Computational Physics
Updating DMD Operators for Changes in Domain Properties
Dimitrios Voulanas and Eduardo Gildin
Fast and reliable surrogate models are critical for optimization, control and uncertainty analysis in geological carbon-storage projects, yet high-fidelity multiphase simulators remain too expensive. Dynamic Mode Decomposition (DMD) offers an attractive data-driven reduction framework, but its operators are trained for a single set of reservoir properties. When permeability or well location changes, conventional practice is to regenerate snapshots and retrain the surrogate, erasing most of the speed advantage. This work presents a lightweight alternative that updates an existing DMD or DMD-with-control model without incorporating new simulation data or retraining. Two complementary update strategies are introduced. For cases where permeability changes uniformly across the domain, the proposed updates adjust the models internal dynamics and control response to match the new flow timescale. When permeability varies in space, the approach modifies the spatial representation so that high-permeability zones are given greater influence on the models reduced basis. Numerical experiments demonstrate that the proposed updates recover plume migration and pressure build-up within three percent of a freshly trained surrogate yet execute hundreds of times faster than full retraining. These methods therefore enable real-time optimization and rapid what-if studies while preserving the physical fidelity demanded by carbon-storage workflows.
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Medical Physics
Referenceless Proton Resonance Frequency Thermometry Using Deep Learning with Self-Attention
Yueran Zhao, Chang-Sheng Mei, Nathan J. McDannold et al. (+2 more)
Background: Accurate
proton resonance frequency (PRF) MR thermometry is essential for monitoring temperature rise during thermal ablation with high intensity focused ultrasound (FUS). Conventional referenceless methods such as complex field estimation (CFE) and phase finite difference (PFD) tend to exhibit errors when susceptibility-induced phase discontinuities occur at tissue interfaces.
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All authors Yueran Zhao, Chang-Sheng Mei, Nathan J. McDannold, Shenyan Zong, Guofeng Shen
History and Philosophy of Physics · Cross-listed from q-bio.NC
Revised comment on the paper titled "The Origin of Quantum Mechanical Statistics: Insights from Research on Human Language
Mikołaj Sienicki and Krzysztof Sienicki
This short note comments on \citet{Aerts2024Origin}, which proposes that ranked word frequencies in texts should be read through the lens of Bose–Einstein (BE) statistics and even used to illuminate the origin of
quantum statistics in physics. The core message here is modest: the paper offers an interesting analogy and an eye-catching fit, but several key steps mix physical claims with definitions and curve-fitting choices. We highlight three such points: (i) a normalization issue that is presented as "bosonic enhancement", (ii) an identification of rank with energy that makes the BE fit only weakly diagnostic of an underlying mechanism, and (iii) a baseline comparison that is too weak to support an ontological conclusion. We also briefly flag a few additional concerns (interpretation drift, parameter semantics, and reproducibility).
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Data Analysis and Statistics · Cross-listed from cs.LG
Softly Symbolifying Kolmogorov-Arnold Networks
James Bagrow and Josh Bongard
Kolmogorov–Arnold Networks (KANs) offer a promising path toward interpretable machine learning: their learnable activations can be studied individually while collectively fitting complex data accurately. In practice, however, trained activations often lack *symbolic fidelity*, learning pathological decompositions with no meaningful correspondence to interpretable forms. We propose Softly Symbolified Kolmogorov–Arnold Networks (S2KAN), which integrate symbolic primitives directly into training. Each activation draws from a dictionary of symbolic and dense terms, with learnable gates that sparsify the representation. Crucially, this sparsification is differentiable, enabling end-to-end optimization, and uses an optimization objective inspired by minimum description length. S2KAN can discover interpretable activation functions while retaining dense splines for flexible approximation. We introduce a quantitative measure of symbolic fidelity, assessing how closely learned activations can be approximated by short expressions from a specified symbolic
language. Across real-world prediction tasks, dynamical-system
forecasting, and synthetic symbolic
benchmarks, S2KAN generally achieves higher symbolic fidelity and often far smaller models, while maintaining competitive predictive accuracy on real-world data and low prediction errors on most symbolic
benchmark configurations. We also examine the models' learned responses on scientific data, including the contributions of their symbolic components. Together, these results show that incorporating symbolic structure during training can yield compact, accurate KAN models whose learned responses can be examined through their symbolic components.
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General Physics
Dual-moon forced dynamics and nonlinear aggregation in Saturn's F ring: From quasi-periodicity to modulated oscillations
Omar El Deeb
We develop a minimal nonlinear model to investigate the oscillatory dynamics of Saturn's F ring under dual-moon forcing from Prometheus and Pandora. The model extends classical predator–prey dynamics by incorporating both a nonlinear mass aggregation term $kM^n$ and explicit dual-frequency forcing, capturing how higher-order coagulation physics interacts with multi-moon perturbations. Through systematic numerical integration and dynamical-systems tools, including time-series, spectral, stroboscopic, and rotation number analysis, we identify distinct dynamical regimes controlled by the parameters $n$ and $k$. For moderate nonlinearity \((n=1.28,k=0.54)\), the numerical diagnostics are consistent with bounded quasiperiodic motion, characterized by smooth amplitude modulation, thin stroboscopic loops, and discrete spectral peaks. For stronger nonlinearity \((n=1.30,k=0.62)\), the same diagnostics indicate a transition toward strongly modulated oscillations, with broadened stroboscopic bands and sideband-rich spectra. A projected rotation-number diagnostic reveals organized regions in parameter space, including smooth quasiperiodic-like domains and near-locking bands analogous to Arnold tongues. Our results show that a reduced deterministic dual-forcing model can generate bounded quasiperiodic-like and strongly modulated aggregation-fragmentation cycles with timescales comparable to relevant moon-ring forcing periods, providing a possible low-dimensional mechanism contributing to F-ring variability.
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Physics and Society
FlockVote: LLM-Empowered Agent-Based Modeling for Simulating U.S. Presidential Elections
Lingfeng Zhou, Yi Xu, Zhenyu Wang et al. (+1 more)
Modeling complex human behavior, such as voter decisions in national elections, is a long-standing challenge for computational social science. Traditional
agent-based models (ABMs) are limited by oversimplified rules, while large-scale statistical models often lack interpretability. We introduce FlockVote, a novel framework that uses Large
Language Models (LLMs) to build a "computational laboratory" of LLM
agents for political simulation. Each
agent is instantiated with a high-fidelity demographic profile and dynamic contextual information (e.g. candidate policies), enabling it to perform nuanced, generative
reasoning to simulate a voting decision. We deploy this framework as a testbed on the 2024 U.S. Presidential Election, focusing on seven key swing states. Our simulation's macro-level results successfully replicate the real-world outcome, demonstrating the high fidelity of our "virtual society". The primary contribution is not only the prediction, but also the framework's utility as an interpretable research tool. FlockVote moves beyond black-box outputs, allowing researchers to probe
agent-level rationale and analyze the stability and sensitivity of LLM-driven social simulations.
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All authors Lingfeng Zhou, Yi Xu, Zhenyu Wang, Dequan Wang
Biological Physics
Nano-capattery: Taming electron traffic for a 367% leap in biohydrogen surge through suppressing competing pathways in photo photo-fermentative system
Muhammad Shahzaib
The electron flux diverts electrons from optimal hydrogen production pathways to competitive pathways, which overall reduces the efficiency of the photo fermentation hydrogen production (PFHP) system. For tackling electron flux and metabolic pathway regulation, a hybrid material (nano-capattery (NC)) was developed based on cobalt-iron-nitrogen doped biochar (Co-Fe-NBC). The NC possessed both the capacitor property (287.91 F/g) and battery-like charge storage 38.3 mC/g with the highest energy density of 159.95 mWh/g. These properties existed due to its Fe2+/Fe3+ and Co2+/Co3+ redox cycle ability, a highly porous surface (291.81 m2/g BET surface area) caused by the defects (AD/AG 3.13) and abundant oxygen vacancies (OVs) observed through electro paramagnetic resonance. During PFHP, there is an 85% reduction in propionic acid, a 65.3% record electron management efficiency, an improved 1.34 NAD+/NADH ratio, along with a 87% increase in dehydrogenase activity, confirming the superior role of NC in efficient regulation of the metabolic pathway and electron flux management. These exceptional properties of biochar-based NC raised the cumulative hydrogen production from 151.03 mL (control) to 589.54 mL, which was an enormous increase of 367%.
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Atmospheric and Oceanic Physics
The Iris Illusion in the Tropical Sky Seen Through Two Decades of Aura MLS Ice Water Contents
Yiguo Zhang
I analyzed ice water content (IWC) data from the Aura Microwave Limb Sounder (MLS) and sea surface temperature (SST) data from NOAA's Optimum Interpolation SST (OISST) product from 2004 to 2024. Using these data, I derived monthly infrared (IR) leakage over the tropics and computed derivatives of both the IR leakage and tropical SST time series from 2005 to 2023. These two derivatives produced a Pearson correlation of -0.49, indicating that IR leakage decreases when SST increases. This behavior contradicts the trend predicted by the Iris hypothesis, suggesting that tropical cirrus clouds strengthen, rather than weaken, as the ocean warms.
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General Physics
CP-violating non-linear electrodynamics and corrections to blackbody radiation thermal laws
L.P.R. Ospedal, R. Turcati and S.B. Duarte
Motivated by ideas from effective field theories, we conduct a twofold investigation in CP-violating non-linear electrodynamics models. On the one hand, features related to field equations and wave propagation in the presence of a
magnetic background field are evaluated. Interestingly, we show that the CP-violating term in our framework induces a bi-anisotropic behavior of the
vacuum. On the other hand, blackbody radiation thermal laws in this situation are studied. Here, we provide a general formalism for
photons at low temperature, namely, with $k_{B}T\ll{m_{e}c^{2}}$. The deviations from standard values of the thermodynamic quantities, such as energy, pressure,
entropy, and specific heat, are discussed. In addition, we investigate the modifications in the Planck distribution and the Stefan-Boltzmann law induced by a non-trivial CP-violating parameter.
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Physics and Society
Roullete curves, coin paradox and Aristotle's wheel paradox
Osvaldo L. Santos-Pereira
This work discusses the concept of roulette, the generated curves that occur when one curve rolls without slipping along another, tracing the path of a fixed point. The coin paradox and Aristotle's wheel paradox are used as pedagogical motivations to discuss the parametric equations of epicycloids and hypocycloids, providing a geometrical intuition for the mathematical derivations and computational implementation of those curves. Python code is provided to motivate the application of the derived parametric equations, resulting in concrete visualizations and animations.
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Chemical Physics
An algorithm for atom-centered lossy compression of the atomic orbital basis in density functional theory calculations
Anthony O. Lara, Justin J. Talbot, Zhe Wang et al. (+1 more)
Large atomic-orbital (AO) basis sets of at least triple and preferably quadruple-
zeta (QZ) size are required to adequately converge Kohn-Sham density functional theory (DFT) calculations towards the complete basis set limit. However, incrementing the cardinal number by one nearly doubles the AO basis dimension, and the computational cost scales as the cube of the AO dimension, so this is very computationally demanding. In this work, we develop and test a natural atomic orbital (NAO) scheme in which the NAOs are obtained as eigenfunctions of atomic blocks of the density
matrix in a one-center orthogonalized representation. The NAO representation enables one-center compression of the AO basis in a manner that is optimal for a given threshold, by discarding NAOs with occupation numbers below that threshold. Extensive tests using the Hartree-Fock functional suggest that a threshold of $10^{-5}$ can yield a compression factor (ratio of AO to compressed NAO dimension) between 2.5 and 4.5 for the QZ pc-3 basis. The errors in relative energies are typically less than 0.1 kcal/mol when the compressed basis is used instead of the uncompressed basis. Between 10 and 100 times smaller errors (i.e., usually less than 0.01 kcal/mol) can be obtained with a threshold $10^{-7}$, while the compression factor is typically between 2 and 2.5.
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All authors Anthony O. Lara, Justin J. Talbot, Zhe Wang, Martin Head-Gordon
Physics and Society
A Survey on Centrality and Importance Measures in Hypergraphs: Categorization and Empirical Insights
Jaewan Chun, Fanchen Bu, Yeongho Kim et al. (+3 more)
Identifying central entities and interactions is a fundamental problem in network science. While well-studied for graphs (pairwise relations), many biological and social systems exhibit higher-order interactions best modeled by hypergraphs. This has led to a proliferation of specialized hypergraph centrality measures, but the field remains fragmented and lacks a unifying framework. This paper addresses this gap by providing the first systematic survey of 39 distinct measures. We introduce a novel taxonomy classifying them as: (1) structural (
topology-based), (2) functional (impact on system dynamics), or (3) contextual (incorporating external features). We also present an experimental assessment comparing their empirical similarity and computation time. Finally, we discuss applications, establishing a coherent roadmap for future research in this area.
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All authors Jaewan Chun, Fanchen Bu, Yeongho Kim, Atsushi Miyauchi, Francesco Bonchi, Kijung Shin
Fluid Dynamics
Learning with Physical Constraints
Miguel A. Mendez, Jan van Den Berghe, Manuel Ratz et al. (+2 more)
This chapter provides three tutorial exercises on physics-constrained regression. These are implemented as toy problems that seek to mimic grand challenges in (1) the super-resolution and data assimilation of the velocity field in image velocimetry, (2) data-driven
turbulence modeling, and (3) system identification and digital twinning for
forecasting and control. The Python codes for all exercises are provided in the course repository.
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All authors Miguel A. Mendez, Jan van Den Berghe, Manuel Ratz, Matilde Fiore, Lorenzo Schena
Medical Physics · Cross-listed from cs.DC
Accelerating mesh-based Monte Carlo simulations using contemporary graphics ray-tracing hardware
Shijie Yan, Douglas Dwyer, David R. Kaeli et al. (+1 more)
Significance: Monte Carlo (MC) methods are the gold-standard for modeling light-tissue interactions due to their accuracy. Mesh-based MC (MMC) offers enhanced precision for complex tissue structures using tetrahedral mesh models. Despite significant speedups achieved on graphics processing units (GPUs), MMC performance remains hindered by the computational cost of frequent ray-boundary intersection tests. Aim: We propose a highly accelerated MMC
algorithm, RT-MMC, that leverages the hardware-accelerated ray traversal and intersection capabilities of ray-tracing cores (RT-cores) on modern GPUs. Approach: Implemented using NVIDIA's OptiX platform, RT-MMC extends graphics ray-tracing pipelines towards volumetric ray-tracing in turbid media, eliminating the need for challenging tetrahedral mesh generation while delivering significant speed improvements through hardware acceleration. It also intrinsically supports wide-field sources without complex mesh retesselation. Results: RT-MMC demonstrates excellent agreement with traditional software-ray-tracing MMC
algorithms while achieving 1.5x to 4.5x speedups across multiple GPU architectures. These performance gains significantly enhance the practicality of MMC for routine simulations. Conclusion: Migration from software- to hardware-based ray-tracing not only greatly simplifies MMC simulation workflows, but also results in significant speedups that are expected to increase further as ray-tracing hardware rapidly gains adoption. Adoption of graphics ray-tracing pipelines in quantitative MMC simulations enables leveraging of emerging hardware resources and benefits a wide range of biophotonics applications.
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All authors Shijie Yan, Douglas Dwyer, David R. Kaeli, Qianqian Fang
Fluid Dynamics
Effect of cross-sectional anisotropy on shock train dynamics in supersonic internal flows
Jagmohan Singh and Venkat Raman
This study investigates the effect of duct aspect ratio ($AR$), defined as the ratio of major to minor axis in an elliptical duct, on shock train dynamics for a freestream Mach number of 2.1. The aspect ratio $AR$ is varied from 1.0 to 3.0 while maintaining a constant cross-sectional area and identical upstream conditions, thereby ensuring the same inlet mass flow and nearly constant boundary-layer-induced blockage across all $AR$. This isolates shape-induced confinement effects. Simulations are performed using an embedded-boundary method with adaptive mesh refinement which enabled a finest resolution of 48$\mu$m resolving the shocks in the shock train. The results show that increasing $AR$ significantly modifies the shock train morphology. The number of discrete shock
cells decreases, and the leading shock front elongates along the major axis while contracting along the minor axis. The normal shock stem prominent in the circular duct (AR=1.0) nearly disappears at AR=3.0. Despite these morphological changes, the wall-pressure trace and stagnation-pressure loss remain largely insensitive to $AR$. These results indicate that while duct cross-section governs the detailed shock train structure, the overall efficiency of flow deceleration and pressure recovery is dictated primarily by the effective blockage imposed by the turbulent boundary layer, rather than the aspect ratio itself for a given mass flow rate and pressure ratio across the pseudo shock.
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Instrumentation and Detectors
Initial Assessment of Second Generation of Large-Area Picosecond Photodetectors with Multi-Channel Systems-on-a-Chip Readout
V. A. Li, O. A. Akindele, M. Bondin et al. (+4 more)
We first briefly describe the history and motivation behind Cherenkov and scintillation light detection. We then discuss the instrumentation needed to detect these
photons as it applies to both photodetectors and readout electronics. One of the motivations is future large
neutrino detectors that could in principle differentiate between Cherenkov and scintillation light if using novel water-based scintillators. In this paper, we present the first measurements utilizing the second generation of Large Area Picosecond Photodetectors (LAPPDs) in conjunction with commercial system-on-a-chip readouts from Nalu Scientific – specifically, the High Density System on Chip (HDSoC) and Advanced ASoC Rapid Digitizer, Variable Adaptive Readout Chip (AARDVARC) platforms. These state-of-the-art full-waveform digitizers feature sampling rates on the order of 1 and 10 samples per nanosecond, respectively. Using a picosecond
laser, we measured the timing jitter between a pair of LAPPD channels, demonstrating the potential of this setup for precise timing applications.
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All authors V. A. Li, O. A. Akindele, M. Bondin, S. R. Durham, J. A. Foot, M. J. Ford, S.-W. Stradleigh
Computational Physics · Cross-listed from cond-mat.mtrl-sci
Cosserat micropolar and couple-stress elasticity models of flexomagnetism at finite deformations
Adam Sky, David Codony, Stephan Rudykh et al. (+3 more)
We propose geometrically nonlinear (finite) continuum models of flexomagnetism based on the Cosserat micropolar and its descendent couple-stress theory. These models introduce the magneto-mechanical interaction by coupling the micro-dislocation tensor of the micropolar model with the magnetisation vector using a Lifshitz invariant. In contrast to conventional formulations that couple strain-gradients to the magnetisation using fourth-order tensors, our approach relies on third-order tensor couplings by virtue of the micro-dislocation being a second-order tensor. Consequently, the models permit centrosymmetric materials with a single new flexomagnetic constant, and more generally allow cubic-symmetric materials with two such constants. We postulate the flexomagnetic action-functionals and derive the corresponding governing equations using both scalar and vectorial
magnetic potential formulations, and present numerical results for a nano-beam geometry, confirming the physical plausibility and computational feasibility of the models.
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All authors Adam Sky, David Codony, Stephan Rudykh, Andreas Zilian, Stéphane P. A. Bordas, Patrizio Neff
Popular Physics
Megastructures of type-III civilizations orbiting galaxies
Zaza N. Osmanov
The article discusses the possibility of a Type-III extraterrestrial civilization constructing megastructures around a
galaxy in regions where the
galactic radiation becomes indistinguishable from the CMB radiation. For a Milky Way-like
galaxy, we estimated the corresponding distance from its center at which a
solar mass megastructure would need to be placed. We also showed that, from an energetic standpoint, placing such a massive object into orbit poses no fundamental difficulties. The detectability of the megastructure was also addressed.
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Fluid Dynamics
U Net LSTM with incremental time-stepping for robust long-horizon unsteady flow prediction
Blaise Madiega and Mathieu Olivier
Transient computational fluid dynamics (CFD) remains expensive when long horizons and multi-scale
turbulence are involved. Data-driven surrogates promise relief, yet many degrade over multiple steps or drift from physical behavior. This work advances a hybrid path: an incremental time-stepping U Net LSTM model that forecasts unsteady dynamics by predicting field updates rather than absolute states. A U-Net encoder decoder extracts multi-scale spatial structures, LSTM layers carry temporal dependencies, and the network is trained on per-step increments of the physical fields, aligning learning with classical time marching and reducing compounding errors. The model is designed to slot into solvers based on projection methods (such as SIMPLE, PISO, etc), either as an initializer that delivers a sharper first guess for pressure-velocity coupling or as a corrective module that refines provisional fields. Across representative test cases, the approach improves long-term stability (54.53 to 84.21 % reduction of cumulative errors) and preserves engineering metrics, integral and averaged quantities, more reliably than standard learning baselines. These properties make it a plausible component of hybrid CFD-ML pipelines designed to accelerate unsteady simulations without compromising quantitative fidelity.
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Chemical Physics · Cross-listed from cond-mat.mtrl-sci
Mechanisms for the Formation of Active Sites in Single-Atom Alloys
Ioannis Karageorgiou, Angelos Michaelides and Fabian Berger
Reactive dopant atoms embedded in inert host metal surfaces define the active sites in single-atom
alloys (SAAs), yet SAA synthesis remains challenging. To address this, we elucidate how dopant adatoms deposited on Cu and Ag surfaces become incorporated into the metal and identify periodic trends from early to late transition metals (TMs) using density functional theory. Adatoms diffuse nearly freely across terraces, as
diffusion barriers are small, whereas direct incorporation into terraces is unfavourable. In line with conventional wisdom, step edges and kink sites strongly facilitate dopant incorporation, confirming their critical role in
alloy formation. Attachment of adatoms to steps and kinks from the lower terrace is favoured. Incorporation then proceeds either from this attached state or when adatoms approach a step edge from above, where reactions often proceed without barrier. Incorporation barriers are generally lower for early and central TMs, increase towards late TMs, and are slightly higher on Cu than on Ag surfaces. Repulsive interactions between Pd adatoms and dopants explain the experimental observation that a dopant-rich brim on the upper terrace of Cu surfaces inhibits incorporation from above. In contrast, attractive interactions, as found for Ru, anchor diffusing adatoms (even on terraces) and promote the formation of adatom islands, yet hinder incorporation next to the dopant and may impede the growth of embedded dopant clusters. By rationalising periodic trends and experimental observations, we show how specific surface sites and adatom–dopant interactions shape dopant incorporation, offering guidance on the surface environments most conducive to SAA synthesis for different dopant elements.
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Fluid Dynamics · Cross-listed from cond-mat.soft
Inferring Surface Slip in Active Colloids from Flow Fields Using Physics-Informed Neural Networks
Parvin Bayati and Stewart A. Mallory
The directed motion of active colloids is governed by spatial variations in surface chemistry and interfacial stress, yet these properties remain extremely difficult to measure directly. We introduce a physics-informed neural network framework that infers the slip distribution driving propulsion from partial observations of the surrounding flow. By combining sparse fluid velocity measurements with the Stokes equations and boundary constraints, the method reconstructs both the near-surface slip and the full velocity and pressure fields. Validation against analytical solutions and Boundary Element Method calculations for canonical active colloid models shows quantitative agreement in both unbounded and confined geometries. Crucially, the framework recovers the surface slip even when no flow data are available near the particle, demonstrating that accessible bulk measurements encode the interfacial stresses responsible for active motion. These results establish physics-informed inference as a powerful tool for characterizing and ultimately controlling interfacially driven transport in colloidal active matter.
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