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At least 1,009 records · Page 56

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Abstract While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii , we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N -glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

59 BASIC BIOLOGICAL SCIENCES↗

Coarse-graining Hamiltonian systems using WSINDy

Abstract Weak form equation learning and surrogate modeling has proven to be computationally efficient and robust to measurement noise in a wide range of applications including ODE, PDE, and SDE discovery, as well as in coarse-graining applications, such as homogenization and mean-field descriptions of interacting particle systems. In this work we extend this coarse-graining capability to the setting of Hamiltonian dynamics which possess approximate symmetries associated with timescale separation. A smooth $$\varepsilon$$ ε -dependent Hamiltonian vector field $$X_\varepsilon$$ X ε possesses an approximate symmetry if the limiting vector field $$X_0=\lim _{\varepsilon \rightarrow 0}X_\varepsilon$$ X 0 = lim ε → 0 X ε possesses an exact symmetry. Such approximate symmetries often lead to the existence of a Hamiltonian system of reduced dimension that may be used to efficiently capture the dynamics of the symmetry-invariant dependent variables. Deriving such reduced systems, or approximating them numerically, is an ongoing challenge. We demonstrate that WSINDy can successfully identify this reduced Hamiltonian system in the presence of large perturbations imparted in the $$\varepsilon >0$$ ε > 0 regime, while remaining robust to extrinsic noise. This is significant in part due to the nontrivial means by which such systems are derived analytically. WSINDy naturally preserves the Hamiltonian structure by restricting to a trial basis of Hamiltonian vector fields. The methodology is computationally efficient, often requiring only a single trajectory to learn the global reduced Hamiltonian, and avoiding forward solves in the learning process. In this way, we argue that weak-form equation learning is particularly well-suited for Hamiltonian coarse-graining. Using nearly-periodic Hamiltonian systems as a prototypical class of systems with approximate symmetries, we show that WSINDy robustly identifies the correct leading-order system, with dimension reduced by at least two, upon observation of the relevant degrees of freedom. While our main contribution is computational, we also provide a contribution to the literature on averaging theory by proving that first-order averaging at the level of vector fields preserves Hamiltonian structure in nearly-periodic Hamiltonian systems. This provides theoretical justification for our approach as WSINDy’s computations occur at the level of Hamiltonian vector fields. We illustrate the efficacy of our proposed method using physically relevant examples, including coupled oscillator dynamics, the Hénon–Heiles system for stellar motion within a galaxy, and the dynamics of charged particles.

97 MATHEMATICS AND COMPUTING↗

Particle physics using reactor antineutrinos

Nuclear reactors are uniquely powerful, abundant, and flavor-pure sources of antineutrinos that have played a central role in the discovery of the neutrinos and in elucidation of their properties. Further, this continues through a broad range of experiments investigating topics including Standard Model and short-baseline oscillations, beyond-the-Standard-Model physics searches, and reactor flux and spectrum modelling. This Report will survey the state of the reactor antineutrino physics field and summarize the ways in which current and future reactor antineutrino experiments can play a critical role in advancing the field of particle physics in the next decade.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

First application of a liquid argon time projection chamber for the search for intranuclear neutron-antineutron transitions and annihilation in 40 Ar using the MicroBooNE detector

We present a novel methodology to search for intranuclear neutron-antineutron transition (n→n̅) followed by n̅-nucleon annihilation within an 40 Ar nucleus, using the MicroBooNE liquid argon time projection chamber (LArTPC) detector. A discovery of n→n̅ transition or a new best limit on the lifetime of this process would either constitute physics beyond the Standard Model or greatly constrain theories of baryogenesis, respectively. The approach presented in this paper makes use of deep learning methods to select n→n̅ events based on their unique features and differentiate them from cosmogenic backgrounds. The achieved signal and background efficiencies are (70.22 ± 6.04)% and (0.0020 ± 0.0003)%, respectively. A demonstration of a search is performed with a data set corresponding to an exposure of 3.32 ×10 26 neutron-years, and where the background rate is constrained through direct measurement, assuming the presence of a negligible signal. With this approach, no excess of events over the background prediction is observed, setting a demonstrative lower bound on the n→n̅ lifetime in 40 Ar of τ m ≳ 1.1×10 26 years, and on the free n→n̅ transition time of τ n→n̅ ≳ 2.6×10 5 s, each at the 90% confidence level. This analysis represents a first-ever proof-of-principle demonstration of the ability to search for this rare process in LArTPCs with high efficiency and low background.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Discovering faint and high apparent motion rate near-Earth asteroids using a deep learning program

ABSTRACT Although many near-Earth objects have been found by ground-based telescopes, some fast-moving ones, especially those near detection limits, have been missed by observatories. We developed a convolutional neural network for detecting faint fast-moving near-Earth objects. It was trained with artificial streaks generated from simulations and was able to find these asteroid streaks with an accuracy of 98.7 per cent and a false positive rate of 0.02 per cent on simulated data. This program was used to search image data from the Zwicky Transient Facility (ZTF) in four nights in 2019, and it identified six previously undiscovered asteroids. The visual magnitudes of our detections range from ∼19.0 to 20.3 and motion rates range from ∼6.8 to 24 deg d−1, which is very faint compared to other ZTF detections moving at similar motion rates. Our asteroids are also ∼1–51 m diameter in size and ∼5–60 lunar distances away at close approach, assuming their albedo values follow the albedo distribution function of known asteroids. The use of a purely simulated data set to train our model enables the program to gain sensitivity in detecting faint and fast-moving objects while still being able to recover nearly all discoveries made by previously designed neural networks which used real detections to train neural networks. Our approach can be adopted by any observatory for detecting fast-moving asteroid streaks.

Wang, Franklin (ORCID:0000000344887355)↗

Preparing an Incompressible-Flow Fluid Dynamics Code for Exascale-Class Wind Energy Simulations

The U.S. Department of Energy has identified exascale-class wind farm simulation as critical to wind energy scientific discovery. A primary objective of the ExaWind project is to build high-performance, predictive computational fluid dynamics (CFD) tools that satisfy these modeling needs. GPU accelerators will serve as the computational thoroughbreds of next-generation, exascale-class supercomputers. Here, we report on our efforts in preparing the ExaWind unstructured mesh solver, Nalu-Wind, for exascale-class machines. For computing at this scale, a simple port of the incompressible-flow algorithms to GPUs is insufficient. To achieve high performance, one needs novel algorithms that are application aware, memory efficient, and optimized for the latest-generation GPU devices. The result of our efforts are unstructured-mesh simulations of wind turbines that can effectively leverage thousands of GPUs. In particular, we demonstrate a first-of-its-kind, incompressible-flow simulation using Algebraic Multigrid solvers that strong scales to more than 4000 GPUs on the Summit supercomputer.

algebraic multigrid↗

Hollow cathode-based plasma contactor experiments for electrodynamic tether

The role plasma contactors play in effective electrodynamic tether operation is discussed. Hollow cathodes and hollow cathode-based plasma sources have been identified as leading candidates for the electrodynamic tether plasma contactor. Present experimental efforts to evaluate the suitability of these devices as plasma contactors are reviewed. This research includes the definition of preliminary plasma contactor designs, and the characterization of their operation as electron collectors from a simulated space plasma. The discovery of an 'ignited mode' regime of high contactor efficiency and low impedance is discussed, as well as is the application of recent models of the plasma coupling process to contactor operation. Results indicate that ampere-level electron currents can be exchanged between hollow cathode-based plasma contactors and a dilute plasma in this regime. A discussion of design considerations for plasma contactors is given which includes expressions defining the total mass flow rate and power requirements of plasma contactors operating in both the cathodic and anodic regimes, and correlation of this to the tether current. Finally, future ground and spaceflight experiments are proposed to resolve critical issues of plasma contactor operation.

Patterson, Michael J.↗

Propagation of Cosmic Rays: Nuclear Physics in Cosmic-ray Studies

The nuclei fraction in cosmic rays (CR) far exceeds the fraction of other CR species, such as antiprotons, electrons, and positrons. Thus the majority of information obtained from CR studies is based on interpretation of isotopic abundances using CR propagation models where the nuclear data and isotopic production cross sections in p- and alpha-induced reactions are the key elements. This paper presents an introduction to the astrophysics of CR and diffuse gamma-rays and dimsses some of the puzzles that have emerged recently due to more precise data and improved propagation models. Merging with cosmology and particle physics, astrophysics of CR has become a very dynamic field with a large potential of breakthrough and discoveries in the near fume. Exploiting the data collected by the CR experiments to the fullest requires accurate nuclear cross sections.

Moskalenko, Igor V.↗

Correlated Topics in a Scalable Multidimensional Text Cube: Algorithms and Aviation Safety Case Study

As world-wide air traffic continues to grow even at a modest pace, the overall complexity of the system will increase significantly. This increased complexity can lead to a larger number of fatalities per year even if the extremely low fatality rate that we currently enjoy is maintained. One important source of information about the safety of the aviation system is in Aviation Safety Text Reports which are written by members of the flight crew, air traffic controllers, and other parties involved with the aviation system. These anonymized narrative reports contain fixed-field contextual information about the flight but also contain free-form narratives that describe, in the author s own words, the nature of the safety incident and, in many cases, the contributing factors that led to the safety incident. Several thousand such reports are filed each month, each of which is read and analyzed by highly trained experts. However, it is possible that there are emerging safety issues due to the fact that they may be reported very infrequently and in different contexts with different descriptions. The goal of this research paper is to develop correlated topic models which uncover correlations in the subspaces defined by the intersection of numerous fixed fields and discovered correlated topics. This task requires the discovery of latent topics in the text reports and the creation of a topic cube. Furthermore, because the number of potential cells in the topic cube is very large, we discuss novel methods of pruning the search space in the topic cells, thereby making the analysis feasible. We demonstrate the new algorithms on an analysis of pilot fatigue and its contributing factors, as well as the safety incidents that are correlated with this phenomenon.

Zhao, Bo↗

Venus High Temperature Atmospheric Dropsonde and Extreme-Environment Seismometer (HADES)

The atmospheric composition and geologic structure of Venus have been identified by the US National Research Council's Decadal Survey for Planetary Science as priority targets for scientific exploration, however the high temperature and pressure at the surface, along with the highly corrosive chemistry of the Venus atmosphere, present significant obstacles to spacecraft design that have severely limited past and proposed landed missions. Following the methodology of the NASA Innovative Advanced Concepts (NIAC) proposal regime and the Collaborative Modeling and Parametric Assessment of Space Systems (COMPASS) design protocol, this paper presents a conceptual study and initial feasibility analysis for a Discovery-class Venus lander capable of an extended-duration mission at ambient temperature and pressure, incorporating emerging technologies within the field of high temperature electronics in combination with novel configurations of proven, high Technology Readiness Level (TRL) systems. Radioisotope Thermal Power (RTG) systems and silicon carbide (SiC) communications and data handling are examined in detail, and various high-temperature instruments are proposed, including a seismometer and an advanced photodiode imager. The study combines this technological analysis with proposals for a descent instrument package and a relay orbiter to demonstrate the viability of an integrated atmospheric and in-situ geologic exploratory mission that differs from previous proposals by greatly reducing the mass, power requirements, and cost, while achieving important scientific goals.

HADES↗

We Should Search for Life in Mars N. Polar Ground Ice

The 2008 Phoenix Mars lander mission sampled ground ice at 68°N latitude. Mission results, considered along with climate modeling studies, suggest that the site is habitable for life during high obliquity periods. The Icebreaker mission has been proposed to the NASA Discovery program to search for biosignatures produced during habitable periods. This paper explores its rationale and approach.

Stoker, C. R.↗

A Joint Measurement of $\nu_{\mu}$-Disappearance and $\nu_{e}$e-Appearance in the NuMI beam using the NOvA Experiment

The discovery of neutrino oscillations provides the first indication of a lepton flavor violating (LFV) process, one that isn't predicted by the Standard Model. As such, NOvA is part of a rich experimental program to constrain unknown parameters in the neutrino oscillation model, described for three neutrino flavors using the PMNS unitary matrix. It is a long baseline experiment utilizing two detectors, a Near Detector at Fermilab and a Far Detector in Ash River, Minnesota for a total baseline of 810 km. It receives a predominantly ${\nu_\mu}/\overline{\bar\nu_\mu}$ beam peaking at 1:8 GeV from the NuMI beam facility at Fermilab. There are four oscillation channels used in the analysis, ${\nu_\mu} \to {\nu_\mu}$, ${\nu_\mu} \to {\nu_e}$, ${\overline{\nu}_\mu} \to {\overline{\nu}_\mu}$ and ${\overline{\nu}_\mu} \to {\overline{\nu}_e }$. With a total exposure of 13:6_10$^{20}$ and 12:5_10$^{20}$ protons on target for the neutrino and anti-neutrino beam modes respectively, 82 candidates are seen in the ${\nu_\mu} \to {\nu_e}$ channel for a total predicted backgroundof 26:8 events. Similarly, 33 candidates are seen in the corresponding anti-neutrino channel for a total predicted background of 14:0 events. In the ${\nu_\mu} \to {\nu_\mu}$ $(\overline{\nu}_\mu \to \overline{\nu}_\mu}$ channel, 211 (105) candidates are seen with an expectation of 1156.1 (488.1) events at no oscillations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Active causal learning for decoding chemical complexities with targeted interventions

Abstract Predicting and enhancing inherent properties based on molecular structures is paramount to design tasks in medicine, materials science, and environmental management. Most of the current machine learning and deep learning approaches have become standard for predictions, but they face challenges when applied across different datasets due to reliance on correlations between molecular representation and target properties. These approaches typically depend on large datasets to capture the diversity within the chemical space, facilitating a more accurate approximation, interpolation, or extrapolation of the chemical behavior of molecules. In our research, we introduce an active learning approach that discerns underlying cause-effect relationships through strategic sampling with the use of a graph loss function. This method identifies the smallest subset of the dataset capable of encoding the most information representative of a much larger chemical space. The identified causal relations are then leveraged to conduct systematic interventions, optimizing the design task within a chemical space that the models have not encountered previously. While our implementation focused on the QM9 quantum-chemical dataset for a specific design task—finding molecules with a large dipole moment—our active causal learning approach, driven by intelligent sampling and interventions, holds potential for broader applications in molecular, materials design and discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

Abstract The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE’s sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Physics-Informed Machine-Learning Prediction of Curie Temperatures and Its Promise for Guiding the Discovery of Functional Magnetic Materials

High-performance permanent magnets with a high Curie temperature, containing less critical materials, are integral to zero-carbon energy solutions. We built a machine-learning model trained over available experimentally measured Curie temperature values to predict the T C of multicomponent magnetic materials. We chose two compositions from a pseudo-binary (Zr 1–x Ce x )Fe 2 system, namely, (Zr 0.16 Ce 0.84 )Fe 2 and (Zr 0.94 Ce 0.06 )Fe 2 , to experimentally validate the ability of our model to predict the Curie temperature of novel compounds. We also provided a detailed discussion on the correlation of the Curie temperature with the de Gennes scaling factor in rare-earth intermetallic compounds and its breakdown below a certain rare-earth content. The electronic structure calculations (density of states and Fermi surface) were performed using the density functional theory on selected compounds (Zr 0.16 Ce 0.84 )Fe 2 and (Zr 0.94 Ce 0.06 )Fe 2 to understand the electronic origin of a strong magnetic exchange. We found that the change in the electronic density of states and electron/hole fillings at the Fermi level directly correlate with the Curie temperature. Notably, our model was able to capture these key electronic structure trends, which show that physics-informed machine learning can play a crucial role in designing new high-performance magnets with improved properties for environmentally sustainable applications.

36 MATERIALS SCIENCE↗

Operations on Graphical Models with Plates

This paper explains how graphical models, for instance Bayesian or Markov networks, can be extended to model problems in data analysis and learning. This provides a unified framework that combines lessons learned from the artificial intelligence, statistical and connectionist communities. This also offers a set of principles for developing a software generator for data analysis, whereby a learning or discovery system can be compiled from specifications. Many of the popular learning algorithms can be compiled in this way from graphical specifications. While in a sense this paper is a multidisciplinary review of learning, the main contribution here is the presentation of the material within the unifying framework of graphical models, and the observation that, as a result, the process of developing learning algorithms can be partly automated.

Buntine, Wray L.↗

Model-Based Approaches to Generate Knowledge from Data in a Plant Reliability Context

One challenge that nuclear power plant system engineers are facing is that the amount of equipment reliability (ER) data being continuously generated are extremely large. These data elements come in different forms: textual (e.g., condition reports) and numeric (e.g., generated by monitoring systems) and they provide system engineers with valuable insights and information regarding the discovery of anomalous behaviors or degradation trends, the identification of the possible causes behind such behaviors and trends, and the prediction of their direct consequences. This paper directly targets the generation of knowledge from ER data by putting “data into context”. Here, we employ model-based system engineering (MBSE) models of systems and assets to represent and capture their architecture and functional (i.e., cause-effect) relations. ER data elements are processed by identifying first which elements of the developed MBSE elements they are referring to. This task is much harder for textual data since the information contained in issue or maintenance reports needs to “be understood” by a computational tool. Here we called this process “knowledge extraction” where our methods to extract knowledge from textual data. Lastly, once numeric and textual ER data elements have been processed and “understood”, we discover possible cause-effect relations among them. This is performed by observing if a logical connection through the MBSE models exists, and if there is a temporal relation among them. The logic and temporal are the two main ingredients to perform “machine reasoning” from ER data.

97 MATHEMATICS AND COMPUTING↗

A new X-ray spectral observation of NGC 1068

A new X-ray observation of NGC 1068, in which improved spectral resolution (R is approximately equal to 40) and broad energy range provide important new constraints on models for this galaxy, is reported. The observed X-ray continuum of NGC 1068 from 0.3 to 10 keV is well fitted as the sum of two power-law spectra with no evidence for absorption intrinsic to the source. Strong Fe K emission lines with a total equivalent width of 2700 eV were detected due to iron less ionized than Fe XX and to iron more ionized than Fe XXIII. No evidence was seen for lines due to the recombination of highly ionized oxygen with an upper limit for the O Ly-alpha emission line of 40 eV. The discovery of multiple Fe K and Fe L emission lines indicates a broad range of ionization states for this gas. The X-ray emission from the two components is modeled for various geometries using a photoionization code that calculates the temperature and ionization state of the gas. Typical model parameters are a total Compton depth of a few percent, an inner boundary of the hot component of about 1 pc, and an inner boundary of the warm component of about 20 pc.

Marshall, F. E.↗