Biological Physics
DNA end tethering through break-induced DNA–protein condensation
Rakesh Das, Tarun Mascarenhas, Nagaraja Chappidi et al. (+2 more)
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show in vitro that upon a DNA double-strand break, a DNA–
protein condensate can tether the broken DNA ends before they disperse away, a critical step for subsequent repair biochemistry. However, it remains puzzling how such condensation reliably achieves spatiotemporal localization at the break site and captures both broken ends despite intrinsic stochasticity. Here, we propose that broken DNA ends can trigger a conversion of
proteins from a soluble state to a condensate-competent state. Combining this idea with Brownian dynamics simulations and theory, we propose a physical mechanism for reliable DNA-end tethering. Simulations show that such break-induced conversion can drive local DNA–
protein condensation with two possible outcomes: successful or failed tethering. To rationalize this, we construct an effective free energy landscape, identify the corresponding stationary states, and demonstrate that tethering is governed by a kinetic competition between
polymer relaxation and condensation dynamics. Together, our study shows that DNA end-dependent conversion, coupled with DNA–
protein condensation, can reliably tether broken DNA ends.
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All authors Rakesh Das, Tarun Mascarenhas, Nagaraja Chappidi, Simon Alberti, Frank Jülicher
Computational Physics · Cross-listed from cs.RO
Learning, locomotion, and navigation of soft synthetic snakes in three-dimensional, heterogeneous environments
Xiaotian Zhang, Ali Albazroun, Tixian Wang et al. (+3 more)
Limbless terrestrial animals exhibit exceptional locomotor versatility and control, currently unmatched by engineered counterparts. Here, we introduce a computational framework that enables soft synthetic snakes to navigate unstructured, heterogeneous 3D terrains. Our approach is grounded in bio-inspired actuation and sensing models that reduce the control complexity inherent to high-degree-of-freedom, continuum bodies. These models are integrated into a reinforcement learning architecture to derive environment-traversing policies. Training first occurs in simplified, homogeneous terrains to learn locomotion primitives. These are then composed into adaptive strategies for complex landscapes. We demonstrate robustness by deploying a snake in high-fidelity 3D environments reconstructed from real-world imaging, achieving reliable
navigation. Overall, this work provides a physically-realistic simulation platform and practical insights for the control of continuum systems in natural terrains.
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All authors Xiaotian Zhang, Ali Albazroun, Tixian Wang, Songyuan Cui, Prashant G. Mehta, Mattia Gazzola
Computational Physics · Cross-listed from math.NA
A Guided Tour of Modern Domain Decomposition: From Schwarz Iterations to Robust Preconditioners and HPC Implementations
Victorita Dolean, Pierre Jolivet, Frédéric Nataf et al. (+1 more)
Domain decomposition methods (DDMs) provide a unifying framework for the scalable numerical solution of partial differential equations. Originating from Schwarz's alternating method, they have evolved into a rich family of
algorithms that combine local robustness with global convergence acceleration and natural parallelism. Over the past decades, domain decomposition has played a central role in enabling large-scale simulations in numerous applications. This chapter presents an overview of modern DDMs, with a particular emphasis on scalable preconditioning techniques for challenging problems, including indefinite and high-frequency regimes. We revisit the fundamental concepts - overlapping decompositions, partition of unity, additive and restricted Schwarz formulations - and explain their algebraic interpretations. We then clarify their role as preconditioners in Krylov subspace solvers and discuss the necessity of coarse space corrections for scalability. Beyond a the survey aspect, the chapter distills key theoretical insights and practical design principles that have emerged over the past twenty years. Special
attention is given to robust coarse spaces (GenEO, DtN-based approaches) and high-performance implementations. The goal is to provide both a coherent overview of the field and a concise, practice-oriented guide for readers seeking to understand and apply domain decomposition methods without navigating the entire literature.
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All authors Victorita Dolean, Pierre Jolivet, Frédéric Nataf, Pierre-Henri Tournier
History and Philosophy of Physics
Physical Coherence and Time's Emergence
Eugene Y. S. Chua
It is often said that time vanishes in
quantum gravity. One general approach to
quantum gravity accepts this fundamental timelessness but seeks to derive time's emergence at a non-fundamental level. To better assess such approaches, I develop the criterion of physical coherence and situate it in context by applying it to two programs for time's emergence, drawing from recent works by Chua and Callender (2021) and Chua (2025): semiclassical time and thermal time. Unlike some recent arguments for the metaphysical incoherence of time's emergence, which rule out all claims of time's emergence 'from on high' once we've fixed a definition of metaphysical emergence, my criterion of physical coherence leaves open the possibility that some programs in
quantum gravity may succeed on their own terms in providing a physically coherent derivation of time from no-time. This sets a challenge for proponents of time's emergence to clarify the conceptual foundations of their program, while at the same time acting as a litmus test for a program's success.
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Atmospheric and Oceanic Physics · Cross-listed from cs.LG
RealBench: Benchmarking Data-Driven Numerical Weather Forecasting Under Operational Conditions and Extreme Event Challenges
Ruize Li, Zhibin Wen, Tao Han et al. (+5 more)
Accurate evaluation of weather
forecasting models is critical for their reliable deployment in real-world applications. However, existing
benchmarks predominantly rely on reanalysis products such as ERA5, which are generated through delayed data assimilation and do not reflect the constraints of real-time operational
forecasting, thereby resulting in a systematic mismatch between
benchmark performance and real-world
forecasting. In this work, we introduce RealBench, a next-generation
benchmark for AI weather
forecasting that emphasizes realistic evaluation under operational conditions. RealBench features a strictly out-of-distribution test set spanning 2025 to eliminate data leakage and capture recent atmospheric regimes. It integrates multiple data sources, including low-latency operational analysis and a large-scale global in-situ observation
dataset comprising over 10,000 stations, enabling direct evaluation against real atmospheric measurements. Beyond standard global metrics, RealBench provides a comprehensive evaluation framework for high-impact extreme events, including heatwaves, cold surges, and tropical cyclones, using event-specific metrics that better reflect real-world
forecasting priorities. The evaluation results reveal substantial discrepancies between reanalysis-based metrics and real-world performance, particularly concerning extreme events. By highlighting the limitations of existing
benchmarks, this work establishes a more faithful and operationally relevant evaluation paradigm, providing a rigorous foundation for advancing next-generation AI weather
forecasting systems. The
benchmark implementation is available at: https://github.com/lixruize-del/NWP-
Benchmark.
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All authors Ruize Li, Zhibin Wen, Tao Han, Hao Chen, Fenghua Ling, Wei Zhang, Song Guo, Lei Bai
Fluid Dynamics
Geometry, elasticity, and activity in the transport of self-propelled filaments in turbulence
Kunal Kumar, Aliv Sahoo, Rahul Kumar Singh et al. (+1 more)
We investigate the transport of elastic active filaments in two-dimensional
turbulence, focusing on how propulsion geometry and elasticity determine
vortex trapping and transport. Using a bead-spring model with activity applied at the filament head, we compare propulsion that follows the instantaneous filament conformation with propulsion imposed along a fixed external direction. We find that activity does not generically enhance transport: when propulsion remains coupled to the filament backbone,
vortex trapping remains dominant and motion stays effectively diffusive, whereas fixed-direction propulsion enables persistent excursions across flow structures and leads to superdiffusive transport. In both cases, activity shifts filament conformations toward more extended states, effectively opposing elastic relaxation without eliminating preferential sampling of coherent vortical regions. At low Weissenberg number, this conformational change is amplified: activity cooperates with elasticity to enhance preferential sampling of vortical regions and strengthen
vortex trapping. Transport therefore emerges from a competition between activity, elasticity, and flow-induced deformation, with elasticity determining how effectively activity-induced extensions can persist against turbulent trapping. These results establish propulsion geometry as the key control parameter for transport, with elasticity and activity acting cooperatively rather than independently to shape filament dynamics in turbulent flows.
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All authors Kunal Kumar, Aliv Sahoo, Rahul Kumar Singh, Samriddhi Sankar Ray
Accelerator Physics
Electron beam evolution in a successive Compton backscattering
D.V. Gavrilenko, A.A. Savchenko, M.N. Strikhanov et al. (+1 more)
Inverse Compton scattering (ICS) is a unique source of highly monochromatic x-ray and gamma radiation. We investigate theoretically the cumulative effects of repeated head-on interactions between the electron beam and a train of powerful
laser pulses inside a linear accelerating structure placed between mirrors of an optical resonator. We find that the longitudinal momentum spread converges exponentially to an
equilibrium value due to the competition between
quantum excitation (heating) and radiation friction (cooling). The predictions of the developed theory coincide very well with computer simulations. Our work establishes the necessity to account for cumulative transverse beam dynamics in the design and optimization of future stable, high-brightness ICS sources.
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All authors D.V. Gavrilenko, A.A. Savchenko, M.N. Strikhanov, A.A. Tishchenko
Atmospheric and Oceanic Physics · Cross-listed from cs.CE
Exascale Hybrid Numerical-AI Ensembles for Operational Flood-Season Forecasting in East Asia: 15-km Decadal Hindcasts and 1-km High-Resolution Capability
Mengxuan Chen, Yunpu Xu, Qiuyan Sun et al. (+19 more)
Seasonal
forecasting of summer rainfall in East Asia remains a grand challenge, as predictability at 3 to 6 month lead times is constrained by the spring predictability barrier, weak large-scale signals, and localized nonlinear convective extremes. We address this challenge with CAPES, which integrates a kilometer-resolution coupled regional model with atmosphere, land, and ocean components and a data-driven AI seasonal
forecasting system. At 15 km resolution, the fused workflow combines 174 numerical members from varying start times, physics schemes, and parameter perturbations with 1,600 AI members generated from initial and physical perturbations. Using the full LineShine system, CAPES completes ten annual 1,774-member hindcasts for 2016 to 2025 within 14.6 hours, improving the mean prediction score from ECMWF's 71.8 to 75.9 and delivering a major gain in operational
forecasting capability. The 1-km configuration further enables fine-scale typhoon simulation and establishes the feasibility of kilometer-scale fused ensemble
forecasting on a one-week timescale.
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All authors Mengxuan Chen, Yunpu Xu, Qiuyan Sun, Han Zhang, Jiayi Lai, Zheng Zhou, Juepeng Zheng, Hongsong Meng, Nan Wei, Jinxiao Zhang, Xiongchuan Tan, Haodong Bian, Yinan Cai, Ge Yang, Fang Wang, Yunyun Liu, Conghui He, Runmin Dong, Lanning Wang, Yutong Lu, Yongjiu Dai, Haohuan Fu
Chemical Physics
Unravelling Chemical Exchanges Through Steady State Free Precession NMR
Sundaresan Jayanthi, Adonis Lupulescu, Mark Shif et al. (+2 more)
NMR is uniquely endowed to analyze dynamics, with line shape and relaxation measurements covering timescales over several orders of magnitude. Further insight arises from pulse sequences like chemical exchange saturation transfer or relaxation dispersion, which facilitate, respectively, the detectability and shift characterization of even lowly populated states, and the pinpointing of the exact exchange rates. The present study demonstrates that Steady State Free Precession (SSFP) experiments involving a train of pulses with flip angle {\alpha} spaced by repetition times TR, combine valuable features from both these experiments. Indeed, in the presence of chemical exchanges, SSFP yields via its offset-dependent excitation and saturation profiles, detailed information about the number, the chemical shifts and the populations of the exchanging sites even when these involve multiple intermediates with dissimilar abundances. Simultaneously SSFP can provide, via its TR dependence, a controllable timescale yielding kinetic information over a variety of slow/intermediate/fast exchange rates. All this is theoretically demonstrated with the aid of a Liouville-space formalism examining the steady state in the presence of chemical exchange. This formalism leads in both the slow and fast exchange regimes to analytical predictions that match well brute-force numerical calculations, which lend themselves to rapid and accurate fittings of exchange rates, chemical shifts, and site populations. The basic features associated to this novel approach to examine chemical kinetics are experimentally verified on simple model compounds; potential extensions are briefly discussed.
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All authors Sundaresan Jayanthi, Adonis Lupulescu, Mark Shif, Zuzana Osifova, Lucio Frydman
Classical Physics · Cross-listed from astro-ph.HE
Pulse Modulation as a Signature of the Asteroid-Neutron Star Collision Model for High-Energy Transients
Partha Bagchi, Biswanath Layek, Dheeraj Saini et al. (+3 more)
Asteroid-
neutron star collision models have been proposed as possible sources of high-energy transients, such as gamma-ray bursts (GRBs) and fast
radio bursts (FRBs). The sequence of events following the impact of the asteroid and finally dissolving into the
neutron star can have several other observable consequences. We propose that due to the development of the off-diagonal moment of inertia (MI) components, the merger's aftermath can lead to the wobbling of the
pulsar (assuming the
neutron star happens to be a
pulsar). Using sample values of various parameters, viz., size, shape, the locations of the deposits, and the pre-existing
pulsar deformation parameter ($\eta$), we calculate the detailed pulse profile modulation of the
pulsar. We observe a distinct pattern of pulse profile modulation on a characteristic timescale enhanced by a factor of $1/\eta$ compared to the pulse timing. Importantly, even small changes in the MI components, of order $\epsilon$, can produce large pulse profile modulations of order $\epsilon/\eta$ (depending on the relative location of asteroid material deposition). Thus, if an asteroid-
neutron star collision is responsible for a high-energy transient, the associated pulse profile modulation may serve as a falsifiable observational signature of such an event.
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All authors Partha Bagchi, Biswanath Layek, Dheeraj Saini, Anjishnu Sarkar, Ajit M. Srivastava, Deepthi Godaba Venkata
Computational Physics
Machine-learned atomistic simulations reveal the basis of hydrogen-induced crack-plane transition in alpha-Fe
Jiaqin Xu, Zhiqiang Zhao, Kazuma Ito et al. (+4 more)
Hydrogen-related fracture in body-centered cubic Fe and ferritic steels often appears as transgranular quasi-cleavage rather than purely intergranular failure, especially at low to moderate hydrogen contents. Fractography has suggested that hydrogen may change the dominant cleavage faceting from {100} toward {110}, but atomic-scale evidence for this possible crack-plane transition remains unclear. Here we construct an efficient neural-network potential for {\alpha}-Fe/H and combine large-scale, three-dimensional molecular dynamics with grand-canonical Monte Carlo (GCMC), allowing the near-tip crack-surface region and crack tip within a defined GCMC domain to exchange hydrogen with a reservoir at fixed chemical potential. A comparison of four crack systems identifies the controlling response: (100)[010], (100)[011], and (110)[001] remain cleavage-dominated, whereas the (110)[1-10] crack changes from dislocation emission in pure Fe to cleavage under hydrogen charging. The energetic origin is twofold. Hydrogen lowers the Griffith cleavage threshold of the {110} cleavage-plane family more strongly than that of {100}, and, for the controlling crack, a Rice-type energetic descriptor indicates that the surface-energy-controlled cleavage resistance decreases faster than the unstable-stacking-fault-controlled emission resistance, consistent with a weakened dislocation-emission shield. These results provide a thermodynamically consistent atomistic basis for a hydrogen-induced transgranular crack-plane transition in Fe.
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All authors Jiaqin Xu, Zhiqiang Zhao, Kazuma Ito, Shuhei Shinzato, Fanshun Meng, Shihao Zhang, Shigenobu Ogata
Computational Physics · Cross-listed from cs.LG
A comparative study of accuracy and rollout stability of temporal surrogate models
Rajarshi Biswas
Temporal surrogate models are effective for predicting chaotic dynamical systems where computational cost can be prohibitive. Several deep neural network architectures can be used for such purposes. In this work, a few commonly used architectures are compared using a common training protocol. The objective is to fairly assess the impact of model architectures for long-horizon prediction stability. Experiments are carried out for three problems, the double pendulum, the Kuramoto-Sivashinsky equations, and the Kolmogorov flow. The experiments are carried out with matching model capacity. Analysis is also carried out for a scenario where each model is individually optimized. It is observed that in both scenarios, the models exhibit categorical differences in long-horizon rollouts. For a concrete quantification, stepwise error injections and perturbation amplifications are analyzed using metrics such as local jacobian, relative one-step bias, and finite-time Lyapunov growth. Additionally, an attractor analysis is also conducted to assess how well the learned models replicate the underlying system geometry. An ablation study to isolate the impact of each component of a continuous-update architecture is also carried out. It is concluded that models that having integrator-like updates show lower bias and perturbation amplification yielding stable long-horizon rollout and more accurate predictions.
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Optics
Vacuum-Sealed Thermal Treatment Regulates Trap States and Red Persistent Luminescence in CaTiO3: Pr3+,Al3+ Phosphors
Ziyi Guo and Duanting Yan
Red persistent phosphors remain less mature than green and blue-green systems because their afterglow is often weak and decays rapidly. Here, CaTiO3:0.3%Pr3+,0.3%Al3+ phosphors were prepared by a high-temperature solid-state route under either air or
vacuum-sealed quartz-tube (QT) conditions. The effects of processing atmosphere and sintering temperature on phase structure, microstructure, steady-state photoluminescence, afterglow, thermoluminescence, and excited-state decay were examined. X-ray diffraction and Raman spectra show that all samples retain the orthorhombic CaTiO3 perovskite phase, with no detectable secondary phase. SEM observations show particle coarsening at higher QT temperatures, while EDS mapping indicates a homogeneous distribution of Ca, Ti, O, Pr, and Al within the examined region. The QT-treated samples exhibit stronger Pr3+ red emission near 612 nm and markedly improved afterglow compared with the air-treated sample. The QT-1300 sample shows the best afterglow among the present samples, with a reported 3.6-fold higher intensity at 1200 s than Air-1200{\deg}C. Thermoluminescence results indicate that QT treatment increases the population of thermally active traps and enhances the deeper trap component. These results suggest that a low-oxygen sealed environment regulates defect-related traps, most likely involving oxygen-vacancy-associated centers, and improves carrier storage and release through the Pr3+ and Ti4+ intervalence charge-transfer pathway. This work provides a practical processing strategy for improving CaTiO3-based red persistent phosphors and offers insight into trap-state regulation under low-oxygen thermal treatment.
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Medical Physics
GRASP MRI: A Decade of Innovation from Bench to Bedside
Li Feng, Kai Tobias Block, Hersh Chandarana et al. (+1 more)
GRASP (Golden-angle RAdial Sparse Parallel) MRI has emerged as one of the most influential motion-robust dynamic MRI frameworks over the past decade. By combining continuous golden-angle radial sampling with compressed sensing and parallel imaging, GRASP enables free-breathing data acquisition with flexible retrospective image reconstruction. Since its original introduction, the framework has evolved substantially and has inspired a broad range of technical developments, including motion-resolved reconstruction, real-time imaging, quantitative MRI, deep learning-enabled reconstruction, and multidimensional cardiovascular imaging. These advances have further expanded the role of GRASP MRI in a range of clinical applications where conventional breath-hold imaging is challenging. This review summarizes the technical
evolution and clinical translation of GRASP MRI over the past decade, with a particular focus on the conceptual advantages of continuous radial acquisition, flexible retrospective reconstruction, and motion-robust imaging. Emerging developments in deep learning reconstruction, real-time volumetric imaging, and quantitative free-breathing MRI are also discussed together with future directions of motion-robust MRI acquisition and reconstruction.
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All authors Li Feng, Kai Tobias Block, Hersh Chandarana, Daniel K Sodickson
Optics · Cross-listed from cond-mat.mtrl-sci
Photoluminescence Identification of Multiple Local Eu3+ Environments in BaTiO3 Ceramics
Yutong Cai, Duanting Yan and Hancheng Zhu
BaTiO3 is a model ferroelectric perovskite whose properties are highly sensitive to local structure, defect chemistry, and dopant distribution. However, conventional diffraction mainly probes the average
lattice and can miss subtle changes in the local coordination environment. Here we use Eu3+ photoluminescence as a local optical probe for BaTiO3 ceramics prepared at 1250, 1300, and 1350 {\deg}C. X-ray diffraction and Raman spectra show that all samples retain the tetragonal BaTiO3 phase within the detection limits of these techniques. Electron microscopy reveals a porous ceramic microstructure with temperature-dependent grain growth, and elemental mapping confirms a spatially distributed Eu signal. The Eu3+ excitation and emission spectra show strong sensitivity to the processing temperature. The sample sintered at 1250 {\deg}C gives the highest emission intensity, while higher sintering temperatures change the relative intensity of the charge-transfer band and the 4f-4f transitions. Most importantly, the 5D0 to 7F0 emission contains two reproducible components near 579.5 nm and 582.2 nm. Their relative weights vary with sintering temperature, and double-exponential decay at 612 nm further supports the presence of multiple Eu-related local environments. These results show that Eu3+ luminescence provides a sensitive route to track local structural heterogeneity in BaTiO3 ceramics.
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Medical Physics
A Wireless Reconfigurable Metasurface for Enhanced Parallel Magnetic Resonance Imaging
Yuhan Liu, Xia Zhu, Ke Wu et al. (+4 more)
Modern
magnetic resonance imaging (MRI) relies on application-specific multi-channel receive coils to achieve high performance, but these coils are typically costly, rigid, and difficult to generalize across anatomies. Recent wireless, low-cost metamaterials offer improved signal-to-noise ratio (SNR) but remain anatomy-dependent, are prone to destructive inter-element interference, and lack demonstrated compatibility with parallel imaging. Herein, a wireless, reconfigurable coaxial loop metasurface (CLM) is introduced as a platform for localized SNR enhancement that can operate either as a standalone element or as an insertable add-on alongside existing clinical receive systems. Through its coaxial architecture and shared current pathways, the CLM establishes a collective in-phase resonant mode that enforces phase-coherent current distributions across all loops, resulting in consistently constructive interference. Benchmarking on a 3.0 T MR system using an 8-loop CLM shows SNR enhancements of up to 14.8-fold and 14.02-fold in the sagittal and axial planes, relative to the birdcage coil (BC). As an add-on to a clinical posterior receive array, it further demonstrates up to 2.9-fold SNR enhancement and compatibility with parallel imaging across ex vivo and in vivo settings. The proposed CLM paves the way toward a new class of reconfigurable and insertable MRI hardware for flexible and system-compatible signal enhancement.
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All authors Yuhan Liu, Xia Zhu, Ke Wu, Artem Kaliaev, Christina A. LeBedis, Stephan W. Anderson, Xin Zhang