shaping (LENS) process. Here by using a Rayleigh-scattering optical frequency domain reflectometer (OFDR), temperature changes, and residual strain in the metal substrate were monitored with 5 mm spatial resolution during the LENS process. Using finite element analysis, temperature and strain profiles induced by the LENS deposition processes were also numerically studied. Discrepancies between the simulated temperature and strain profiles and those measured directly were less than 10%. Results presented in this article demonstrates a digital twin approach to fuse modeling results with distributed fiber sensor measurement data to study additive manufacturing process toward design and fabrication process optimization.

36 MATERIALS SCIENCE↗

HAPPA: A Modular Platform for HPC Application Resilience Analysis with LLMs Embedded

High-performance computing (HPC) systems are increasingly vulnerable to soft errors, which pose significant challenges in maintaining computational accuracy and reliability. Predicting the resilience of HPC applications to these errors is crucial for robust code protection and detailed resilience analysis. In this study, we present HAppA, a modular platform designed for HPC Application Resilience Analysis. Embedding Large Language Models (LLMs), HAppA addresses understanding the context information of long code sequences typical in HPC applications. HAppA implements a novel code representation module that chunks the code into fixed-size segments and aggregates the embeddings of these segments. Three aggregation methods have been explored: MeanPooling, MaxPooling, and LSTM-based techniques. We built a DAtaset for REsilience analysis using Fault Injection (FI), named DARE. Using our DARE dataset, HAppA is trained for regression prediction tasks. Our evaluation results demonstrate the predictive accuracy of HAppA compared to other models, particularly noting that the LSTM-based aggregation method -- HAppA-LSTM -- achieves a mean squared error (MSE) of 0.078 for SDC prediction, surpassing the existing state-of-the-art PARIS model, which recorded an MSE of 0.1172. Additionally, HAppA with the KeyBERT model extracts a list of keywords representing the source code. A comprehensive importance analysis of these keywords further elucidates the code patterns contributing to the error rate. These findings highlight the effectiveness of HAppA in analyzing the resilience of HPC applications and establish a new benchmark for predictive accuracy in resilience.

Jiang, Hailong [Kent State University]↗

Marker-free registration of forest terrestrial laser scanner data pairs with embedded confidence metrics

Terrestrial laser scanning (TLS) has emerged as an effective tool for rapid comprehensive measurement of object structure. Registration of TLS data is an important prerequisite to overcome the limitations of occlusion. However, due to the high dissimilarity of point cloud data collected from disparate viewpoints in the forest environment, adequate marker-free registration approaches have not been developed. The majority of studies instead rely on the utilization of artificial tie points (e.g., reflective tooling balls) placed within a scene to aid in coordinate transformation. We present a technique for generating view-invariant feature descriptors that are intrinsic to the point cloud data and, thus, enable blind marker-free registration in forest environments. To overcome the limitation of initial pose estimation, we employ a voting method to blindly determine the optimal pairwise transformation parameters, without an a priori estimate of the initial sensor pose. To provide embedded error metrics, we developed a set theory framework in which a circular transformation is traversed between disjoint tie point subsets. This provides an upper estimate of the Root Mean Square Error (RMSE) confidence associated with each pairwise transformation. Output RMSE errors are commensurate with the RMSE of input tie points locations. Thus, while the mean output RMSE=16.3cm, improved results could be achieved with a more precise laser scanning system. This study 1) quantifies the RMSE of the proposed marker-free registration approach, 2) assesses the validity of embedded confidence metrics using receiver operator characteristic (ROC) curves, and 3) informs optimal sample spacing considerations for TLS data collection in New England forests. Furthermore, while the implications for rapid, accurate, and precise forest inventory are obvious, the conceptual framework outlined here could potentially be extended to built environments.

47 OTHER INSTRUMENTATION↗

Multiview marker-free registration of forest terrestrial laser scanner data with embedded confidence metrics

Terrestrial laser scanning has demonstrated increasing potential for rapid comprehensive measurement of forest structure, especially when multiple scans are spatially registered in order to reduce the limitations of occlusion. Although marker-based registration techniques (based on retro-reflective spherical targets) are commonly used in practice, a blind marker-free approach is preferable, insofar as it supports rapid operational data acquisition. To support these efforts, we extend the pairwise registration approach of our earlier work, and develop a graph-theoretical framework to perform blind marker-free global registration of multiple point cloud data sets. Pairwise pose estimates are weighted based on their estimated error, in order to overcome pose conflict while exploiting redundant information and improving precision. The proposed approach was tested for eight diverse New England forest sites, with 25 scans collected at each site. Quantitative assessment was provided via a novel embedded confidence metric, with a mean estimated root-mean-square error of 7.2 cm and 89% of scans connected to the reference node. Lastly, this paper assesses the validity of the embedded multiview registration confidence metric and evaluates the performance of the proposed registration algorithm.

47 OTHER INSTRUMENTATION↗