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At least 847 records · Page 47

Graph-based featurization methods for classifying small molecule compounds

For over a decade, drug-induced liver injury (DILI) has posed significant drawbacks in the synthesis and development of drugs and remains a consequential concern. With finite success within the existing preclinical models, DILI is one of the main causes of drug withdrawal or termination from the market. Particularly, this withdrawal occurs during the late stages of drug development (Kullak-Ublick, 2017). Since DILI is difficult to diagnose and treat, it has become an obstacle in the drug production market that in turn affects clinicians, pharmaceutical companies, and consumers. We propose a method for learning features of DILI-positive drugs based on the graphical relationships and patterns they possess within a network of biological databases. We also train various statistical and machine learning models on these learned features in order to classify the drugs as DILI-positive or negative. Our methods include Random Forest, Neural networks, and logistic regression classification. We utilize labeled DILI-positive and DILI-negative datasets, which were developed by the FDA and the National center for toxicological research, as well as additional literature datasets (Thakkar, 2020) in order to validate our results and assess our featurization and model accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monomer-dimer tensor-network basis for qubit-regularized lattice gauge theories

Traditional SU⁡(𝑁) lattice gauge theories (LGTs) can be formulated using an orthonormal basis constructed from the irreducible representations (irreps) 𝑉 𝜆 of the SU⁡(𝑁) gauge symmetry. On a lattice, the elements of this basis are tensor networks comprising dimer tensors on the links labeled by a set of irreps {𝜆 ℓ } and monomer tensors on sites labeled by {𝜆 𝑠 }. These tensors naturally define a local site Hilbert space, ℋ$^𝑔_𝑠$, on which gauge transformations act. Gauss’s law introduces an additional index 𝛼 𝑠 =1,2,…,𝒟⁡(ℋ$^𝑔_𝑠$) that labels an orthonormal basis of the gauge-invariant subspace of ℋ$^𝑔_𝑠$. This monomer-dimer tensor-network (MDTN) basis, |{𝜆 𝑠 },{𝜆 ℓ },{𝛼 𝑠 }⟩, of the physical Hilbert space enables the construction of new qubit-regularized SU⁡(𝑁) gauge theories that are free of sign problems while preserving key features of traditional LGTs. Here, we investigate finite-temperature confinement-deconfinement transitions in a simple qubit-regularized SU(2) and SU(3) gauge theory in 𝑑 =2 and 𝑑 =3 spatial dimensions, formulated using the MDTN basis, and show that they reproduce the universal results of traditional LGTs at these transitions. Additionally, in 𝑑 =1, we demonstrate using a plaquette chain that the string tension at zero temperature can be continuously tuned to zero by adjusting a model parameter that plays the role of the gauge coupling in traditional LGTs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Controllable vortex shedding from dissipative exchange flows in ferromagnetic channels

Ferromagnetic channels subject to spin injection at one extremum sustain long-range coherent textures that carry spin currents known as dissipative exchange flows (DEFs). In the weak injection regime, spin currents carried by DEFs decay algebraically and extend through the length of the channel, a regime known as spin superfluidity. Similar to fluids, these structures are prone to phase slips that manifest as vortex-antivortex pairs. In this work, we numerically study vortex shedding from DEFs excited in a magnetic nanowire with a physical obstacle. Using micromagnetic simulations, we find regimes of laminar flow and vortex shedding as a function of obstacle position tunable by the spin injection sign and magnitude. Vortex-antivortex pairs translate forward (VF regime) or backward (VB regime) with respect to the detector's extremum, resulting in well-defined spectral features. Qualitatively similar results are obtained when temperature, anisotropy, and weak nonlocal dipole fields are included in the simulations. These results provide clear features associated with DEFs that may be detected experimentally in devices with nominally identical boundary conditions. Furthermore, our results suggest that obstacles can be considered as DEF control gates, opening an avenue to manipulate DEFs via physical defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

On the Sensitivity of Coastal Hypoxia to Its External Physical Forcings

Abstract The development of low‐oxygen zones threatening marine life (hypoxia) occurs annually in multiple coastal regions of the world. The largest estuary of the continental United States, the Chesapeake Bay, typically has ≈10 km 3 of water with dioxygen concentrations <3 mg L −1 in July. As numerical methods for refining model resolutions in targeted areas are becoming common, there is interest in assessing the feasibility of simulating coastal hazards such as hypoxia in Earth System Models (ESMs). These coupled models are typically not constrained by observations and thus likely to feature systematic biases in their land, atmosphere, or ocean components. This study relies on four numerical experiments to evaluate the sensitivity of Chesapeake Bay hypoxia to changes or biases in its external physical forcings. Hypoxia exhibits only a minor decrease (−1.6%) after reducing the Bay's terrestrial freshwater discharge by 9.5% (but keeping terrestrial nutrient loadings the same). Changes in freshwater discharges have their largest impact on hypoxia during one extreme event (−37% during 2011 tropical storm Lee). Similarly, changing oceanic conditions on the shelf or their temporal frequency impact hypoxia by only 5%–6%, indicating that the latter is predominantly dictated by local conditions. Although these results are promising from the perspective of ESMs, additional components of ESMs will need to be evaluated before general conclusions can be reached. We notably speculate that the Bay's hypoxia would exhibit higher sensitivity to other forcings not examined here, notably air temperatures and nutrient loadings.

Meteorology & Atmospheric Sciences↗

Coupling physics in machine learning to predict properties of high-temperatures alloys

Abstract High-temperature alloy design requires a concurrent consideration of multiple mechanisms at different length scales. We propose a workflow that couples highly relevant physics into machine learning (ML) to predict properties of complex high-temperature alloys with an example of the 9–12 wt% Cr steels yield strength. We have incorporated synthetic alloy features that capture microstructure and phase transformations into the dataset. Identified high impact features that affect yield strength of 9Cr from correlation analysis agree well with the generally accepted strengthening mechanism. As a part of the verification process, the consistency of sub-datasets has been extensively evaluated with respect to temperature and then refined for the boundary conditions of trained ML models. The predicted yield strength of 9Cr steels using the ML models is in excellent agreement with experiments. The current approach introduces physically meaningful constraints in interrogating the trained ML models to predict properties of hypothetical alloys when applied to data-driven materials.

36 MATERIALS SCIENCE↗

NUMERICAL MODELING OF A SOLID OXIDE FUEL CELL FOR USE IN REAL-TIME SIMULATION AND CYBER-PHYSICAL SYSTEMS

Cyber-physical systems provide a mechanism with which to investigate the physical phenomena and behavior of traditionally cost-prohibitive or otherwise fragile equipment. For the National Energy Technology Laboratory (NETL), this approach resulted in the Hybrid Performance (Hyper) facility which features a gas turbine-SOFC hybrid cycle utilizing real turbomachinery and a simulated SOFC stack. This allows for the investigation of combined cycle performance and control strategies, in an exhaustive manner, both without fear of destroying delicate state-of-the-art fuel cells, and with the full accuracy of real-world turbomachinery. Issues arose between the transient response of the SOFC model being limited to a sample time of 80 milliseconds, due to the calculation time of the SOFC model taking on average 40 milliseconds to calculate for a given timestep with spikes in calculation time reaching the 80 millisecond threshold. In order to be able to match the speed of transients from the turbomachinery and likewise better discern transient behavior, it was determined that the SOFC model must be optimized to operate at a sample time of 5 milliseconds. Therefore, it is necessary to optimize the SOFC model in order to decrease the calculation time from around 40 milliseconds, down to at the most 5 milliseconds. To do this, both the electrochemical algorithm and the thermal algorithm used to simulate the physical behavior of the SOFC are investigated to determine where improvements can be made. To this end the rootfinding numerical recipes of the electrochemical algorithm are investigated as the complex electrochemistry requires a highly iterative nested dual convergence loop to resolve the voltage-current relationship, and likewise the temporal discretization of the thermal algorithm is modified for the sake of higher accuracy and stability. Ultimately the new electrochemical algorithm featuring higher order rootfinding schemes proves to be efficient enough to reach the sub 5 millisecond target, signifying an order of magnitude reduction in calculation time, and when coupled with the new temporal discretization similar calculation time characteristics show that a fully implicit, higher order temporal discretization can also successfully be used if desired. Ultimately this result means that the cyber-physical simulation system can operate at higher sample rates, and resolve transient events at significantly higher resolution and fidelity.

Arias, Jesus↗

Design and Preparation of Nematic Colloidal Particles

Colloidal systems are abundant in technology, in biomedical settings, and in our daily life. The so-called “colloidal atoms” paradigm exploits interparticle interactions to self-assemble colloidal analogs of atomic and molecular crystals, liquid crystal glasses, and other types of condensed matter from nanometer- or micrometer-sized colloidal building blocks. Nematic colloids, which comprise colloidal particles dispersed within an anisotropic nematic fluid host medium, provide a particularly rich variety of physical behaviors at the mesoscale, not only matching but even exceeding the diversity of structural and phase behavior in conventional atomic and molecular systems. This feature article, using primarily examples of works from our own group, highlights recent developments in the design, fabrication, and self-assembly of nematic colloidal particles, including the capabilities of preprogramming their behavior by controlling the particle’s surface boundary conditions for liquid crystal molecules at the colloidal surfaces as well as by defining the shape and topology of the colloidal particles. Here recent progress in defining particle-induced defects, elastic multipoles, self-assembly, and dynamics is discussed along with open issues and challenges within this research field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recent progress on the mesoscale modeling of architected thin-films via phase-field formulations of physical vapor deposition

Thin-film coatings can be found everywhere in modern technological applications due to desirable electrical, mechanical, chemical, and optical properties. These properties directly depend upon the thin-film’s microstructural features, which are themselves influenced by the materials and vapor-deposition processing conditions used for fabrication. As such, understanding processing-microstructure relationships is essential to designing thin-films with optimized properties, and discovering new processing conditions that allow for novel thin-films with multifunctional microstructures. Here, a short review is presented on recent developments that utilize the phase-field method to simultaneously model the vapor-deposition process and corresponding microstructure formation at the mesoscale. Also phase-field-based vapor-deposition models that simulate thin-film growth of immiscible alloy and polycrystalline systems are highlighted in addition to machine-learning-based surrogate models that can facilitate accelerated high-fidelity simulations along with materials design and exploration studies.

36 MATERIALS SCIENCE↗

Feature Engineering and Ensemble Methods for Imbalanced ICS Intrusion Detection: Pipeline Audit and Constrained Evaluation

Industries are becoming increasingly connected and are more vulnerable to cyberattacks due to the widened attack surface. Industrial Control Systems (ICS) are among the most critical sectors that malicious actors can target, as such attacks can cause significant operational disruption and physical damage. It is imperative to detect such attacks as early as possible. This paper evaluates constraint-conditioned optimistic performance estimates for traditional ML models in ICS intrusion detection (i.e., estimates obtained under contiguous, non-shuffled temporal evaluation without test-set alteration, but with pre-split feature engineering that may introduce temporal leakage, due to dataset constraints). Our findings are threefold. First, we quantify how iterative feature engineering affects tree-based ensemble performance and examine how pipeline decisions (split strategy, sampling scope, and cleaning policy) can inflate or reduce reported IDS results under constraint-bound evaluation. Second, we compare intrinsic class-imbalance handling across ensemble models. Third, under our current pipeline constraints (including pre-split feature engineering), CatBoost achieves the best performance on Water Storage Tank (accuracy: 0.9831, class-1 F1: 0.9682), while Light- GBM achieves the best performance on Gas Pipeline (accuracy: 0.9618, class-1 F1: 0.9086).

97 MATHEMATICS AND COMPUTING↗

Machine-learning predictions of the shale wells’ performance

The ultra-low permeability nature of shale reservoirs leads to an extended linear flow and necessitates horizontal wells with multi-stage engineered fractures to efficiently extract hydrocarbons resources. These artificially-generated and naturally-occurring fractures form complex networks that create complex flow regimes which control oil production. These fractures are neither identical nor equally-spaced, which leads to a production profile with a masked onset of the boundary-dominated flow. The combination of the extended linear flow with the indeterminate onset of the boundary-dominated flow challenges the current deterministic analytic approaches to forecast the estimated ultimate recovery (EUR). In this work, we propose a novel machine-learning approach which overcomes these challenges and provides reliable EUR estimates based on field-wide analyses. We implement a novel unsupervised machine learning (ML) methodology, which allows for automatic identification of the optimal number of features (signals) present in the data based on non-negative matrix/tensor factorization coupled with k-means clustering incorporating regularization and physics constraints. In the presented analyses, the input data to the ML algorithm is the available (public) production history from the field collected at existing unconventional reservoirs. We validate our approach through hindcasting of the production data, where we achieved an excellent agreement. In addition, our approach is able to identify the poorly-performing wells, which could benefit from early refracing. Our approach provides fast and accurate estimations of the well performance without presumptions about the state of the well or the flow regime.

03 NATURAL GAS↗

Signatures of chiral superconductivity in rhombohedral graphene

Chiral superconductors are unconventional superconducting states that break time-reversal symmetry spontaneously and typically feature Cooper pairing at non-zero angular momentum. Such states may host Majorana fermions and provide an important platform for topological physics research and fault-tolerant quantum computing. Despite intensive search and prolonged studies of several candidate systems, chiral superconductivity has remained elusive so far. Here we report the discovery of robust unconventional superconductivity in rhombohedral tetralayer and pentalayer graphene without moiré superlattice effects. We observed two superconducting states in the gate-induced flat conduction bands with T c up to 300 mK and charge density n e down to 2.4 ×10 11 cm −2 in five devices. Spontaneous time-reversal-symmetry breaking (TRSB) owing to orbital motion of the electron is found and several observations indicate the chiral nature of these superconducting states, including: (1) in the superconducting state, R xx shows magnetic hysteresis in varying out-of-plane magnetic field B ⊥ —absent from all other superconductors; (2) the superconducting states are robust against in-plane magnetic field and are developed within a spin-polarized and valley-polarized quarter-metal (QM) phase; (3) the normal states show anomalous Hall signals at zero magnetic field and magnetic hysteresis. Here, we also observed a critical B ⊥ of 1.4 T, higher than any graphene superconductivity, which indicates a strong-coupling superconductivity close to the Bardeen–Cooper–Schrieffer (BCS)–Bose–Einstein condensate (BEC) crossover. Our observations establish a pure carbon material for the study of topological superconductivity, with the promise to explore Majorana modes and topological quantum computing.

36 MATERIALS SCIENCE↗

Arctic soil patterns analogous to fluid instabilities

Significance Slow-moving arctic soils form patterns resembling those found in common fluids, such as paint and cake icing drips. Inspired by fluid instabilities, we develop a conceptual model for soil patterns and use mathematical analysis to predict their wavelength. In particular, we propose that soil patterns arise due to competition between gravity and cohesion or the “stickiness” of soil grains. We compare our theoretical predictions with a dataset of soil features from Norway, finding that soil patterns are controlled by fluid-like properties as well as climate. Our work provides a physical explanation for a common pattern on both Earth and Mars, with implications for our understanding of landscapes and complex materials composed of both granular and fluid components.

54 ENVIRONMENTAL SCIENCES↗

Asymmetric jet shapes with two-dimensional jet tomography

Two-dimensional (2D) jet tomography is a promising tool to study jet medium modification in high-energy heavy-ion collisions. It combines gradient (transverse) and longitudinal jet tomography for selection of events with localized initial jet production positions. It exploits the transverse asymmetry and energy loss that depend, respectively, on the transverse gradient and jet path length inside the quark-gluon plasma (QGP). In this study, we employ 2D jet tomography to study medium modification of the jet shape of γ -triggered jets within the linear Boltzmann transport (LBT) model for jet propagation in heavy-ion collisions. Our results show that jets with small transverse asymmetry ( A N n ⃗ ) or small γ -jet asymmetry ( x J γ = p T jet / p T γ ) exhibit a broader jet shape than those with larger A N n ⃗ or x J γ , since the former are produced at the center and go through longer path lengths while the later are off center and close to the surface of the QGP fireball. In events with finite values of A N n ⃗ , jet shapes are asymmetric with respect to the event plane. Hard partons at the core of the jet are deflected away from the denser region while soft partons from the medium response at large angles flow toward the denser part of QGP. Future experimental measurements of these asymmetric features of the jet shape can be used to study the transport properties of jets and medium responses. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Addition of tabulated equation of state and neutrino leakage support to illinoisgrmhd

Here we have added support for realistic, microphysical, finite-temperature equations of state (EOS) and neutrino physics via a leakage scheme to illinoisgrmhd, an open-source GRMHD code for dynamical spacetimes in the einstein toolkit. These new features are provided by two new, nrpy+-based codes: nrpyeos, which performs highly efficient EOS table lookups and interpolations, and nrpyleakage, which implements a new, adaptive mesh refinement (AMR)-capable neutrino leakage scheme in the einstein toolkit. We have performed a series of strenuous validation tests that demonstrate the robustness of these new codes, particularly on the Cartesian AMR grids provided by carpet. Furthermore, we show results from fully dynamical GRMHD simulations of single unmagnetized neutron stars, and magnetized binary neutron star mergers. This new version of illinoisgrmhd, as well as nrpyeos and nrpyleakage, is pedagogically documented in jupyter notebooks and fully open source. The codes will be proposed for inclusion in an upcoming version of the einstein toolkit.

79 ASTRONOMY AND ASTROPHYSICS↗

Quantized Information in Spectral Cyberspace

The constant-Q Gabor atom is developed for spectral power, information, and uncertainty quantification from time–frequency representations. Stable multiresolution spectral entropy algorithms are constructed with continuous wavelet and Stockwell transforms. The recommended processing and scaling method will depend on the signature of interest, the desired information, and the acceptable levels of uncertainty of signal and noise features. Selected Lamb wave signatures and information spectra from the 2022 Tonga eruption are presented as representative case studies. Resilient transformations from physical to information metrics are provided for sensor-agnostic signal processing, pattern recognition, and machine learning applications.

74 ATOMIC AND MOLECULAR PHYSICS↗

Hardware-Based Emulator with Deep Learning Model for Building Energy Control and Prediction Based on Occupancy Sensors’ Data

Heating, ventilation, and air conditioning (HVAC) is the largest source of residential energy consumption. Occupancy sensors’ data can be used for HVAC control since it indicates the number of people in the building. HVAC and sensors form a typical cyber-physical system (CPS). In this paper, we aim to build a hardware-based emulation platform to study the occupancy data’s features, which can be further extracted by using machine learning models. In particular, we propose two hardware-based emulators to investigate the use of wired/wireless communication interfaces for occupancy sensor-based building CPS control, and the use of deep learning to predict the building energy consumption with the sensor data. We hypothesize is that the building energy consumption may be predicted by using the occupancy data collected by the sensors, and question what type of prediction model should be used to accurately predict the energy load. Another hypothesis is that an in-lab hardware/software platform could be built to emulate the occupancy sensing process. The machine learning algorithms can then be used to analyze the energy load based on the sensing data. To test the emulator, the occupancy data from the sensors is used to predict energy consumption. The synchronization scheme between sensors and the HVAC server will be discussed. We have built two hardware/software emulation platforms to investigate the sensor/HVAC integration strategies, and used an enhanced deep learning model—which has sequence-to-sequence long short-term memory (Seq2Seq LSTM)—with an attention model to predict the building energy consumption with the preservation of the intrinsic patterns. Because the long-range temporal dependencies are captured, the Seq2Seq models may provide a higher accuracy by using LSTM architectures with encoder and decoder. Meanwhile, LSTMs can capture the temporal and spatial patterns of time series data. The attention model can highlight the most relevant input information in the energy prediction by allocating the attention weights. The communication overhead between the sensors and the HVAC control server can also be alleviated via the attention mechanism, which can automatically ignore the irrelevant information and amplify the relevant information during CNN training. Our experiments and performance analysis show that, compared with the traditional LSTM neural network, the performance of the proposed method has a 30% higher prediction accuracy.

Ye, Zhijing↗