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At least 613 records · Page 34

Predicting Metabolic Reaction Networks with Perturbation-Theory Machine Learning (PTML) Models

Background: Checking the connectivity (structure) of complex Metabolic Reaction Networks(MRNs) models proposed for new microorganisms with promising properties is an importantgoal for chemical biology. Objective: In principle, we can perform a hand-on checking (Manual Curation). However, this is achallenging task due to the high number of combinations of pairs of nodes (possible metabolic reactions). Results: The CPTML linear model obtained using the LDA algorithm is able to discriminate nodes(metabolites) with the correct assignation of reactions from incorrect nodes with values of accuracy,specificity, and sensitivity in the range of 85-100% in both training and external validation dataseries. Methods: In this work, we used Combinatorial Perturbation Theory and Machine Learning techniquesto seek a CPTML model for MRNs >40 organisms compiled by Barabasis’ group. First, wequantified the local structure of a very large set of nodes in each MRN using a new class of node indexcalled Markov linear indices fk. Next, we calculated CPT operators for 150000 combinationsof query and reference nodes of MRNs. Last, we used these CPT operators as inputs of differentML algorithms. Conclusion: Meanwhile, PTML models based on Bayesian network, J48-Decision Tree and RandomForest algorithms were identified as the three best non-linear models with accuracy greaterthan 97.5%. The present work opens the door to the study of MRNs of multiple organisms usingPTML models.

Pharmacology & Pharmacy↗

Electric Vehicle Charging Management in Smart Energy Communities to Increase Renewable Energy Hosting Capacity

Abnormal climates due to global warming have emerged as a big concern in the global community. To mitigate climate change and achieve sustainability, distributed energy resources (DERs), including solar and wind, have been recently deployed in power systems. As the penetration level of DERs has increased, however, it caused a multitude of issues in the power systems, such as voltage fluctuation in the distribution network limiting renewable hosting capacity. On the other hand, the electric vehicle (EV) industry is rapidly growing to facilitate the transition to a carbon-neutral community, illuminating the potential of EVs as a flexible grid asset to mitigate some of the issues and improve grid operation, if properly exploited. To explore the potential of EVs, this paper proposes an EV scheduling strategy. By using an optimal EV charging scheduling proposed, distribution system operators (DSOs) can minimize their operating costs and stably operate the system with a high level of DERs. To validate the method, a modified IEEE 33-bus system with DERs is developed. The case study shows the proposed scheduling strategizes EV charging to reduce the cost of PV curtailment. In the study, the method outperforms the renewable-only case with curtailment by 4.97% in DSO cost. It also demonstrates its potential to increase the renewable hosting capacity by harmonizing EV charging with renewables.

ADVANCED PROPULSION SYSTEMS,POWER TRANSMISSION AND↗

Coordinated Control of Wind Turbine and Energy Storage System for Reducing Wind Power Fluctuation

This paper proposes a coordinated control of wind turbine and energy storage system (ESS). Because wind power (WP) is highly dependent on variable wind speed and could induce a severe stability problem to power system especially when the WP has high penetration level. To solve this problem, many power generation corporations or grid operators recently use the ESS. It has very quick response and good performance for reducing the impact of WP fluctuation but has high cost for its installation. Therefore, it is very important to design the control algorithm considering both ESS capacity and grid reliability. Thus, we propose the control algorithm to mitigate the WP fluctuation by using the coordinated control between wind turbine and ESS considering ESS state of charge (SoC) and the WP fluctuation. From deloaded control according to WP fluctuation and ESS SoC management, we can expect the ESS lifespan expansion and improved grid reliability. The effectiveness of the proposed method is validated in MATLAB/Simulink considering power system including both wind turbine generator and conventional generators which react to system frequency deviation.

17 WIND ENERGY↗

Simultaneous Forward-Backward Prony Estimation

Power system dynamic stability can be evaluated through the analysis of transient oscillations that occur following significant system events. One of the earliest methods for this type of study is Prony analysis, which estimates the system's electromechanical modes. While previous studies have highlighted advantages of performing Prony analysis on data in the forward and backward directions, the proposed method does so simultaneously. As a result, signal poles corresponding to electromechanical modes can be distinguished from spurious poles more reliably. The method also produces a single mode estimate, where independent application in the forward and backward directions would produce two estimates for each mode. The method is validated using simulated and measured power system data.

Follum, James D.↗

Time Delay of Wide Area Damping Control in Urban Power Grid: Model-Based Analysis and Data-Driven Compensation

Due to the rapid development of economies, large urban cities consume an increasing amount of energy and have a higher requirement for power quality. Voltage source converter based high voltage direct current (VSC-HVDC) is a promising device to transmit clean power from remote regions to urban power systems, while also providing wide area damping control (WADC) for frequency stabilization. However, the time-delay naturally existing in the VSC-HVDC system may degrade the performance of WADC and even result in instability. To address this issue, this paper develops a time-delay correction control strategy for VSC-HVDC damping control in urban power grids. First, a small signal model of WADC is built to analyze the negative impacts of time delay. Then, a data-driven approach is proposed to compensate for the inherent time delay in VSC-HVDC damping control. The extensive training data will be generated under various disturbances. After offline training, the long short-term memory network (LSTM) can be implemented online to predict the actual frequency deviation based on real-time measurements. Finally, the proposed method is validated through MATLAB-Simulink in a two-area four-machine system. The results indicate that the data-driven compensation has a strong generalization ability for random delay time constants and can improve the performance of WADC significantly.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Characterizing the Reproducibility of Noisy Quantum Circuits

The ability of a quantum computer to reproduce or replicate the results of a quantum circuit is a key concern for verifying and validating applications of quantum computing. Statistical variations in circuit outcomes that arise from ill-characterized fluctuations in device noise may lead to computational errors and irreproducible results. While device characterization offers a direct assessment of noise, an outstanding concern is how such metrics bound the reproducibility of a given quantum circuit. Here, we first directly assess the reproducibility of a noisy quantum circuit, in terms of the Hellinger distance between the computational results, and then we show that device characterization offers an analytic bound on the observed variability. We validate the method using an ensemble of single qubit test circuits, executed on a superconducting transmon processor with well-characterized readout and gate error rates. The resulting description for circuit reproducibility, in terms of a composite device parameter, is confirmed to define an upper bound on the observed Hellinger distance, across the variable test circuits. This predictive correlation between circuit outcomes and device characterization offers an efficient method for assessing the reproducibility of noisy quantum circuits.

97 MATHEMATICS AND COMPUTING↗

A Qualitative Strategy for Fusion of Physics into Empirical Models for Process Anomaly Detection

To facilitate the automated online monitoring of power plants, a systematic and qualitative strategy for anomaly detection is presented. This strategy is essential to provide credible reasoning on why and when an empirical versus hybrid (i.e., physics-supported) approach should be used and to determine the ideal mix of these two approaches for a defined anomaly detection scope. Empirical methods are usually based on pattern, statistical, and causal inference. Hybrid methods include the use of physics models to train and test data methods, reduce data dimensionality, reduce data-model complexity, augment data, and reduce empirical uncertainty; hybrid methods also include the use of data to tune physics models. The presented strategy is driven by key decision points related to data relevance, simple modeling feasibility, data inference, physics-modeling value, data dimensionality, physics knowledge, method of validation, performance, data availability, and suitability for training and testing, cause-effect, entropy inference, and model fitting. The strategy is demonstrated through a pilot use case for the application of anomaly detection to capture a valve packing leak at the high-pressure coolant injection system of a nuclear power plant.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Estimating and Calibrating DER Model Parameters Using Levenberg–Marquardt Algorithm in Renewable Rich Power Grid

The proliferation of inverter-based distributed energy resources (IBDERs) has increased the number of control variables and dynamic interactions, leading to new grid control challenges. For stability analysis and designing appropriate protection controls, it is important that IBDER models are accurate. This paper focuses on the accurate estimation and parameter calibration of DER_A, a recently proposed aggregated IBDER model. In particular, we focus on the parameters of the reactive power–voltage regulation module. We formulate the problem of parameter tuning as a non-linear least square minimization problem and solve it using the Levenberg–Marquardt (LM) method. The LM method is primarily chosen due to its flexibility in adaptively selecting between the steepest descent and Gauss–Newton methods through a damping parameter. The LM approach is used to minimize the error between the actual measurements and the estimated response of the model. Further, the computational challenges posed by the numerical calculation of the Jacobian are tackled using a quasi-Newton root-finding approach. The proposed method is validated on a real feeder model in the northeastern part of the United States. The feeder is modeled in OpenDSS and the measurements thus obtained are fed to the DER_A model for calibration. The simulation results indicate that our approach is able to successfully calibrate the relevant model parameters quickly and with high accuracy, with a total sum of square error of 3.57 × 10 –7 .

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability

Predicting how a point mutation alters a protein’s stability can guide pharmaceutical drug design initiatives which aim to counter the effects of serious diseases. Conducting mutagenesis studies in physical proteins can give insights about the effects of amino acid substitutions, but such wet-lab work is prohibitive due to the time as well as financial resources needed to assess the effect of even a single amino acid substitution. Computational methods for predicting the effects of a mutation on a protein structure can complement wet-lab work, and varying approaches are available with promising accuracy rates. In this work we compare and assess the utility of several machine learning methods and their ability to predict the effects of single and double mutations. We in silico generate mutant protein structures, and compute several rigidity metrics for each of them. We use these as features for our Support Vector Regression (SVR), Random Forest (RF), and Deep Neural Network (DNN) methods. We validate the predictions of our in silico mutations against experimental ΔΔG stability data, and attain Pearson Correlation values upwards of 0.71 for single mutations, and 0.81 for double mutations. We perform ablation studies to assess which features contribute most to a model’s success, and also introduce a voting scheme to synthesize a single prediction from the individual predictions of the three models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparative Evaluation of U.S. Brand and Generic Intravenous Sodium Ferric Gluconate Complex in Sucrose Injection: Biodistribution after Intravenous Dosing in Rats

Relative biodistribution of FDA-approved innovator and generic sodium ferric gluconate (SFG) drug products was investigated to identify differences in tissue distribution of iron after intravenous dosing to rats. Three equal cohorts of 42 male Sprague-Dawley rats were created with each cohort receiving one of three treatments: (1) the innovator SFG product dosed intravenously at a concentration of 40 mg/kg; (2) the generic SFG product dosed intravenously at a concentration of 40 mg/kg; (3) saline dosed intravenously at equivalent volume to SFG products. Sampling time points were 15 min, 1 h, 8 h, 1 week, two weeks, four weeks, and six weeks post-treatment. Six rats from each group were sacrificed at each time point. Serum, femoral bone marrow, lungs, brain, heart, kidneys, liver, and spleen were harvested and evaluated for total iron concentration by ICP-MS. The ICP-MS analytical method was validated with linearity, range, accuracy, and precision. Results were determined for mean iron concentrations (µg/g) and mean total iron (whole tissue) content (µg/tissue) for each tissue of all groups at each time point. A percent of total distribution to each tissue was calculated for both products. At any given time point, the overall percent iron concentration distribution did not vary between the two SFG drugs by more than 7% in any tissue. Overall, this study demonstrated similar tissue biodistribution for the two SFG products in the examined tissues.

59 BASIC BIOLOGICAL SCIENCES↗

The evolution of the galaxy stellar mass function at z = 4-8: a steepening low-mass-end slope with increasing redshift

We present galaxy stellar mass functions (GSMFs) at z = 4–8 from a rest-frame ultraviolet (UV) selected sample of ∼4500 galaxies, found via photometric redshifts over an area of ∼280 arcmin{sup 2} in the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS)/Great Observatories Origins Deep Survey (GOODS) fields and the Hubble Ultra Deep Field. The deepest Spitzer/IRAC data to date and the relatively large volume allow us to place a better constraint at both the low- and high-mass ends of the GSMFs compared to previous space-based studies from pre-CANDELS observations. Supplemented by a stacking analysis, we find a linear correlation between the rest-frame UV absolute magnitude at 1500 Å (M{sub UV}) and logarithmic stellar mass (logM{sub ∗}) that holds for galaxies with log(M{sub ∗}/M{sub ⊙})≲10. We use simulations to validate our method of measuring the slope of the logM{sub ∗}–M {sub UV} relation, finding that the bias is minimized with a hybrid technique combining photometry of individual bright galaxies with stacked photometry for faint galaxies. The resultant measured slopes do not significantly evolve over z = 4–8, while the normalization of the trend exhibits a weak evolution toward lower masses at higher redshift. We combine the logM{sub ∗}–M {sub UV} distribution with observed rest-frame UV luminosity functions at each redshift to derive the GSMFs, finding that the low-mass-end slope becomes steeper with increasing redshift from α=−1.55{sub −0.07}{sup +0.08} at z = 4 to α=−2.25{sub −0.35}{sup +0.72} at z = 8. The inferred stellar mass density, when integrated over M{sub ∗}=10{sup 8}–10{sup 13} M {sub ⊙}, increases by a factor of 10{sub −2}{sup +30} between z = 7 and z = 4 and is in good agreement with the time integral of the cosmic star formation rate density.

79 ASTRONOMY AND ASTROPHYSICS↗

CHARGED DUST GRAIN DYNAMICS SUBJECT TO SOLAR WIND, POYNTING–ROBERTSON DRAG, AND THE INTERPLANETARY MAGNETIC FIELD

We investigate the combined effect of solar wind, Poynting–Robertson drag, and the frozen-in interplanetary magnetic field on the motion of charged dust grains in our solar system. For this reason, we derive a secular theory of motion by the means of an averaging method and validate it with numerical simulations of the unaveraged equations of motions. The theory predicts that the secular motion of charged particles is mainly affected by the z -component of the solar magnetic axis, or the normal component of the interplanetary magnetic field. The normal component of the interplanetary magnetic field leads to an increase or decrease of semimajor axis depending on its functional form and sign of charge of the dust grain. It is generally accepted that the combined effects of solar wind and photon absorption and re-emmision (Poynting–Robertson drag) lead to a decrease in semimajor axis on secular timescales. On the contrary, we demonstrate that the interplanetary magnetic field may counteract these drag forces under certain circumstances. We derive a simple relation between the parameters of the magnetic field, the physical properties of the dust grain, as well as the shape and orientation of the orbital ellipse of the particle, which is a necessary conditions for the stabilization in semimajor axis.

79 ASTRONOMY AND ASTROPHYSICS↗

Higher Compact Multiple Occurrence around Metal-poor M-dwarfs and Late-K-dwarfs

The planet–metallicity correlation serves as a potential link between exoplanet systems as we observe them today and the effects of bulk composition on the planet formation process. Many observers have noted a tendency for Jovian planets to form around stars with higher metallicities; however, there is no consensus on a trend for smaller planets. Here, we investigate the planet–metallicity correlation for rocky planets in single- and multi-planet systems around Kepler M-dwarf and late-K-dwarf stars. Due to molecular blanketing and the dim nature of these low-mass stars, it is difficult to make direct elemental abundance measurements via spectroscopy. We instead use a combination of accurate and uniformly measured parallaxes and photometry to obtain relative metallicities and validate this method with a subsample of spectroscopically determined metallicities. We use the Kolmogorov–Smirnov (K-S) test, Mann–Whitney U-test, and Anderson–Darling (AD) test to compare the compact multiple planetary systems with single-transiting planet systems and systems with no detected transiting planets. We find that the compact multiple planetary systems are derived from a statistically more metal-poor population, with a p-value of 0.015 in the K-S test, a p-value of 0.005 in the Mann–Whitney U-test, and a value of 2.574 in the AD test statistic, which exceeds the derived threshold for significance by a factor of 25. We conclude that metallicity plays a significant role in determining the architecture of rocky planet systems. Compact multiples either form more readily, or are more likely to survive on gigayear timescales, around metal-poor stars.

47 OTHER INSTRUMENTATION↗

General Relativistic Implicit Monte Carlo Radiation-hydrodynamics

Abstract We report on a new capability added to our general relativistic radiation-magnetohydrodynamics code, Cosmos++ : an implicit Monte Carlo (IMC) treatment for radiation transport. The method is based on a Fleck-type implicit discretization of the radiation-hydrodynamics equations, but generalized for both Newtonian and relativistic regimes. A multiple reference frame approach is used to geodesically transport photon packets (and solve the hydrodynamics equations) in the coordinate frame, while radiation–matter interactions are handled either in the fluid or electron frames then communicated via Lorentz boosts and orthonormal tetrad bases attached to the fluid. We describe a method for constructing estimators of radiation moments using path-weighting that generalizes to arbitrary coordinate systems in flat or curved spacetime. Absorption, emission, scattering, and relativistic Comptonization are among the matter interactions considered in this report. We discuss our formulations and numerical methods, and validate our models against a suite of radiation and coupled radiation-hydrodynamics test problems in both flat and curved spacetimes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Enabling Robust Exoplanet Atmospheric Retrievals with Gaussian Processes

Atmospheric retrievals are essential tools for interpreting exoplanet transmission and eclipse spectra, enabling quantitative constraints on the chemical composition, aerosol properties, and thermal structure of planetary atmospheres. The James Webb Space Telescope (JWST) offers unprecedented spectral precision, resolution, and wavelength coverage, unlocking transformative insights into the formation, evolution, climate, and potential habitability of planetary systems. However, this opportunity is accompanied by challenges: modeling assumptions and unaccounted-for noise or signal sources can bias retrieval outcomes and their interpretation. To address these limitations, we introduce a Gaussian process (GP)-aided atmospheric retrieval framework that flexibly accounts for unmodeled features and correlated noise in exoplanet spectra. We validate this method on synthetic JWST observations, and show that GP-aided retrievals reduce bias in inferred abundances and better capture model–data mismatches than traditional approaches. We also introduce the concept of mean squared error to quantify the trade-off between bias and variance, arguing that this metric more accurately reflects retrieval performance than bias alone. We then reanalyze the NIRISS/SOSS JWST transmission spectrum of WASP-96 b, finding that GP-aided retrievals yield broader constraints on CO 2 and H 2 O, possibly alleviating tension between previous retrieval results and equilibrium predictions. Our GP framework provides precise and accurate constraints while highlighting regions where models fail to explain the data. As JWST matures and future facilities come online, a deeper understanding of the limitations of both data and models will be essential, and GP-enabled retrievals like the one presented here offer a principled path forward.

Rotman, Yoav [Arizona State Univ., Tempe, AZ (Unit↗

MicroRNAs as diagnostic and therapeutic tools for Alzheimer’s disease: advances and limitations

Alzheimer’s disease (AD) is the most common age-related, progressive neurodegenerative disease. It is characterized by memory loss and cognitive decline and responsible for most cases of dementia in the elderly. Late-onset or sporadic AD accounts for > 95% of cases, with age at onset > 65 years. Currently there are no drugs or other therapeutic agents available to prevent or delay the progression of AD. The cellular and molecular changes occurring in the brains of individuals with AD include accumulation of β-amyloid peptide and hyperphosphorylated tau protein, decrease of acetylcholine neurotransmitter, inflammation, and oxidative stress. Aggregation of β-amyloid peptide in extracellular plaques and the hyperphosphorylated tau protein in intracellular neurofibrillary tangles are characteristic of AD. A major challenge is identifying molecular biomarkers of the early-stage AD in patients as most studies have been performed with blood or brain tissue samples (postmortem) at late-stage AD. Subjects with mild cognitive impairment almost always have the neuropathologic features of AD with about 50% of mild cognitive impairment patients progressing to AD. They could provide important information about AD pathomechanism and potentially also highlight minimally or noninvasive, easy-to-access biomarkers. MicroRNAs are dysregulated in AD, and may facilitate the early detection of the disease and potentially the continual monitoring of disease progression and allow therapeutic interventions to be evaluated. Four recent reviews have been published of microRNAs in AD, each of which identified areas of weakness or limitations in the reported studies. Importantly, studies in the last three years have shown considerable progress in overcoming some of these limitations and identifying specific microRNAs as biomarkers for AD and mild cognitive impairment. Further large-scale human studies are warranted with less disparity in the study populations, and using an appropriate method to validate the findings.

Cell Biology↗

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

Computational Engineering, Finance, and Science (c↗

High-resolution mapping of nitrogen oxide emissions in large US cities from TROPOMI retrievals of tropospheric nitrogen dioxide columns

Satellite-derived spatiotemporal patterns of nitrogen oxide (NOx) emissions can improve accuracy of emission inventories to better support air quality and climate research and policy studies. In this study, we develop a new method by coupling the chemical transport Model-Independent SATellite-derived Emission estimation Algorithm for Mixed-sources (MISATEAM) with a divergence method to map high-resolution NO x emissions across US cities using TROPOspheric Monitoring Instrument (TROPOMI) tropospheric nitrogen dioxide (NO 2 ) retrievals. The accuracy of the coupled method is validated through application to synthetic NO 2 observations from the NASA-Unified Weather Research and Forecasting (NU-WRF) model, with a horizontal spatial resolution of 4 km × 4 km for 33 large and mid-size US cities. Validation reveals excellent agreement between inferred and NU-WRF-provided emission magnitudes (R= 0.99, normalized mean bias, NMB = —0.01) and a consistent spatial pattern when comparing emissions for individual grid cells (R = 0.88 ± 0.06). We then develop a TROPOMI-based database reporting annual emissions for 39 US cities at a horizontal spatial resolution of 0.05° × 0.05° from 2018 to 2021. This database demonstrates a strong correlation (R= 0.90) with the National Emission Inventory (NEI) but reveals some bias (NMB = —0.24). There are noticeable differences in the spatial patterns of emissions in some cities. Our analysis suggests that uncertainties in TROPOMI-based emissions and potential misallocation of emissions and/or missing sources in bottom-up emission inventories both contribute to these differences.

54 ENVIRONMENTAL SCIENCES↗