Instrumentation and Detectors
Multi-scale reconstruction of single-ion damage tracks in diamond via nitrogen-vacancy centers
Daniel G. Ang, Jiashen Tang, Maximilian Shen et al. (+9 more)
Understanding particle-induced damage tracks in solid-state materials underpins emerging applications in rare-event detection and
quantum defect engineering. Resolving these tracks requires multi-scale readout, from event localization at the millimeter scale to track-morphology reconstruction at the nanoscale. Nitrogen-vacancy (NV) centers in diamond provide such a platform, combining optical localization with
quantum sensing of track morphology. Here, we implant sub-MeV carbon ions into nitrogen-rich diamond and detect individual
recoil events via spatially localized NV formation. We develop a simulation framework that explains the observed NV yield and predicts that directional information is retained in the NV distribution after annealing. Machine learning further recovers much of the information lost to defect
diffusion and limited NV yield, improving head-tail classification to a level comparable to pre-annealed vacancy tracks. Measurements of NV
spin coherence indicate compatibility with nanoscale track reconstruction via NV strain mapping and
magnetic gradient-based techniques. These results identify promising pathways toward NV-diamond directional detectors for rare events, while the track-modeling framework has broader implications for paleodetection and
quantum material synthesis.
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All authors Daniel G. Ang, Jiashen Tang, Maximilian Shen, Michael Titze, Gavishta Liyanage, Jordan Chapman, Chinmay Bharathulwar, Andrew T. Gilpin, Tanguy Terlier, Edward S. Bielejec, Vsevolod Ivanov, Ronald L. Walsworth
Biological Physics · Cross-listed from cond-mat.stat-mech
Thermodynamic inference from noisy single-molecule time series
Todd R. Gingrich, Oleg A. Igoshin, Anatoly B. Kolomeisky et al. (+1 more)
Single-molecule or single-particle tracking measurements inherently yield noisy microscopic trajectories, often significantly constrained by the diffraction limit and by the finite rate at which
photons are emitted and counted. Here we study systematically the resulting effects of finite spatial and temporal resolution on one's ability to discern and quantify the arrow of time in microscopic trajectories. Given an experimental time series Y(t) degraded by noise, we consider the problem of estimating the
entropy production associated with the corresponding microscopic variable X(t) using two strategies. The first attempts to infer the statistical properties of X(t) from those of Y(t) before estimating the
entropy production. The second uses the experimental observable as a proxy for the true microscopic observable, with the
entropy production
estimator applied directly to Y(t). We prove that both strategies result in lower bounds on the true
entropy production. Importantly, noise-degraded observables Y(t) undergo non-Markovian dynamics even when X(t) are Markovian, and non-Markovian
entropy production
estimators are advantageous. We further note nontrivial interplay between spatial and temporal resolution: in the presence of detection noise, improving the temporal resolution alone may lead to poorer rather than better
entropy production estimates.
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All authors Todd R. Gingrich, Oleg A. Igoshin, Anatoly B. Kolomeisky, Dmitrii E. Makarov
Physics and Society
One country, multiple portraits: representativeness in GPS-based mobility data is source-specific and spatially dependent
Carmen Cabrera, Francisco Rowe, Miguel González-Leonardo et al. (+3 more)
Anonymised GPS-based mobile phone data are increasingly used to estimate population distribution and human mobility, supporting applications across disaster response, public health, urban planning and migration research. Yet whether these data fairly represent the populations they describe, particularly outside high-income countries, remains poorly understood. We quantify coverage bias for 2,478 municipalities in Mexico by comparing population estimates from a single-platform source (Facebook) and a multi-app aggregator (Veraset) against the 2020 Mexican Population Census. We find that the magnitude and spatial distribution of coverage bias differ substantially across sources. Facebook provides higher and more evenly distributed coverage, whereas the multi-app data concentrate users in larger, wealthier and more digitally connected places. Coverage bias is also spatially structured, with neighbouring municipalities showing similar levels of over- or under-coverage. Using explainable machine learning, we show that digital access and material resources are the dominant drivers of bias for the multi-app data, while demographic and population structure dominate for Facebook. Explicitly modelling spatial dependence improves the performance of statistical models for explaining bias and reveals that an appreciable share of spatial variation remains unexplained by observed
covariates. These findings show that coverage bias is source-specific and spatially dependent, and provide a foundation for adjustments that improve the representativeness of mobile phone data in unequal, data-scarce settings.
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All authors Carmen Cabrera, Francisco Rowe, Miguel González-Leonardo, Juan Ignacio Vilchis-García, Elisa Omodei, Maribel Hernández-Rosales
Applied Physics · Cross-listed from cond-mat.mtrl-sci
Data analysis methods for powder x-ray diffraction intensity under laser-driven dynamic compression at Omega and NIF laser facilities
Marius Millot, Federica Coppari, Amy Lazicki et al. (+1 more)
Powder x-ray diffraction (PXRD) under
laser-driven dynamic compression is a powerful tool to investigate material response to extreme pressure, temperature and strain rates. Robust PXRD platforms have been developed at kJ and MJ
laser facilities worldwide including the Powder X-Ray Diffraction Image Plate (PXRDIP) at the Omega
Laser Facility at the Laboratory for
Laser Energetics (LLE) and the TARget Diffraction In Situ (TARDIS) at the National Ignition Facility (NIF). Here we present further developments of data analysis methods focused towards improving the fidelity of the PXRD intensity determination for these platforms. We illustrate these methods by discussing how they can be implemented in a data analysis package and applied to shock compression data on diamond near 1 TPa. We discuss using the XRD signal from the collimating pinhole or a layer of un-compressed material in the sample package as in-situ references for XRD intensity. We detail how to compare data collected with different x-ray sources and how to account for thermal damping of XRD signal when comparing XRD from a shock-compressed, hot material with the reference material at ambient.
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All authors Marius Millot, Federica Coppari, Amy Lazicki, Jon H. Eggert
Biological Physics
Electrochemical DNA Hairpin Sensors for Differentiating Small Molecule Intercalation from Minor Groove Binding
Kiara Thompson, Kian Barnes, Saron Yoseph et al. (+5 more)
Small molecule double-stranded DNA intercalators have significant potential for therapeutic applications. However, screening for and confirming a drug candidate's intercalative behavior remains labor-intensive and costly. To address this, we investigated the sequence and biophysical parameters that affect the performance of electrochemical DNA hairpin sensors for streamlined identification of structural intercalators. These sensors utilize oligonucleotide (oligo) sequences that form hairpins upon intercalator binding. The 3
prime end of the oligo is modified with alkylthiol linkers for gold electrode surface monolayer self-assembly, while the 5
prime end carries a methylene blue redox reporter. Hairpin formation enhances electron transfer between methylene blue and the gold electrode, which can be detected via voltammetry. We tested seven hairpin structures varying in stem length and sequence. Our optimal oligo, HP4, features a four-base-pair stem and responds to five DNA intercalators over a broad detection range, with EC50 in close agreement with published affinity (KD) values for these interactions. We further demonstrate HP4s ability to discriminate intercalator binding from a series of minor groove binders through significant differences in signal gain upon incubation. Altogether, our strategy establishes a platform for identifying intercalative compounds that should support the development of DNA-targeting therapeutics.
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All authors Kiara Thompson, Kian Barnes, Saron Yoseph, Vincent Clark, J.D. Mahlum, Ananya Majumdar, Philip S Lukeman, Netzahualcóyotl Arroyo-Currás
Optics · Cross-listed from cs.NI
Protection Switching in Hybrid Hollow-Core and Single-Mode Fiber Networks: Challenges, Analysis, and Mitigation Strategies
Md Ghulam Saber and Zhiping Jiang
Hollow-core fibers (HCF) are transitioning from laboratory curiosities to production-deployed infrastructure, with cloud providers operating thousands of kilometers of hollow-core links. As operators upgrade their networks, working and protection paths will inevitably traverse different fiber types, creating a class of protection switching challenges absent in homogeneous single-mode fiber networks. This article provides a comprehensive overview of these challenges and presents a comparative analysis of protection switching under two architectures - 1+1 dedicated and shared backup path protection (SBPP) - in hybrid hollow-core and single-mode fiber networks. Using Monte Carlo simulation with random per-link fiber assignment across six reference
topologies (1,602 node pairs), we quantify chromatic dispersion (CD) steps, generalized signal-to-noise ratio (GSNR) penalties, and modulation-format degradation for both architectures. At 50% HCF deployment mean CD steps range from 4,000 to 22,000 ps/nm, with GSNR penalties of 1.6-3.1 dB and 38-59% of node pairs requiring modulation downgrade under 1+1 protection. A complementary cross-fiber extreme analysis reveals that the two switching directions are fundamentally asymmetric: HCF-to-SMF switching doubles the CD step and inflicts about a 10 dB GSNR penalty while SMF-to-HCF switching delivers a negative GSNR penalty (the protection path is higher quality than the working path). SBPP shows up to 7% higher CD steps and 4 percentage points more downgrade in sparsely connected
topologies due to its greedy shortest-first path selection. Capacity retention improves with HCF penetration for both architectures, reaching 85-99% at full HCF deployment. We present mitigation strategies including DSP pre-loading, spectral pre-equalization, and network planning guidelines, concluding that 1+1 dedicated protection is preferable to SBPP for hybrid deployments.
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Accelerator Physics
SuperCond-GNN: Scalable Graph Neural Network Surrogate for Superconducting Circuit Simulations
Nandana Menon and Giorgio Vallone
This paper presents SuperCond-GNN, a graph neural network-based surrogate model for predicting the voltage distribution in high-temperature superconducting (HTS) magnets. HTS magnets are modeled as lumped-element equivalent
circuits and mapped onto graph representations, enabling message passing GNNs to learn the electrical response as a function of
circuit topology, material properties, and operating current. As a proof of concept, tape stacks of up to 10 tapes are considered across a range of
circuit topologies and operating conditions. The surrogate is trained on data generated from
circuit simulations and achieves a mean MAPE of 4.3 % within the prescribed design space. The predicted nodal voltages enable fast and scalable inference of current redistribution and local operating conditions across a wide range of
circuit configurations. The effect of incorporating physics-informed regularization via Kirchhoff's current law is also evaluated, and generalizability to unseen
topologies is assessed through zero-shot inference and few-shot fine-tuning. While demonstrated on tape stack
circuits, the graph-based framework is
topology-agnostic and naturally extensible to more complex HTS cable and magnet configurations, offering a scalable alternative to conventional
circuit solvers for downstream applications such as design space exploration, current sharing analysis, and real-time magnet monitoring.
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Instrumentation and Detectors
HeteroViT: A Versatile Single-Layer Vision Transformer Concept, Co-Designed for Distributed Real-Time Data Reduction on Scientific Detectors
Abhilasha Dave, Weijian Zheng, Antonino Miceli et al. (+3 more)
Next-generation X-ray detectors generate data faster than any system can affordably store or process. LCLS-II, the upgraded Linac Coherent Light Source at SLAC, produces data on the order of terabytes per second, with raw-data transfer and storage projected to be prohibitively costly, even though much of the data is not scientifically useful. This concept paper focuses on two major points. The first is versatility: a deliberately tiny, single-layer
Vision Transformer (ViT) is enough to serve distinct scientific quick-evaluation tasks. We demonstrate this on two very different problems: (a) a supervised hit/miss/maybe classification on the CSPAD
dataset, made to resemble ePixUHR-like detector frames, and (b) a self-supervised latent space for rare-event detection in X-ray diffraction spanning two learning paradigms, two output types, and two detector modalities, with one small backbone. The second is hardware co-design: because the ViT's blocks are structurally uniform, the model maps cleanly onto the heterogeneous hardware already present in the LCLS detector pipeline (ASIC -> FPGA -> GPU) under a simple rule one ASIC is one
token so the data is reduced progressively at each stage and a keep/discard decision is produced in real time at the edge. The two claims reinforce each other: versatility is precisely what justifies freezing the front-end in silicon, since a reusable front-end is only worth committing to hardware if it serves many tasks. We are explicit that this is a concept supported by early software analysis, not a hardware demonstration. The natural and primary next phase is the hardware implementation of this distributed pipeline. The decisive evidence still owed an end-to-end latency budget, ASIC feasibility of the in-sensor
embedding, and the false-negative behavior that matters for a data veto defines that program. HeteroViT is our first step toward it.
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All authors Abhilasha Dave, Weijian Zheng, Antonino Miceli, Dionisio Doering, Ryan Herbst, Angelo Dragone
Atomic Physics · Cross-listed from quant-ph
Structure and information measures of few-electron systems under a spherically symmetric Gaussian potential within a density functional approach
Raveena Arya, Santanu Mondal and Amlan K. Roy
Energies of H, He-like ($Z=2-18$) ions, Li, and Be are investigated under a spherically symmetric Gaussian potential through a density functional formalism. The radial Kohn-Sham equation has been solved by invoking a work function-based exchange potential. The effect of electron correlation is analyzed by incorporating two functionals: a local parameterized Wigner functional and a non-linear gradient- and
Laplacian-dependent Lee-Yang-Parr (LYP) functional. The generalized pseudospectral method is employed to provide accurate numerical eigenfunctions and
eigenvalues. This allows nonuniform, optimal spatial discretization fulfilling the Dirichlet boundary conditions. This work demonstrates a possible manipulation of energy by controlling dot parameters. Apart from ground states, exploratory results are also reported for low-lying excited state $1s2s$ ($^{1,3}S$) of He atom. Companion calculations are also performed for various information-theoretic measures, such as Shannon
entropy in position ($S_{r}$), momentum ($S_{p}$) spaces, and Fisher information in position space ($I_{r}$). The behavior of correlation functionals in presence of Gaussian potential is examined critically. We find that energy increases, $S_{r}$ exhibits minima, while $S_{p}$, $I_{r}$ attain maxima for a decrease in the width of potential, whereas an increase in potential depth further amplifies these effects across all properties. The Fisher-Shannon plane reveals a progressive localization as well as the compression of electronic density, and thereby indicates a weakening of relative electron-correlation effects. In the Collin's
conjecture, it gives rise to a non-linear loop-like feature. Much of the results are presented here for the first time.
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Physics and Society · Cross-listed from cs.SI
Direct and Indirect Influence on Likes in Social Media
Ivan Kozitsin and Anton V. Proskurnikov
The present study investigates direct and indirect social contagion mechanisms in an online social network environment. Using a large-scale
dataset comprising approximately 290,000 users from the VKontakte platform, we examine the factors associated with the probability that a user likes a post. Our analysis shows that, while demographic and structural characteristics of individual nodes, such as gender and degree, contribute to the observed dynamics, the strongest associations arise from activity in the user's local network. In particular, active nodes (users who have already liked the post) at distances d = 1 and d = 2 play a central role in shaping liking behavior. We find a substantial association between second-order activity and liking probability, which persists even in the absence of active direct neighbors and is consistent with indirect influence pathways in the network. No significant association is detected for nodes at distance three or beyond. The results also support the structural diversity hypothesis: the number of connected components among active friends is a significant predictor of liking.
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Atomic Physics · Cross-listed from cond-mat.quant-gas
A dipolar Bose-Bose mixture of Dysprosium isotopes with controllable interspecies interactions
M. Duerbeck, L. Reihs, J.P. Marulanda-Serna et al. (+5 more)
We report on the realization of a
quantum-degenerate Bose-Bose mixture of 162Dy and 164Dy. Owing to the near-identical mass and polarizability of the two isotopes, the mixture thermalizes efficiently, with evaporation trajectories closely following those of the single-isotope case. Using a broad interspecies Feshbach resonance, we explore a miscible-immiscible transition between the two Bose-Einstein condensates. The tunability of the interspecies interaction, combined with the large
magnetic dipole moment of Dy, makes this platform well suited for exploring dipolar effects in ultracold mixtures, including multi-component supersolidity.
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All authors M. Duerbeck, L. Reihs, J.P. Marulanda-Serna, B. Choudhari, J. Seifert, N. Werum, G. Meijer, G. Valtolina
Optics
System-Level Limits of Higher-Order QAM in Hollow-Core Fiber Systems
Md Ghulam Saber and Zhiping Jiang
Hollow-core fiber (HCF) is widely expected to enable higher-order quadrature amplitude modulation (QAM) because of its near-
vacuum Kerr nonlinearity and higher launch power. We develop a per-channel effective signal-to-noise ratio (SNR) budget that combines, in reciprocal form, optical-link impairments including amplified spontaneous emission, Kerr nonlinear interference (NLI), inter-modal interference (IMI), pigtail NLI, and CO2 gas absorption; a parameterized, symbol-rate-dependent transceiver back-to-back SNR ceiling determined by effective-number-of-bits at rate, analog bandwidth, and Tx/Rx nonlinearity; and the remaining transceiver and line impairments, including
laser phase noise, equalization-enhanced phase noise, timing jitter, polarization-dependent loss, and amplifier gain ripple with filter narrowing, each expressed as an equivalent SNR floor. The central result, at a representative 64GBaud system with 75GHz channel spacing over 6THz, is that once HCF removes the fiber limits, the transceiver ceiling rather than the fiber sets the achievable modulation order: a roughly 25dB ceiling at 64GBaud makes 1024-QAM and above infeasible on either fiber, confining ultra-high-order QAM to low baud rates. HCF therefore provides its main advantage in reach and achievable baud rate at a given modulation order: at an IMI coefficient of kappa=-55dB/km, 256-QAM reach increases from about 45km to about 170km and 64-QAM reach from about 415km to about 2275km when moving from single-mode fiber to HCF. In the C-band, CO2 absorption lines are weak and sparse, so channels placed away from the lines follow the gas-free baseline, while only worst-case placements lose reach at long distances. In the L-band, the stronger absorption bands are denser than the channel bandwidth, making line avoidance spectrally costly, and a channel placed on a line loses one to two QAM orders.
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Fluid Dynamics
Scaling patch analysis of turbulent kinetic energy budget equation in wall-bounded flows
Tie Wei, Zhaorui Li and Sergio Pirozzoli
The scaling patch approach is applied to analyze the turbulent kinetic energy (TKE) budget equation in wall-bounded turbulent flows. The balance of the TKE equation is divided into several distinct regions, or scaling patches, each characterized by a dominant balance among the governing terms and its own appropriate scaling parameters. In the near-wall viscous sublayer, the TKE balance is primarily between viscous
diffusion and dissipation, and the characteristic scales are set by the kinematic viscosity and the wall dissipation rate. The thickness of this sublayer is on the order of the Kolmogorov length scale. Moving away from the wall, the peak TKE production provides a natural reference scale for the inner layer, yielding the traditional inner scaling. Grouping the viscous
diffusion and dissipation terms in the inner layer enhances the collapse across different Reynolds numbers. In the outer region, Prandtl's mixing-length model is used to derive a characteristic scale for TKE production. A new meso-scaling is further introduced to describe the intermediate region, ensuring a smooth transition between the inner and outer layers. The scaling patch framework offers a unified interpretation of the structure and scaling behavior of the TKE budget across all regions of wall-bounded
turbulence.
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Optics
Hollow-Core Fiber in Direct-Detection Optical Networks: Technology Readiness, Deployment Drivers, and Adoption Outlook
Md Ghulam Saber and Zhiping Jiang
This paper presents a comprehensive analysis of hollow-core fiber (HCF) for intensity-modulation and direct-detection (IMDD) optical networks, covering fiber-level physics, system-level performance, and deployment economics. We quantify the three principal advantages of anti-resonant HCF over standard single-mode fiber (SMF) for IMDD: (i) chromatic dispersion of 2-4 ps/(nm km) versus 17 ps/(nm km), which shifts the first dispersion-induced power-fading null from about 10 GHz to 20-28 GHz at 40 km, extending the dispersion-limited reach by 4-8x; (ii) a nonlinear coefficient approximately 1,000x lower than silica, permitting launch powers of +10 to +20 dBm and yielding 7-17 dB of additional link budget; and (iii) a group index near unity (ng about 1.003), reducing propagation latency by 31%. We further analyze inter-modal interference (IMI) as the dominant impairment for HCF-based IMDD. We show that differential modal attenuation (DMA) exceeding 12 dB/km suppresses IMI-induced crosstalk below the -30 dB multipath interference threshold required for PAM4. The reduced dispersion also lowers the required feed-forward equalizer (FFE) tap count by 3-6x, directly decreasing noise enhancement penalty and DSP complexity. A deployment cost model across five application scenarios - intra-data center, campus DCI, metro DCI, 5G fronthaul, and PON - reveals that fiber cable constitutes only 5-10% of outside-plant deployment cost, and that coherent transceiver avoidance savings of $1000 to $2000 per transceiver can offset the current HCF premium at metro distances. We provide a technology adoption roadmap indicating that HCF is economically justified now for intra-DC and campus DCI, with metro DCI following in 2027-2030 as manufacturing costs continue to decline.
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Physics Education
Analysis of quantum-related courses and textbooks for potential integration of quantum sensing
Namitha Pradeep and Ben Zwickl
The second
quantum revolution is driving advancements in
quantum computing, communication, and sensing. While
quantum computing has gained significant
attention in education,
quantum sensing remains largely overlooked. In order to find ways of integrating sensing into existing
quantum-related curricula, we performed an analysis of six of the most commonly used textbooks in modern physics,
quantum mechanics, and
quantum computing. We identified a set of keywords related to
quantum sensing and tagged all excerpts in which these concepts appeared. For each excerpt, we also recorded the context in which it was presented within the textbook. Network maps were constructed to visualize which keywords appeared in which contexts and the frequency of these occurrences within each subject area. We then developed an analytic rubric to evaluate the conceptual and mathematical depth of these excerpts as well as the extent of sensing-related discussions. Our results show that there is significant variation in how different subjects address these concepts, both in the nature of the content covered and the depth of coverage. We also observe notable differences in how
spin-first and position-first textbooks discuss these keywords, particularly in the coverage and contexts in which core concepts such as superposition and
entanglement appear. Additionally, we analyzed course titles and descriptions from a database of over 8,000
quantum-related courses, focusing on those that mentioned “sensing” or “sensor”. Together, these analyses of textbook content and course descriptions inform the
quantum information science and engineering education community about potential opportunities to integrate
quantum sensing topics into
quantum-related courses in physics and adjacent disciplines.
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Optics
Fractality-induced photonic topological insulators
Shuming Zhang, Zhaoxin Wu, Lumen Eek et al. (+2 more)
Fractal
lattices have recently emerged as a promising setting for topological wave physics, but in most realizations the topological character is inherited from externally engineered couplings, gauge fields, or temporal modulation rather than from the fractal geometry itself. Here, we experimentally realize a photonic higher-order topological
insulator in which the
topology is induced solely by the self-similar geometry of a Sierpiński-gasket
lattice. Following the isospectral reduction method recently proposed by Eek et al.~\cite{Eek2025}, we show that the fractal waveguide array with uniform nearest-neighbor couplings can be mapped onto an effective breathing Kagome model that supports corner states. We selectively excite these modes with a weakly coupled detuned auxiliary waveguide and directly observe robust corner localization in real space, whereas an otherwise equivalent uniform triangular
lattice exhibits only bulk diffraction under the same protocol. Spectral analysis and open-boundary calculations associate the observed states with nontrivial $C_3$ rotational
topology, and disorder measurements further show that the corner localization persists over a finite range of random and
symmetry-preserving disorder. Our results establish fractal geometry itself as a mechanism for generating topological boundary states in photonic
lattices.
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All authors Shuming Zhang, Zhaoxin Wu, Lumen Eek, Cristiane Morais Smith, Zhaoju Yang
Computational Physics · Cross-listed from math.NA
Projection-Based Reconstruction for Achieving High-Order Accuracy from Low-Order DGSEM Simulations
Xukun Wang, Suyash Shrestha, Oscar A. Marino et al. (+1 more)
High-order discontinuous Galerkin spectral element methods (DGSEM) based on Legendre-Gauss-Lobatto (LGL) nodes provide accurate and efficient discretizations for conservation laws. However, their cost,
memory footprint, and time-step restrictions increase rapidly when the degree of the
polynomial increases. This paper develops a corrected $\mathbb{P}_n\mathbb{P}_m$ ($c\mathbb{P}_n\mathbb{P}_m$) approach for DGSEM-LGL discretizations that aims to recover the accuracy of an $m^{th}$-order approximation while evolving only the degrees of freedom associated with an $n^{th}$-order representation, with $n<m$. The projected
evolution of the high-order components is derived first at the continuous level and then in the fully discrete DGSEM-LGL setting. The discrete analysis shows that because LGL quadrature is not exact for the highest Legendre mode, a correction term for that mode is required to preserve the order of convergence. A compact projection-based reconstruction operator is then introduced to recover high-order components without solving the enlarged constrained least-squares systems used in standard reconstruction procedures. For sufficiently smooth solutions, the resulting $c\mathbb{P}_n\mathbb{P}_m$ scheme is shown to achieve the expected $m+1^{th}$ convergence order. Numerical experiments for one- and two-dimensional conservation laws, including Euler, viscous Burgers, and 2D decaying homogeneous isotropic
turbulence, confirm theoretical convergence behavior and demonstrate competitive accuracy relative to computational cost, with particularly clear efficiency gains for viscous flows.
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All authors Xukun Wang, Suyash Shrestha, Oscar A. Marino, Esteban Ferrer
Classical Physics · Cross-listed from nlin.CD
Recurrence time entropy and weak chaos in Hamiltonian flows
Matheus Rolim Sales, Leonardo Costa de Souza, Iberê Luiz Caldas et al. (+2 more)
Stickiness in mixed
Hamiltonian systems causes chaotic trajectories to remain temporarily trapped near regular structures, making it difficult to distinguish regular, weakly chaotic, and strongly chaotic motion over finite times. We show that the recurrence time
entropy (RTE), previously used in discrete maps, also characterizes weak chaos in
Hamiltonian flows. In the Hénon-Heiles system, the RTE reproduces the structures identified by the largest Lyapunov exponent, taking intermediate values in the sticky layers, and yields a proportion of chaotic trajectories consistent with the smaller
alignment index. The finite-time RTE identifies low-
entropy episodes near regular islands, whose durations decay algebraically, whereas high-
entropy episodes decay exponentially. The same characterization holds for a periodically driven system and for a
Hamiltonian system with three degrees of freedom, whose section is four-dimensional. The RTE is thus an effective diagnostic of weak chaos and stickiness in
Hamiltonian flows.
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All authors Matheus Rolim Sales, Leonardo Costa de Souza, Iberê Luiz Caldas, Edson Denis Leonel, José Danilo Szezech Jr
Fluid Dynamics
Continuity equations in the Generalised Lagrangian Mean theory
Vladimir A. Vladimirov
Generalised Lagrangian Mean (GLM) theory describes the joint
evolution of the mean flow and its perturbations. This paper analyses the exact GLM continuity equations (GLM-CEs), presents them in new forms, and adds new equations to complete them. Our three-dimensional results include: (i) A modified approach to GLM theory that uses only the basic notions of classical fluid dynamics. The only tools used are Lagrangian X, Eulerian x, averaged (mean) Eulerian x' coordinates of fluid particles, and an averaging parameter a. The targeted forms of GLM-CEs are expressed with functions x(x',t, a) and r(x',t, a), where r is the fluid density. (ii) Actual velocity divergence div u expressed through div'u', where u and u' are the actual and mean fluid velocities. (iii) Three new forms of GLM-CEs. Each version represents a sum of a mean and an a-dependent (tilde) part. The latter addition makes each form mathematically complete. (iv) The original Andrews-McIntyre transformation (AMT) is also complemented by its tilde part. Then it also gives the full version of the exact GLM-CEs. However, it works only for a special class of fluid flows. Its structure explains why the tilde equations have been overlooked. (v) Our generalisation of AMT, which repeats the results (i)-(iii) but requires a more complex derivation. (vi) Examples of flows with small but finite Lagrangian perturbations, linking our exposition to the classical GLM theory. Keywords: continuity equations, general Lagrangian mean theory, average (mean) coordinates, Eulerian description, tilde equations, Andrews-McIntyre transformation.
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Applied Physics
High performance construction materials fracture and high cycle fatigue assessment based on accelerated PF-CZM
Jiaqi Li, Zhihua Xiong, Xuyao Liu et al. (+1 more)
Given the widespread application of high-performance materials in cyclic loaded infrastructure, a thorough understanding of the fracture and high-cycle fatigue behavior of high-performance materials is of critical importance. However, these behaviors predominantly rely on experimental methods, which are often costly, time-consuming and limited in generalizability. To address these issues, this paper proposes the constitution and high-cycle fatigue of Ultra-High Performance Concrete (UHPC) and High Strength Steel (HSS) within the Phase-Field Cohesive Zone Model (PF-CZM) framework. A generic stress-based failure criterion for UHPC is derived from the biaxial tensile test results to calculate crack driving force. Furthermore, a fatigue degradation function and an acceleration
algorithm are integrated into the PF-CZM framework to enable efficient high-cycle fatigue simulations. In the acceleration
algorithm, the envelope load is used to approximate the real cyclic load to avoid the simulation of each cycle, and the three-stage fatigue process is simulated through adjusting the cyclic increment adaptively. The proposed model successfully captures mixed-mode fracture and high-cycle fatigue behavior of UHPC and HSS, with validation provided through relevant experimental comparisons.
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All authors Jiaqi Li, Zhihua Xiong, Xuyao Liu, Hongyu Liu
Atmospheric and Oceanic Physics · Cross-listed from astro-ph.SR
Phase-mixing of acoustic waves: From the solar tachocline to marine vessel hydroacoustics
D. Tsiklauri
We adapt the magnetohydrodynamic wave phase-mixing paradigm [Tsiklauri et al. (2003)] to investigate harmonic wave, Gaussian pulse, and
hyperbolic pulse propagation and damping in media governed by transverse sound speed gradients. This universal mechanism is applied to two distinct problems using the harmonic wave phase-mixed solutions. First, we resolve the 26-year-old helioseismic mystery of low-degree global $p$-mode linewidth anomalies observed by BiSON above $\nu \approx 3000\,\mu\text{Hz}$, demonstrating that a localised, non-turbulent sound speed gradient in the
solar tachocline shear zone acts as the necessary high-efficiency energy sink. Second, we translate this formalism into a terrestrial metamaterial fluid engineering design. We show that an engineered microstructured mesh or stern cowl generating a controlled radial sound speed gradient induces severe near-field phase-mixing. This collapses the traditional bulk viscous damping length of $100\text{-kHz}$ propeller acoustic signatures from several kilometres down to a practical design envelope of approximately $10\text{ metres}$, providing an actionable paradigm for compact stealth shielding. Finally, as an independent theoretical extension, we establish a new power-law scaling governing a
hyperbolic secant-squared pulse
evolution: under developed-stage phase-mixing, its peak wave envelope decays as $\max(P_1) \propto x^{-9/2}$.
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Chemical Physics · Cross-listed from cs.LG
What Does a Chemical Language Model Know About Molecules?
Christian Kenneth, Etowah Adams, Liam Bai et al. (+1 more)
Chemical
language models (cLMs) are widely assumed to learn surface-level syntactic patterns rather than learning meaningful molecular semantics. Here, we apply sparse autoencoders (SAEs) to MolFormer, an encoder-only cLM, to mechanistically examine how molecular representations are built across layers. We discover that early layers rely on position-tracking latents to parse molecular grammar, while later layers encode atom-in-substructure and pharmacologically relevant features. Additionally, we show that non-canonical SMILES produce more disruptive representation shifts than invalid SMILES, driven by position-latent disruption propagating across layers. To support further exploration, we develop InterMol, an interactive visualizer for SAE activations on molecular strings and structures.
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All authors Christian Kenneth, Etowah Adams, Liam Bai, Gerard JP van Westen
Optics
Full-Field Mode Sorter for Optical Knots
Tareq Jaouni, Roohollah Ghobadi and Ebrahim Karimi
Optical
knots are topologically structured light fields whose phase or polarization singularities trace linked or knotted trajectories during propagation, making them promising candidates for high-dimensional optical information carriers. Their use in communication or
quantum-information protocols, however, requires a practical readout method that can distinguish a chosen
knot alphabet with low crosstalk. Here, we demonstrate a proof-of-principle full-field sorter for optical
knots using one or two optimized phase-only elements. The sorter maps each input
knot to a predefined output region and is optimized directly from the output intensity distributions to enhance correct assignment, suppress crosstalk, and avoid degenerate mappings between distinct
knots. We apply the method to an alphabet composed of the
Hopf link, trefoil, and cinquefoil optical
knots. Two optimized phase planes improve the sorting performance relative to a single plane and enable high distinguishability for the three-
knot alphabet. We further
benchmark the sorter under common experimental imperfections. These results extend full-field optical mode sorting to topologically structured light and provide a readout route for
knot-based high-dimensional optical communication.
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Optics
Free-running single-cavity dual combs with Hz-level relative linewidth
Yuan Chen, Ming Yan, Jia Xu et al. (+7 more)
Single-cavity dual-comb
lasers provide a compact and efficient source for dual-comb spectroscopy in gas sensing applications; however, achieving sufficient free-running mutual coherence for comb-line-resolved, high-resolution measurements remains challenging. Here, we present a
symmetry-engineered bidirectional single-cavity dual-comb
laser based on an all-polarization-maintaining fiber architecture. The system exhibits exceptional free-running mutual coherence, achieving Hz-level relative linewidths without active feedback or phase correction. The time-averaged absolute jitter of the dual-comb repetition-rate difference reaches 4.7*10^-7 min-1, representing an improvement of nearly two orders of magnitude over previously reported free-running systems. As a spectroscopic demonstration, we resolve ~49,000 comb lines over a 5.4 THz optical bandwidth and measure the absorption spectrum of carbon monoxide (12CO), faithfully retrieving molecular line shapes with millisecond acquisition times. This architecture provides a compact and robust free-running platform for broadband molecular spectroscopy and millisecond-scale, line-shape-resolved gas sensing.
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All authors Yuan Chen, Ming Yan, Jia Xu, Yueting Hu, Jieming Zhang, Zhaoyang Wen, Zijian Wang, Xiangze Ma, Min Li, Heping Zeng
Plasma Physics
Detachment dynamics and disturbance rejection in the TCV X-Point Target divertor
M. Winkel, K. Verhaegh, B. Kool et al. (+11 more)
The X-Point Target divertor is an alternative divertor configuration with a secondary X-point in its divertor volume. In this work, we investigate the dynamic response and disturbance rejection capacity of the XPT configuration on the TCV tokamak, comparing it to a single null (SN) divertor. We employ a system identification approach using multi-sine perturbations to measure the dynamic response of the detached state in both Ohmic and auxiliary-heated L-mode scenarios upon D$_2$ fuelling, N$_2$ seeding and Electron Resonance Cyclotron Heating (ECRH) power modulations. We demonstrate an inherent disturbance rejection capacity of the XPT at its secondary X-point compared to a SN configuration for all perturbation scenarios. Upstream of its secondary X-point, the dynamic response of the detached state between the XPT and SN appears similar. The disturbance rejection capacity of the XPT could be highly beneficial for passively buffering disturbances that cannot be effectively managed by power exhaust controllers. At the same time, it presents a challenge for monitoring the detached state close to the secondary x-point.
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All authors M. Winkel, K. Verhaegh, B. Kool, K. Lee, M. Carpita, A. Perek, R. Morgan, G. Derks, O. Février, C. Theiler, D. Brida, M. van Berkel, the TCV team, the EUROfusion tokamak exploitation team
Plasma Physics
Disambiguation of magnetic sensors in ITER
M. J. Hole, S. D. Pinches, G. Vayakis et al. (+3 more)
ITER will possess approximately 500
magnetic sensors (mainly measuring poloidal flux) distributed across the first wall. The coils are at known locations but the matching signals not necessarily known. There may also be mistakes in the wiring of the coil polarity. The existing strategy to disambiguate coils uses combinatoric programming of poloidal field coil waveforms of up to 48 discharges of
plasma-less operation. An alternate strategy explored in this work is the energisation of a combination of both poloidal and toroidally asymmetric active coils, and Biot-Savart computation of the field solution from all active coils at the sensor coils. A direct brute force permutation of all $N$ coil combinations scales as $O(2^N N!) $ which is intractable for $N>10$. The mathematically formulated optimisation problem was analysed using AI-assisted coding tools, which identified the problem structure as a signed assignment problem and suggested a Hungarian-
algorithm-based optimisation strategy, which scales as $O(N^3)$. This search
algorithm, when embedded into the
magnetic-diagnostic identification problem, was able to disambiguate randomly connected and polarised coils in a regularly spaced array in the ITER first wall (where the the coils are located) down to a signal-to-noise ratio of 50. The computation took 2 seconds. Reconstruction of the actual coil positions in the ITER first wall was achieved high confidence, $C>0.97$. Reconstruction of the second wall poloidal flux coils, which comprised multiple arrays at near constant $\phi$ (each of which is regularly spaced in $\theta$) had a much lower confidence, of $C > 0.15$. By adding the active poloidal field coils to the combined cost function, the confidence increased to $C > 0.59$. This provides the opportunity to reduce the commissioning time of ITER, and is a strategy that could be tested on other toroidal
magnetic confinement devices.
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All authors M. J. Hole, S. D. Pinches, G. Vayakis, S. C. McIntosh, O. Hoenen, P. Abreu
Fluid Dynamics · Cross-listed from astro-ph.SR
Phase-space averaging for stellar convection I. Liouvillian dynamics
P. S. Houdayer and M. Rieutord
Convection remains one of the main uncertain links between multidimensional hydrodynamics and one-dimensional
stellar evolution. In particular, transition regions such as near-surface layers or convective boundaries require mean-field descriptions that remain connected to the underlying dynamics rather than to a prescribed mixing length. We describe the flow as a distribution of mesoscopic fluid particles in position-velocity space. A conservation law for this distribution defines the average and yields the Reynolds-Favre mean-field equations as velocity-space moments. Under standard interior conditions, the same dynamics can be written in Liouvillian form, which extends the
Hamiltonian structure to stratified and dissipative media. The Liouvillian formulation identifies the phase-space divergence, $\{s, T\}$, as a local measure of contraction or expansion of nearby trajectories. In the quasi-adiabatic limit, its sign reduces to the classical Schwarzschild stability criterion. Away from this limit, the diagnostic remains velocity-resolved and can distinguish different parts of the convective population within the same layer, for example in surface and penetration regions. Appendices show how rotation,
magnetic fields, and composition changes can be incorporated through modifications of the phase-space structure. Phase-space averaging provides a dynamically grounded route from hydrodynamics to mean-field
stellar convection equations. It also supplies a local trajectory-based stability diagnostic and a natural starting point for the maximum-
entropy closures constructed in the companion paper.
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Medical Physics
Dosimetric Quantification of a Commercial Dual-Tube kV X-Ray System for Preclinical FLASH Research
Luka Matej Devenica, Lixiang Guo, Mohammad Rezaee et al. (+1 more)
A kV dual tube system has been disseminated as a commercial research platform for preclinical FLASH radiotherapy (RT). Because the tubes are arranged in a parallel opposed geometry, both output
symmetry and time resolved tube synchronization are critical for achieving sufficiently high dose rates (DR) and reproducible study results. We quantified tube output asymmetry observed in depth dose measurements as well as tube synchronization and evaluated their impact on FLASH studies. The dual-tube system defines dose per pulse as the combined single pulse output from both tubes, with DR given by dose per pulse/pulse length. 3D dose distributions were reconstructed from film measurements to assess the impact of output discrepancies. Pulse synchronization between tubes was characterized using a scintillator with 1 ms resolution. We showed >20% discrepancies in output at nominally equal mA/ms settings. After we compensated such discrepancy by decreasing the current of the tube with higher output, the inter tube output difference was reduced to <1%, restoring symmetrical depth dose. We further simulated an in vivo intestinal irradiation in which naive tube settings resulted in >22% of the organ volume receiving >102% of the prescribed dose, compared with <7% when output compensation was applied. We identified a 10.2 +/- 7.0ms synchronization jitter between tubes, which disproportionately impacts the DR at low dose-per-pulse settings, particularly relevant for fractionated studies. Corresponding quality assurance (QA) was designed to monitor tube synchronization over time. We quantified the dosimetric impact of asymmetric output and synchronization and demonstrated implications for preclinical studies. The proposed methodology and QA would mitigate and monitor these effects, ensuring study reproducibility.
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All authors Luka Matej Devenica, Lixiang Guo, Mohammad Rezaee, Ken Kang-Hsin Wang
Biological Physics
Imaging aerosolized viruses with an X-ray free-electron laser using single-particle rotational invariants
Tim B. Berberich, Johan Bielecki, Jonas A. Sellberg et al. (+12 more)
X-ray free-electron
lasers (XFELs) enable diffraction-before-destruction measurements of individual nanosized bioparticles, making it possible to study the structure and dynamics of non-crystalline targets under near-biologically relevant conditions. In this work, we employ rotational invariants for model-guided and ab initio three-dimensional (3D) structure determination of aerosolized bacteriophages PR772 measured with an XFEL. The rotational invariants derived from diffraction patterns collected during multiple independent XFEL experiments facilitate the characterization of similarities and structural variations within the measured ensembles of PR772 particles. Despite modest experimental resolution, we can identify various structural features of the viruses, including the asymmetric nature of capsid distortions from the perfect icosahedral shape, density variations in the encapsulated content, and an extension at one of the capsid vertices. Rotational invariants combine structural sensitivity with applicability to forward-scattering modeling and inverse problem solving, making them powerful tools for probing the structure and temporal
evolution of nano- and bioparticles using an XFEL, particularly enhancing the fidelity of structural analysis at limited experimental resolution.
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All authors Tim B. Berberich, Johan Bielecki, Jonas A. Sellberg, Benedikt J. Daurer, Carl Nettelblad, Paul Lourdu Xavier, Ivan A. Vartanyants, Garth J. Williams, Luca Gelisio, Richard Bean, Serguei L. Molodtsov, Petra Fromme, Andrew Aquila, Adrian P. Mancuso, Ruslan P. Kurta
Plasma Physics
On the accuracy of measurements of electron temperature by Thomson scattering diagnostic in the plasma core of the ITER tokamak
M.Yu. Kantor
The ITER tokamak project includes a Thomson scattering diagnostic designed to measure electron temperature and density in the
plasma core. The system is required to provide measurements over a wide temperature range while meeting stringent accuracy requirements. A previous study analyzed the errors of electron temperature measurements to assess the feasibility of these requirements. The analysis concluded that the central electron temperature could be measured with the required accuracy of 10% for temperatures up to 40 keV at a minimum electron density of 3*10^19 m^-3. However, those results were based on an overestimation of the number of photoelectrons generated in detectors by the scattered radiation due to the incorrect application of the Thomson scattering cross-section. As a consequence, the temperature measurement errors were significantly underestimated. In the present work, the accuracy of electron temperature measurements in the ITER
plasma core is reassessed using the corrected photoelectron yield derived from published data and incorporating the effects of background radiation. The revised analysis shows that the proposed diagnostic system can achieve the required accuracy of 10% for temperatures up to 20 keV at low
plasma background radiation, whereas under high background radiation this accuracy can only be maintained up to 1 keV. To achieve the 10% accuracy across the full temperature range while preserving the current diagnostic configuration, either the energy of the probing
laser pulse must be increased by a factor of 2-4 or the least electron density must be raised to 6*10^19 m^-3.
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