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At least 1,063 records · Page 59

Combining Physics and Machine Learning for the Next Generation of Molecular Simulation

Simulating molecules and atomic systems at quantum accuracy is a grand challenge for science in the 21 st century. Quantum-accurate simulations would enable the design of new medicines and the discovery of new materials. The defining problem in this challenge is that quantum calculations on large molecules, like proteins or DNA, are fundamentally impossible with current algorithms. In this work, we explore a range of different methods that aim to make large, quantum-accurate simulations possible. We show that using advanced classical models, we can accurately simulate ion channels, an important biomolecular system. We show how advanced classical models can be implemented in an exascale-ready software package. Lastly, we show how machine learning can learn the laws of quantum mechanics from data and enable quantum electronic structure calculations on thousands of atoms, a feat that is impossible for current algorithms. Altogether, this work shows that combining advances in physics models, computing, and machine learning, we are moving closer to the reality of accurately simulating our molecular world.

74 ATOMIC AND MOLECULAR PHYSICS↗

Understanding palladium–tellurium cluster formation on WTe2: From a kinetically hindered distribution to thermodynamically controlled monodispersity

Abstract A fundamental understanding of the transition metal dichalcogenide (TMDC)–metal interface is critical for their utilization in a broad range of applications. We investigate how the deposition of palladium (Pd), as a model metal, on WTe2(001), leads to the assembly of Pd into clusters and nanoparticles. Using X-ray photoemission spectroscopy, scanning tunneling microscopy imaging, and ab initio simulations, we find that Pd nucleation is driven by the interaction with and the availability of mobile excess tellurium (Te) leading to the formation of Pd-Te clusters at room temperature. Surprisingly, the nucleation of Pd-Te clusters is not affected by intrinsic surface defects, even at elevated temperatures. Upon annealing, the Pd-Te nanoclusters adopt an identical nanostructure and are stable up to ∼523 K. Density functional theory calculations provide a foundation for our understanding of the mobility of Pd and Te atoms, preferential nucleation of Pd-Te clusters, and the origin of their annealing-induced monodispersity. These results highlight the role the excess chalcogenide atoms may play in the metal deposition process. More broadly, the discoveries of synthetic pathways yielding thermally robust monodispersed nanostructures on TMDCs are critical to the manufacturing of novel quantum and microelectronics devices and catalytically active nano-alloy centers.

36 MATERIALS SCIENCE↗

Discovery of compact disc galaxies with high-surface brightness in the Sloan Digital Sky Survey

Compact disc galaxies (CDGs) with high-surface brightness were identified in the Sloan Digital Sky Survey data. We determined the surface profiles of the CDGs and compared them to those of normal-sized disc galaxies (NDGs). The CDGs have higher central brightness and older stellar age than the NDGs. Furthermore, the brightness profiles of the CDGs fit a Sérsic model with n ≈ 2.11 and have a zero g′ − r′ colour gradient on average. By contrast, the NDGs fit an exponential profile and have a negative colour gradient on average. These results indicate that the structure and stellar population of the CDGs and NDGs differ. We suggest that the CDGs are ancient galaxies in the quenching phase following the initial central starburst.

79 ASTRONOMY AND ASTROPHYSICS↗

ExaWind: Opportunity for Discovery

The predictive simulation of the dynamics of modern wind turbines and wind farms is a high-performance-computing (HPC) grand challenge. Modern wind turbines are the largest rotating machines in the world, with rotor diameters exceeding 200 meters, and with heights well into the atmospheric boundary layer. To address this grand challenge, the U.S. Department of Energy (DOE) Wind Energy Technologies Office and the Exascale Computing Project have been supporting the creation of the ExaWind modeling and simulation environment since 2016. ExaWind is composed of the incompressible-flow computational-fluid-dynamics (CFD) solvers AMR-Wind and Nalu-Wind and the wind-turbine-dynamics solver OpenFAST. In our hybrid CFD approach, Nalu-Wind unstructured-grid models resolve the near-body flow around the turbine; those models are embedded in, and two-way coupled to, an AMR-Wind structured-grid mesh through overset meshes. In this talk I give an overview of ExaWind software stack and describe how it is being used to address important problems in wind energy.

computational fluid dynamics↗

Detecting thermodynamic phase transition via explainable machine learning of photoemission spectroscopy

Identifying thermodynamic signatures of electronic phases, such as superconductivity, is challenging in low-dimensional materials due to strong fluctuations and low probing volume. Spectroscopic methods are often used to identify new bulk phases, but their main measurable quantity—electronic energy gaps—is no longer an effective order parameter in low-dimensional and fluctuating systems. Combining angle-resolved photoemission with a domain-adversarial neural network, we report a data-driven method to identify thermodynamic phase transitions solely based on single-particle spectra. We demonstrate 97.6% accuracy in cuprate superconductor Bi 2 Sr 2 CaCu 2 O 8+δ with strong superconducting fluctuations. This model notably compensates for the scarcity of experimental data by leveraging virtually inexhaustible simulated data. Further, its explainability reveals the crucial role of in-gap spectral weight in detecting phase fluctuations and thermodynamic transitions. Our work pinpoints the spectroscopic signatures of fluctuating orders and enables using spectroscopy for machine-learning-assisted material discovery for low-dimensional and strong coupling systems.

2D materials↗

The joint automated repository for various integrated simulations (JARVIS) for data-driven materials design

The Joint Automated Repository for Various Integrated Simulations (JARVIS) is an integrated infrastructure to accelerate materials discovery and design using density functional theory (DFT), classical force-fields (FF), and machine learning (ML) techniques. JARVIS is motivated by the Materials Genome Initiative (MGI) principles of developing open-access databases and tools to reduce the cost and development time of materials discovery, optimization, and deployment. The major features of JARVIS are: JARVIS-DFT, JARVIS-FF, JARVIS-ML, and JARVIS-tools. To date, JARVIS consists of ≈40,000 materials and ≈1 million calculated properties in JARVIS-DFT, ≈500 materials and ≈110 force-fields in JARVIS-FF, and ≈25 ML models for material-property predictions in JARVIS-ML, all of which are continuously expanding. JARVIS-tools provides scripts and workflows for running and analyzing various simulations. We compare our computational data to experiments or high-fidelity computational methods wherever applicable to evaluate error/uncertainty in predictions. In addition to the existing workflows, the infrastructure can support a wide variety of other technologically important applications as part of the data-driven materials design paradigm. The JARVIS datasets and tools are publicly available at the website: https://jarvis.nist.gov .

36 MATERIALS SCIENCE↗

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. In this work, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. Furthermore ,this hybrid ‘Ribosolve’ pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

Understanding the interactions and regulatory relationships among biomolecules is essential for deciphering complex biological systems and elucidating the mechanisms behind diverse biological functions. Traditionally, the collection of such molecular interaction data has relied on expert curation, a process that is both time-consuming and labor-intensive. To address these limitations, this study explores the use of large language models (LLMs) to automate the genome-scale extraction of molecular interaction knowledge. Here, we evaluate the performance of various LLMs on key biological tasks, including the identification of protein-protein interactions, detection of genes associated with pathways influenced by low-dose radiation, and inference of gene regulatory relationships. Our findings demonstrate that larger LLMs tend to perform better, particularly in extracting intricate gene and protein interactions. Despite their strengths, these models face challenges in recognizing functionally diverse gene groups and highly correlated regulatory relationships. Through a comprehensive analysis using established molecular interaction and pathway databases, we show that LLMs possess the potential to identify relevant biomolecules and predict their interactions, offering valuable insights and marking a significant step toward AI-driven biological knowledge discovery.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of Quantum Machine Learning to High Energy Physics Analysis at LHC using IBM Quantum Computer Simulators and IBM Quantum Computer Hardware

One of the major objectives of the experimental programs at the LHC is the discovery of new physics. This requires the identification of rare signals in immense backgrounds. Using machine learning algorithms greatly enhances our ability to achieve this objective. With the progress of quantum technologies, quantum machine learning could become a powerful tool for data analysis in high energy physics. In this study, using IBM gate-model quantum computing systems, we employ the quantum variational classifier method and the quantum kernel estimator method in two recent LHC flagship physics analyses: $t\bar{t}H$ (Higgs boson production in association with a top quark pair) and $H\rightarrow\mu\mu$ (Higgs boson decays to two muons). We have obtained early results with 10 qubits on the IBM quantum simulator and the IBM quantum hardware. On the quantum simulator, the quantum machine learning methods perform similarly to classical algorithms such as SVM (support vector machine) and BDT (boosted decision tree), which are often employed in LHC physics analyses. On the quantum hardware, the quantum machine learning methods have shown promising discrimination power, comparable to that on the quantum simulator. This study demonstrates that quantum machine learning has the ability to differentiate between signal and background in realistic physics datasets.

Chan, Jay↗

Verification, Validation, and Calibration Through a Causal Lens

While typical validation and verification approaches focus on identifying the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on identifying causal relationships between data elements. Statistical and machine-learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between data sets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify, and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles, it is known as a directed acyclic graph. A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts can identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗

VALIDATION, VERIFICATION, AND CALIBRATION THROUGH A CAUSAL LENS

This paper presents an alternative method based on causal inference to perform validation, verification, and calibration of simulation models. While classical validation and verification approaches focus on the identification of the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on the identification of causal relationships between data elements. Statistical and machine learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between datasets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, then the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles it is known as a directed acyclic graph (DAG). A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and from experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts have a means to identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗

New physics in single resonant top quarks

Abstract Searches for new physics in the top quark sector are of great theoretical interest, yet some powerful avenues for discovery remain unexplored. We characterize the expected statistical power of the LHC dataset to constrain the single production of heavy top partnersTdecaying to a top quark and a photon or a top quark and a gluon. We describe an effective interaction which could generate such production, though the limits apply to a range of theoretical models. We find sensitivity to cross sections in the 10 2 − 10 5 fb range, forTmasses between 300 and 1000 GeV, depending on decay mode.

Physics↗

Interlayer pairing in bilayer nickelates

The discovery of T c ~ 80 K superconductivity in pressurized La 3 Ni 2 O 7 has launched a new platform to study high-temperature superconductivity. Using non-perturbative dynamic cluster approximation quantum Monte Carlo calculations, we characterize the magnetic and superconducting pairing behavior of a realistic bilayer two-orbital Hubbard-Hund model of this system that describes the relevant Ni e g states with physically relevant interaction strengths. We find a leading s ± superconducting instability in this model at a temperature T ~ 100 K close to the experimentally observed T c . Analyzing the orbital and spatial structure of the effective pairing interaction giving rise to this state reveals that the interaction predominantly acts between local interlayer pairs of the $d_{3z^2-r^2}$ orbital. By correlating the strength of the interaction with that of the magnetic spin fluctuations we show that it is driven by strong interlayer spin-fluctuations arising from the $d_{3z^2-r^2}$ orbital. These results provide first-time non-perturbative evidence supporting the picture that a simple single-orbital bilayer Hubbard model for the Ni $d_{3z^2-r^2}$ orbital provides an excellent low-energy effective description of the superconducting behavior of La 3 Ni 2 O 7 .

Maier, Thomas A. [Oak Ridge National Laboratory (O↗

Identification of mobile genetic elements with geNomad

Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad’s speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad.

59 BASIC BIOLOGICAL SCIENCES↗

Timing of pulsars in the globular cluster omega centauri

We present the timing of the first five millisecond pulsars discovered in the globular cluster Omega Centauri and the discovery of a pulsar with a spin period of 3.68 ms. With a timing baseline of ~3.5 yr we are able to measure the derivative of the spin frequency ($\dot{\nu }$) for the first five pulsars. Upper limits on the pulsar line-of-sight acceleration are estimated and compared with predictions based on analytical models of the cluster. We find that PSRs J1326-4728B and D show large negative accelerations, which are in tension with the minimum acceleration predicted by analytical models. We searched for pulsed γ-ray signals using 14.3 yr of data from the Fermi Large Area Telescope. Although we found no evidence for γ-ray pulsations, PSRs J1326-4728A, B, C, and E are associated with X-ray sources. This suggests that the observed γ-ray emission from Omega Centauri is likely caused by the emission of the ensemble of MSPs. Finally, the linearly polarized emission from PSR J1326-4728A yields a rotation measure of -18 ± 8 rad m -2 .

79 ASTRONOMY AND ASTROPHYSICS↗

Visualizing strange metallic correlations in the two-dimensional Fermi-Hubbard model with artificial intelligence

Strongly correlated phases of matter are often described in terms of straightforward electronic patterns. This has so far been the basis for studying the Fermi-Hubbard model realized with ultracold atoms. Here, we show that artificial intelligence (AI) can provide an unbiased alternative to this paradigm for phases with subtle, or even unknown, patterns. Long- and short-range spin correlations spontaneously emerge in filters of a convolutional neural network trained on snapshots of single atomic species. In the less well-understood strange metallic phase of the model, we find that a more complex network trained on snapshots of local moments produces an effective order parameter for the non-Fermi-liquid behavior. We report our technique can be employed to characterize correlations unique to other phases with no obvious order parameters or signatures in projective measurements, and has implications for science discovery through AI beyond strongly correlated systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

IceCube high-energy starting event sample: Description and flux characterization with 7.5 years of data

The IceCube Neutrino Observatory has established the existence of a high-energy all-sky neutrino flux of astrophysical origin. This discovery was made using events interacting within a fiducial region of the detector surrounded by an active veto and with reconstructed energy above 60 TeV, commonly known as the high-energy starting event sample (HESE). Here, we revisit the analysis of the HESE sample with an additional 4.5 years of data, newer glacial ice models, and improved systematics treatment. This paper describes the sample in detail, reports on the latest astrophysical neutrino flux measurements, and presents a source search for astrophysical neutrinos. We give the compatibility of these observations with specific isotropic flux models proposed in the literature as well as generic power-law-like scenarios. Assuming ν e :ν μ :ν τ =1:1:1, and an equal flux of neutrinos and antineutrinos, we find that the astrophysical neutrino spectrum is compatible with an unbroken power law, with a preferred spectral index of $2.87_{-0.19}^{+0.20}$ for the 68% confidence interval.

79 ASTRONOMY AND ASTROPHYSICS↗