Biological Physics · Cross-listed from cond-mat.stat-mech
Nonequilibrium Theory for Molecular Machine Design
Ying-Jen Yang and Ken A. Dill
Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with
entropy production. But this alone is not sufficient for design, optimization and
evolution because it doesn't treat cost-benefit tradeoffs, or small-system misflows (backsteps, futile cycles, ineffective actions), or differential properties for flow design. Here we develop CFT Design, based on the recently developed Caliber Force Theory (CFT). We apply it to: designing faster molecular motors through “traffic control”; optimizing speed, energy, and accuracy in kinetic proofreaders; and designing better enzyme inhibitors. CFT Design provides a general framework for optimizing nonequilibrium flow networks.
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Computational Physics · Cross-listed from cs.CE
An Overlapping Schwarz Space-Time Refinement Framework for Material Point Method
Zhaofeng Luo, Minchen Li and Yupeng Jiang
We propose an overlapping Schwarz space-time refinement framework for the material point method (OS-MPM) to improve computational efficiency in problems with strongly localized deformation, contact, and large
geometric nonlinearity. The method decomposes the domain into overlapping coarse and fine subdomains with heterogeneous spatial and temporal resolutions, while retaining standard MPM discretizations within each subdomain. Coarse-fine coupling is achieved through an MPM-specific Schwarz iteration combining mass-weighted spatial transmission and temporal interpolation for sub-cycling. In contrast to refinement strategies based on modified basis functions, transition kernels, or strongly enforced interface constraints, the proposed approach preserves the modular structure of standard MPM and shifts the coupling complexity to nonmatching-grid interface operators within the Schwarz alternating procedure. Numerical examples, including a
gravity-driven cantilever beam, Hertzian contact, and an elastic inclusion problem, show that the method reproduces analytical or fine-resolution reference solutions with good accuracy and convergence behavior. In the inclusion
benchmark, the proposed framework achieves comparable or slightly lower error than single-domain fine simulations at the finest tested resolutions, while reducing computational cost by up to 9.15 times. A three-dimensional folding example further demonstrates the generality of the framework. These results indicate that the proposed method provides an accurate, modular, and efficient route for local space-time refinement in MPM.
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Medical Physics
Combined Diffusion-Relaxation MRI to Assess Muscle Microstructure and Composition
Matteo Figini, Paddy J. Slator, Valeria E. Contarino et al. (+3 more)
Quantifying muscle tissue properties is crucial for understanding pathophysiological changes occurring in skeletal muscle (SM). In particular, T2 relaxation and
diffusion MRI (dMRI) are promising techniques. However, typical methods measure T2 and
diffusion separately, making them less specific to microstructure than emerging combined
diffusion-relaxation techniques. Here we demonstrate a combined
diffusion-relaxation MRI approach for disentangling T2 and diffusivity properties in SM. A
diffusion-relaxation acquisition was implemented on a 3 T scanner, combining six b-values and four echo times within a 12-min single-slice protocol. Five healthy participants were enrolled. Data were analysed with six microstructural
diffusion and
diffusion-relaxation models. Mean parameter values were extracted from manually segmented calf muscles. Models neglecting T2 relaxation showed strong TE dependence: mean diffusivity (MD) decreased by up to 47%, fractional anisotropy (FA) increased by up to 75%, and vascular fraction fv increased by up to 297% when TE increased from 50 to 90 ms.
Diffusion-relaxation models produced TE-independent estimates. Tissue and vascular relaxation times ranged 31-36 ms T2t and 66-86 ms T2v, respectively. Simulations confirmed improved accuracy for fv estimation (r=0.95; RMSE=0.03) and reduced TE-related bias. Combined
diffusion-relaxation MRI provides robust, TE-independent estimates of muscle microstructural and perfusion-related biomarkers. The quantitative improvements observed - particularly in the estimation of fv - show its potential to provide non-invasive biomarkers for the assessment of muscle physiology, exercise adaptation, rehabilitation, and neuromuscular pathology.
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All authors Matteo Figini, Paddy J. Slator, Valeria E. Contarino, Eleftheria Panagiotaki, Giovanna Rizzo, Alfonso Mastropietro
Computational Physics
Nonlinear GENERIC-Embedded Neural Networks (N-GENNs): Learning GENERIC dynamics with non-quadratic dissipation potentials
Vojtěch Votruba, Zequn He, Weilun Qiu et al. (+2 more)
We introduce Nonlinear GENERIC-Embedded Neural Networks (N-GENNs), a deep learning framework for discovering
evolution equations of systems governed by the nonlinear GENERIC formalism (General Equation for Non-
Equilibrium Reversible-Irreversible Coupling). Such systems exhibit coupled conservative and dissipative dynamics, and can be described via the superposition of a
Hamiltonian flow and a generalized gradient flow. In contrast to existing approaches, our formulation incorporates generalized gradient flows via convex dissipation potentials, enabling the identification of a broader class of thermodynamically consistent dynamics, including systems with non-quadratic dissipation potentials. Thermodynamic structure is strongly enforced by construction through suitable reparameterizations of both the reversible operator and the dissipation potential, ensuring exact compliance with the first and second laws of thermodynamics. We validate the proposed approach on three representative examples: a harmonic oscillator coupled to a heat bath, an idealized chemical motor, and a one-dimensional viscoplastic model of Perzyna type. These results demonstrate the method's ability to accurately infer thermodynamically consistent models from data for systems incorporating both conservative and nonlinear dissipative dynamics.
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All authors Vojtěch Votruba, Zequn He, Weilun Qiu, Celia Reina, Michal Pavelka
Geophysics · Cross-listed from astro-ph.EP
Exploring Enceladus's Interior Structure Using Electromagnetic Induction
Alexander Grayver and Joachim Saur
Electromagnetic (EM) sounding can constrain the electrical structure of Enceladus and, in turn, the salinity of its ocean and the porosity, fluid content, and thermal state of its hydrothermally active core. Here, we assess the feasibility of EM sounding at Enceladus using both global (orbiter) and local (lander) EM induction transfer functions. We provide a physical framework for modeling EM induction for 1-D and 3-D subsurface conductivity models and discuss how transfer functions can be estimated from global or local measurements of the
magnetic and electric fields. We simulate 3-D induction effects arising from variations in ice-shell thickness. The magnitude of these effects in the
magnetic field correlates with the ice-shell thickness at the surface and is strongly dependent on the ocean's conductivity. These
magnetic variations, if observed, would favor a moderately to highly conductive ocean, providing lower bounds on salinity and volatile content. The absence of these effects indicates a thicker, more homogeneous ice shell and/or a lower-conductivity ocean. Given plausible magnitudes, a polar-orbiting mission with low-altitude measurements will be required to detect these effects. In summary, an orbiter will constrain global ocean conductivity using long-period induction and possibly map the ice thickness variations. The detailed EM sounding of both the hydrosphere and the core can be achieved by a lander-based broadband EM sounding at periods $\approx 10^1-10^5$ s to probe ocean salinity and thickness, as well as core properties including porosity, fluid content, and temperature.
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Accelerator Physics
Status report towards implementation of a Compton polarimeter at BEPCII
Mengyu Su, Zhe Duan, Jie Gao et al. (+26 more)
Precision beam polarization measurements based on Compton polarimeters are essential for the physics program of future high-energy
colliders. In order to prepare for these and to extend the scope of physics measurements of the BESIII experiment at the BEPCII, a diagnostic of electron beam transverse polarization at BEPCII is of interest. The design and status report of the commissioning, until July 2025, of this device is reported in this paper. We report unambiguous observation of Compton interaction, discuss current limitations of the experimental setup and draw prospects for improvements and actual measurement of electron beam polarization in the near future.
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All authors Mengyu Su, Zhe Duan, Jie Gao, Qingfu Han, Daheng Ji, Dazhang Li, Qi Li, Xiaodong Li, Yanchun Li, Zhijun Liang, Ge Lei, Zhonghui Ma, Aurélien Martens, Lingling Men, Xianjing Sun, Guangyi Tang, Huan Wang, Jianli Wang, Lin Wang, Qi Yang, Lingda Yu, Chenghui Yu, Jianyong Zhang, Wan Zhang, Yandong Zhang, Yuelei Zhang, Ningchuang Zhou, Dechong Zhu, Fabian Zomer
Chemical Physics
Beyond the Black Box: An Interpretable Machine Learning Framework for Predicting Electronic Structure Microdescriptors and Structure-Performance Relationships in Fe-based Catalytic Systems
Oyinkansola Romiluyi
The current catalyst discovery and development pipeline for energy-intensive applications like methane conversion remains bottlenecked by expensive trial-and-error experimentation, irreproducible chemical intuition, and a lack of frameworks linking complex catalytic design spaces to performance. This work presents an interpretable machine learning framework that integrates SHAP-based feature importance analysis (Explainable AI) with tree-based ensembles (Random Forest and
Bayesian-optimized CatBoost) to characterize Fe-zeolite and
oxide-supported catalysts for the partial oxidation of methane (POM). Despite limited data, the framework decodes complex structure-performance relationships by identifying and ranking thermodynamic, structural, and
geometric microdescriptors that influence the electronic band gap and govern macroscale performance metrics such as selectivity, activity, and stability. This work explicitly demonstrates that thermodynamic
lattice stability and
geometric factors are the primary drivers of electronic band gap (a critical proxy for redox reactivity) rather than bulk stoichiometry. Non-linear models achieve an R2 of 0.61 - 0.77, significantly outperforming traditional linear baselines (R2 = 0.32). This workflow provides both a light-weight generalizable methodology and a prioritized list of physical features for accelerated catalyst screening - and these features can subsequently be integrated into microkinetic and reaction engineering models to create digital twins of complex reactor systems and to enable predictive optimization in autonomous R&D laboratories.
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Chemical Physics · Cross-listed from cond-mat.mtrl-sci
CrystalREPA: Transferring Physical Priors from Universal MLIPs to Crystal Generative Models
Chengqian Zhang, Yucheng Jin, Duo Zhang et al. (+2 more)
Crystal generative models mainly learn what stable
crystals look like, with little explicit supervision for what makes them stable. We reveal a substantial representation gap between state-of-the-art
crystal generative models and pretrained universal machine learning interatomic potentials (MLIPs) via energy probing, and show this gap can be closed by a simple training-time
alignment. We propose
Crystal REPresentation
Alignment (CrystalREPA), a plug-and-play framework that aligns the atom-wise hidden states of generative encoders with frozen MLIP representations through an element-aware contrastive objective, transferring stability-aware atomistic priors with marginal training overhead and no additional inference cost. Across three generative frameworks, ten MLIP teachers, and two
benchmark datasets, CrystalREPA consistently improves the thermodynamic stability, structural validity, and structural fidelity of generated
crystals. Equally important, we find that an MLIP's transfer effectiveness is poorly predicted by its accuracy on standard leaderboards (e.g., Matbench Discovery) but strongly predicted by the distinguishability of its atom-wise representation space, yielding a practical, accuracy-independent criterion for selecting MLIP teachers for generative transfer. Code is available at https://github.com/Chengqian-Zhang/CrystalREPA.
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All authors Chengqian Zhang, Yucheng Jin, Duo Zhang, Tiejun Li, Han Wang
Medical Physics
Bilateral breast gradient insert prototype for strong diffusion encoding at 3T
Gerrit Arends, Edwin Versteeg, Feng Jia et al. (+4 more)
Purpose:
Diffusion MRI has shown promise for breast cancer screening, lesion characterization,and treatment response monitoring without contrast
agents, but further translation is constraint by the gradient performance of conventional systems. The aim of this work is to develop a single-axis high performance bilateral plug-and-play breast gradient insert to enable strong-gradient
diffusion MRI. Methods: An in-house breast gradient insert and bed-tabletop was constructed entirely from commercially available materials, providing a cost-effective solution compatible with existing MRI systems. Its wiring pattern was optimized for torque and force balancing, power dissipation, and target field performance. Evaluation included gradient field characterization, peripheral nerve stimulation simulation verification, and temperature and eddy current assessment. The setup was used for imaging of a
diffusion phantom based on soy lecithin across a range of b-values. Results: Gradient efficiency reached 2.8 mT/m/A, enabling local strengths up to 1850 mT/m (660 A). No peripheral nerve stimulation was observed during tests on five healthy volunteers. Eddy currents were successfully characterized employed in standard correction methods. Imaging showed the feasibility of $b = 10 000 s/mm^2$ acquisitions at TE = 78 ms versus 161 ms with scanner gradients. Conclusion: This work demonstrates a dedicated bilateral breast gradient insert for safe and feasible strong-gradient breast
diffusion MRI, and represents a first step toward dedicated hardware for breast cancer detection and characterization without contrast
agents.
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All authors Gerrit Arends, Edwin Versteeg, Feng Jia, Dennis Klomp, Maxim Zaitsev, Sebastian Littin, Chantal Tax
Biological Physics · Cross-listed from q-bio.BM
A putative, computationally stable structure of homotrimeric BP180/collagen XVII
Congzhou M Sha
Background: BP180, also known as collagen XVII and BPAG2 (bullous pemphigoid antigen 2), is a 180-kDa transmembrane
protein within the hemidesmosomal plaque complex, and which is known to be a major antigen in bullous pemphigoid, gestational pemphigoid, cicatricial (mucous membrane) pemphigoid, and linear IgA bullous disease. Objective: At present, the 3D structure of BP180 is not known. The goal is to predict a reasonable structure for BP180 through machine learning and molecular dynamics. Methods: In this work, we use the recent Boltz-2 model to predict a putative structure for the intracellular, transmembrane, and proximal extracellular domains, including the NC16A antigenic region and a portion of its first extracellular collagenous domain, Col-15. We computationally embed BP180 in a simple phospholipid
bilayer, demonstrate that the putative structure is stable using molecular dynamics, and analyze its allosteric properties. Results: The structures presented satisfy
symmetry and secondary structure properties which are expected from homology modelling. Over three 500 ns trajectories, there is minor instability of the predicted globular head domain, but the homotrimer otherwise stays mostly folded. The putative NC16A domain is stiff, whereas the truncated Col-15 domain is highly flexible. There does not appear to be a nearby stable conformation distinct from the initial state. Conclusion: The structure presented is a useful starting point for targeting BP180 pharmacologically, for further experimental characterization of BP180, and for generating hypotheses regarding the relevant epitopes contributing to bullous disease.
Diffusion models such as Boltz-2 and AlphaFold3 are useful, but their results must be evaluated carefully.
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Optics
Integrated lithium niobate microwave photonics: Driving next-generation wireless technologies
Hanke Feng, Yuansong Zeng, Kaixuan Ye et al. (+7 more)
Integrated microwave photonics (MWP) offers a powerful paradigm for handling high-speed microwave signals within chip-scale optical systems. It provides a cost-effective solution to address bandwidth, tunability, and loss bottlenecks of electronics-based
radio frequency (RF) systems. The recently emerged thin-film lithium niobate (TFLN) photonic platform, with its exceptional electro-optic (EO) properties, low loss, and scalability, has shown promise to reshape the MWP landscape. Here, we discuss the performance implications of state-of-the-art TFLN photonic devices for MWP applications and offer insights into the emerging trends for next-generation wireless networks. In particular, the unparalleled EO bandwidth enables direct optical generation, processing, and reception of millimeter-wave or even terahertz (THz) signals, significantly expanding the operation frequency range of MWP systems. The low drive voltages and linearity of TFLN modulators lead to an unprecedented operation regime of
radio-over-fiber (RoF) systems, featuring net gain, low noise figure and large dynamic range, simultaneously. The availability of a versatile device toolkit, combined with low optical loss and scalability, further supports the transition from traditional tabletop MWP systems to chip-scale solutions, with advanced functionalities, compact footprint, and enhanced system robustness. As the TFLN industrial ecosystem rapidly matures, TFLN-based MWP technology has the potential to deliver transformative solutions to future 6G integrated sensing and communication networks.
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All authors Hanke Feng, Yuansong Zeng, Kaixuan Ye, Yuansheng Tao, Zihan Tao, Tong Ge, Haowen Shu, Xingjun Wang, David Marpaung, Cheng Wang
Instrumentation and Detectors · Cross-listed from hep-ex
A study of multicavity concept applied to hexagonal coaxial haloscopes
J.M. García-Barceló, Jose R. Navarro-Madrid and Alejandro Díaz-Morcillo
In this work, a study on the development of scalable multicavity architectures for
axion haloscopes, based on a hexagonal coaxial geometry operating at $30$ GHz frequencies, is presented. To enhance the scanning rate and sensitivity within the limited volume of experimental magnet bores, the transition from a baseline single-cavity design to dual and triple-subcavity configurations is investigated. A novel tuning mechanism based on the rotation of one or two inner hexagonal prisms is implemented, providing a robust method to shift the resonant frequency while maintaining high form and quality factors. The results show that the triple-subcavity design achieves an improvement of $\times3$ over the single-cavity baseline. The scaling potential of quad-subcavity architectures under a strict radial constraint of $25$ mm is further explored. Theoretical analysis confirms that a four-subcavity system is feasible within a certain radial clearance, provided that wall thicknesses are strategically optimised to ensure frequency stability. The practical challenges associated with mode splitting, manufacturing tolerances, and thermal management in these high-order systems are also discussed. This one-port multicavity approach offers a viable path toward increasing the sensitive volume of haloscopes, enabling more efficient exploration of the
axion dark matter parameter space in high-frequency regimes.
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Applied Physics · Cross-listed from cond-mat.mtrl-sci
Thermodynamic Approach for Deciphering Magneto-Structural Phase Transitions: Proof of Concept in Heusler Alloys
Eleonora Rusconi, Lorenzo Gallo, Victor A. L'vov et al. (+7 more)
Ferromagnetic solids acquire nontrivial
magnetic and caloric properties when the temperature of the structural phase transition approaches the Curie point. Deciphering magneto-structural transitions, i.e. determining their characteristic temperatures and elucidating the related properties, remains challenging. In the present paper, three types of transformational behaviour of Ni50Mn25-xCuxGa25 (x = 6.25, 6.5, 6.75, 7) and Ni50.5Mn18.5Cu6.5Ga24.5
alloys have been identified, arising from small variations in chemical composition: (i) structural martensitic transformation (MT) in the
ferromagnetic phase; (ii) magneto-structural phase transition from paramagnetic austenite to
ferromagnetic martensite; (iii) MT in paramagnetic phase. The temperature-dependent values of magnetization, M(T), and of
magnetic susceptibility, $\chi(T)$, were measured for each
alloy. A novel thermodynamic analysis was used to determine the Curie points and MT temperatures. The novelty lies in considering the interplay between structural and
magnetic characteristics of the
alloys through the impact of the structural transition on the
spin-exchange parameter. The theoretical analysis of experimental data revealed that this impact results in a large difference ($\geq$ 50 K) between the Curie temperatures computed for the austenitic and martensitic states of each
alloy. The characteristic temperatures, corresponding to the extrema of the dM(T)/dT and $\chi(T)$ functions, were calculated. The correlation of these temperatures with the Curie temperatures and the MT temperatures is not straightforward and depends strongly on the type of transformational behaviour (i) - (iii). The proposed approach provides a robust framework for extracting unmeasurable characteristic temperatures from standard magnetization data, applicable to
ferromagnetic Heusler systems and other multiferroic
ferromagnetic materials.
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All authors Eleonora Rusconi, Lorenzo Gallo, Victor A. L'vov, Anna Kosogor, Simone Fabbrici, Giovanna Trevisi, Francesco Cugini, Massimo Solzi, Thomas Schrefl, Franca Albertini
Fluid Dynamics
Viscoelastic control of acoustic particle migration and trapping in microchannels
T. Sujith and A. K. Sen
Particle migration and trapping in ultrasonically actuated microscale flows arise from the competition between acoustic radiation forces and streaming-induced drag. While these mechanisms are well understood in Newtonian fluids, the role of fluid viscoelasticity in governing particle dynamics remains largely unexplored. Here, we investigate particle transport and trapping in a viscoelastic fluid within an ultrasonically excited microchannel under the combined action of acoustic streaming and radiation forces. Using a perturbation framework, we solve the continuity, momentum and constitutive equations for an Oldroyd-B fluid to obtain the oscillatory acoustic field and the resulting steady streaming flows in the bulk and near-wall boundary layers. Acoustic radiation forces, incorporated through a semi-analytical model, drives particle migration, while streaming-induced drag can oppose, alter or suppress trapping. We show that particle trajectories and
equilibrium trapping locations are governed primarily by the Deborah number ($De$) and viscous
diffusion number ($Dv$). At high $Dv$, increasing $De$ shifts the trapping location from the bulk region to the channel wall, pressure nodal line, channel centre or ultrasound
symmetry line. We further determine the critical particle size governing the transition between radiation-dominated and streaming-dominated regimes as a function of $De$ and $Dv$. The critical particle size can become significantly smaller than that in a Newtonian fluid, enabling effective manipulation of submicron particles and overcoming a key limitation of conventional acoustofluidics. These results demonstrate how viscoelasticity fundamentally modifies acoustophoretic transport and establish new mechanisms for tunable particle migration and trapping in complex fluids.
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Optics
Geometrical Tuning of Light-Matter Interaction in Atomic Trimer Antennas: A Symmetry-Resolved Modal Analysis
Linsa G. J., Pushpender Singh, Rohit Dhir et al. (+1 more)
Atomic trimers constitute the smallest geometry in which collective electric and
magnetic responses emerge from coupled electric dipoles. We present a theoretical study of collective mode excitation in atomic trimers as the geometry is continuously tuned from linear to equilateral, using the coupled-dipole method with a multipole expansion formulated about the optimal scattering center. By combining eigenmode analysis and
symmetry classification, we provide a complete
symmetry-resolved map of the six in-plane and three out-of-plane modes, revealing how
symmetry reduction across the $D_{\infty h}$, $C_{2v}$, and $D_{3h}$ configurations governs the
evolution of eigenmodes and their spectral features, lifting degeneracies, activating dark modes, and enabling full access to the modal spectrum. Based on this modal understanding, we demonstrate that forward-backward scattering can be switched solely by frequency detuning in a nearly linear trimer, without
geometric reconfiguration. Furthermore, a linear trimer under s-polarized excitation supports a
magnetic mode with a strongly enhanced
magnetic field and a large Purcell factor, making it a promising platform for probing
magnetic dipole transitions in atoms, with emission preferentially directed into the transverse plane. These results establish atomic trimers as a minimal platform where
symmetry-controlled electric-
magnetic mode engineering can be fully resolved and exploited for tailoring light-matter interaction at the atomic level.
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All authors Linsa G. J., Pushpender Singh, Rohit Dhir, M. Ameen Poyli
Optics
Metasurface spaceplates reach a millimeter-scale squeezed length of free space
Imon Kalyan, Raghvendra P. Chaudhary and Nir Shitrit
Metasurfaces offer compact flat lenses (metalenses) for miniaturized imaging systems; however, the utmost miniaturization requires not only metalenses but also a substantial reduction of free space. A Spaceplate is a flat-optics element designed to mimic free-space propagation, effectively propagating light over a distance far exceeding its physical thickness, with the induced squeezed length serving as the key figure of merit. Despite substantial progress, most existing spaceplate designs have been fundamentally constrained by a trade-off between squeezed length and numerical aperture, and none has demonstrated a feasible structure supporting both a moderate numerical aperture and a millimeter-scale squeezed length. We report a metasurface spaceplate reaching the milestone of a millimeter-scale squeezed length with a practical numerical aperture. We achieved this by combining advantageous elements from existing approaches: high compression ratios and inverse-design flexibility in optimized multilayer metasurfaces, serving as the spaceplate unit structure, and preserving its numerical aperture by coupling its replicas, to construct a coupled cascaded spaceplate with an increased thickness. For operation in the mid-wave infrared, we demonstrated an optimized spaceplate exhibiting a high compression ratio of ~14 with a physical thickness of ~80 {\mu}m, resulting in a squeezed length of 1.09 mm, for a numerical aperture of 0.13. We developed a general framework for calculating the transmission characteristics of multilayered spaceplates while optimizing their layer thicknesses to accurately reproduce the target free space. Strikingly, millimeter-scale squeezed lengths with practical numerical apertures via metasurface spaceplates pave the way for ultrathin imaging systems through their utmost miniaturization, opening a new paradigm for augmented reality headsets, cellphones, and many more.
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Atomic Physics · Cross-listed from quant-ph
Bloch Siegert Physics in a Reconfigurable Photonic Binary Lattice
Ze-Sheng Xu, Liwei Duan, Rohan Yadgirkar et al. (+4 more)
The Bloch Siegert shift, a hallmark correction arising from counter-rotating interactions in driven two-level systems, has an exact counterpart in binary
lattices under static forcing, where it governs resonant long-range tunneling between sites separated by odd
lattice spacings. Here we report the first experimental realization of this correspondence using a 12 mode programmable photonic integrated
circuit. By implementing a reconfigurable binary
lattice with sub-percent control of on-site detuning, we observe coherent periodic jumps across four resonance orders and quantitatively verify the predicted period law over the full parameter space. The measured dynamics exhibit the extreme resonance sensitivity characteristic of Bloch Siegert physics and agree closely with the level-anticrossing picture of the semiclassical Rabi model. Exploiting the underlying parity structure, we further convert intrinsically bidirectional oscillations into cascaded unidirectional transport through adaptive sign reversal of the staggered potential, achieving fidelities exceeding 0.95 and 0.98 on the same hardware platform. Our results establish programmable photonic
lattices as a scalable testbed for strongly driven
quantum-optical phenomena and Floquet-engineered transport.
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All authors Ze-Sheng Xu, Liwei Duan, Rohan Yadgirkar, Andrea Cataldo, Adrian Iovan, Jun Gao, Ali W. Elshaari
Fluid Dynamics
Data-driven Symbolic Closure for Turbulence Modeling in the Lattice Boltzmann Framework
Yujie Fu, Yihan Zhang, Wanru Deng et al. (+1 more)
Turbulence modeling within the
Lattice Boltzmann Method (LBM) framework has long relied on traditional algebraic sub-grid scale (SGS) models, which often suffer from over-dissipation and lack of spatial selectivity near solid boundaries. In this work, we utilize Physical Symbolic Optimization (Phi-SO) to discover explicit analytical closures from high-fidelity DNS
datasets of Taylor-Green
Vortex (TGV) and Lid-Driven Cavity (LDC) flows. Central to our methodology is the integration of virtual dimensional analysis and non-linear tensor invariants, a strategy that enforces physical scaling laws directly within the symbolic search process. The resulting model exhibits a highly non-linear dependency on both strain-rate and rotation-rate invariants. Numerical validations confirm that this symbolic closure outperforms the standard Smagorinsky approach in capturing kinetic energy dissipation rate peaks and resolving delicate secondary corner
vortices. Furthermore, the model exhibits robust zero-shot generalization to wall-bounded turbulent channel flow (Re_tau = 180) without the aid of any supplemental wall-damping corrections. This work highlights the potential of symbolic regression to uncover robust, interpretable physical laws for the next generation of intelligent computational fluid dynamics solvers.
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All authors Yujie Fu, Yihan Zhang, Wanru Deng, Yuanjun Dai
Fluid Dynamics
Disentangling coherent structures and the origin of swirl-switching
Eman Bagheri, Riccardo Casali, Stefan Becker et al. (+1 more)
The physical origin of swirl-switching in turbulent bent-pipe flow remains the subject of ongoing research. We perform three direct numerical simulations (DNS) of flow through a $180^{\circ}$ bent pipe for
curvature $\gamma=0.2$ at $Re_D=5,300$ and $Re_D=10,000$, and for
curvature $\gamma=0.4$ at $Re_D=5,300$. Here, $Re_D$ is the Reynolds number based on the bulk velocity $U_b$ and pipe diameter $D$. The DNS data are subsequently used to conduct modal decompositions and local stability analysis (LSA). We discuss the limitations of common modal decomposition methods and introduce a new decomposition method, filtered
Hilbert proper orthogonal decomposition (FHPOD), enabling us to isolate different instabilities as distinct FHPOD modes. FHPOD reveals seven modes belonging to four distinct families: a low-frequency axial mode, two swirl-switching modes, two swirl-breathing modes and a pair of downstream shear-layer modes. The swirl-switching and swirl-breathing modes are localised to the curved section of the bent-pipe flow and represent the sinuous and varicose instabilities of the Dean
vortices, respectively. The DNS data are used to perform local stability analysis of the mean flow using the frozen eddy-viscosity method at the two streamwise wavenumbers associated with the two swirl-switching and swirl-breathing modes. The linear stability analysis reveals six unstable branches, with the swirl-switching mode being the most unstable branch. Another unstable branch represents the swirl-breathing mode. The modes obtained from the local stability analysis are in close agreement with their FHPOD counterparts in both spatial features and the range of Strouhal numbers. The results support the interpretation that swirl-switching arises as an intrinsic instability of the bent-pipe mean flow, which can be excited by incoming turbulent structures.
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All authors Eman Bagheri, Riccardo Casali, Stefan Becker, Philipp Schlatter
Instrumentation and Detectors
A Modular Zero-Dead-Time Data Acquisition and Real-Time GPU Processing Platform for High Throughput Physics Experiments
Toma-Stefan Cezar, Marios Maroudas and Dieter Horns
High-throughput physics experiments require efficient and increasingly complex real-time processing. This paper presents a modular, software-defined platform combining high-bandwidth PCIe digitizers with consumer GPUs to achieve continuous, zero-dead-time data acquisition. Utilizing NVIDIA CUDA, the system provides a scalable pipeline for real-time fast
Fourier transforms and statistical averaging.
Benchmarks demonstrate that the platform can sustain continuous processing at sampling rates up to 500 MSa/s, effectively managing data throughputs of 1 GB/s. To validate the in-situ zero-dead-time architecture, end-to-end phase continuity tests were conducted, constraining fractional data loss to below $10^{-12}$. Furthermore, long-term system stability was demonstrated through an uninterrupted one-month data acquisition run. In its current deployment for the WISPLC dark matter experiment, the platform operates at 124 MSa/s with a resolution bandwidth of 0.1 Hz. This implementation enabled a significant reduction in data storage requirements using real-time spectral averaging. The callback-driven software architecture, multi-GPU workload distribution, and custom hardware shielding solutions are detailed, establishing this platform as a flexible and cost-effective alternative to traditional hardware-based pipelines.
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Fluid Dynamics · Cross-listed from cs.LG
Inpainting physics: self-supervised learning for context-driven fluid simulation
Jonas Weidner, Yeray Martin-Ruisanchez, Daniel Rueckert et al. (+2 more)
Neural surrogate models for computational fluid dynamics (CFD) are typically trained as forward operators that map explicit problem specifications, such as geometry and boundary conditions, to solution fields. This ties the model to the conditioning variables seen during training and limits reuse under boundary-condition shifts or local geometry changes. We propose to reformulate steady CFD inference as an inpainting problem: instead of training on explicit boundary conditions, we learn a self-supervised prior over velocity fields and impose boundary constraints only during inference by fixing known regions such as inlet, outlet or unchanged regions from previous simulations. To scale this idea to large 3D meshes, we introduce a local neighbourhood tokeniser that represents high-resolution velocity fields as compact spatial latent
tokens and train latent flow-matching and masked-autoencoder models on these
tokens. On intracranial aneurysm hemodynamics, our method reconstructs full velocity fields from sparse boundary context, outperforms supervised neural surrogates under boundary-condition and
dataset shift and enables local geometry editing by reusing unchanged simulation context. These results suggest that viewing CFD inference as context-conditioned inpainting can turn neural surrogates from task-specific predictors into reusable flow priors.
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All authors Jonas Weidner, Yeray Martin-Ruisanchez, Daniel Rueckert, Benedikt Wiestler, Julian Suk
Optics
Ultra-BroadBand Electromagnetic Control Using a Triple Circular Ring Metasurface: Surface Wave Propagation, Beam Steering, and RCS reduction (50-100 Ghz)
Md. Al Amin Chy, Tasnimul Hasan Tasneem, Sabbir Ahmad Chowdhury et al. (+1 more)
Traditional metasurfaces often face challenges in achieving broadband functionality and dynamic adaptability, limiting their use in advanced electromagnetic systems. This paper presents a triple circular ring metasurface designed for multifunctional electromagnetic applications, including surface wave propagation, beam shaping, and ultra-broadband radar cross-section (RCS) reduction. The proposed structure uses a cost-effective FR-4 substrate and demonstrates strong electromagnetic reflection characteristics across 50-100 GHz. Except near 91 GHz, the metasurface exhibits amplitude and phase responses comparable to a conventional copper plate while maintaining efficient surface wave propagation. Significant electric and
magnetic field amplitudes of nearly 1 V/m and 5x10^-3 A/m are sustained across the surface, unlike a standard copper plate. The metasurface also redirects incident energy toward a predefined direction of 67 degrees in the phi plane while minimizing radiation over a 360-degree angular range. In addition, it achieves a stable monostatic RCS reduction from -40 dB to -30 dB across a broad frequency range, outperforming conventional copper structures. Numerical simulations validate the proposed design. The results demonstrate strong potential for stealth technology, radar systems, and next-generation wireless communications.
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All authors Md. Al Amin Chy, Tasnimul Hasan Tasneem, Sabbir Ahmad Chowdhury, M.R.C. Mahdy
Optics
Reconfigurable Magnetic Nanopore Platform for Selective Trapping
Nageswar Reddy Sanamreddy, Jeanne Maunier, Malavika Kayyil Veedu et al. (+5 more)
Solid-state nanopores offer a powerful platform for nanoscale analysis of individual analytes, including biomolecules and functionalized nanoparticles, by confining them within a precisely defined sensing region. However, their inherently passive operation restricts practical applications, as they cannot precisely control particle position or dynamics inside the pore. Here, we introduce
magnetic nanopore architectures that integrate a
ferromagnetic layer into the nanopore system. Acting as a
magnetic discontinuity within an otherwise uniformly magnetized film, the nanopore generates localized stray
magnetic fields that enable
magnetic tweezing of
magnetic nanoparticles, which can be functionalized with fluorescent biomolecules. Importantly, the nanopore geometry is designed to reversibly switch between a nearly uniform magnetization state and a
magnetic flux-closure state through the application of short
magnetic field pulses of controlled amplitude. This capability allows the
magnetic tweezing effect to be selectively activated or deactivated, enabling controlled capture and release of tagged biomolecules on demand. As a proof of concept, we demonstrate the selective
magnetic trapping of fluorescent
magnetic particles. These findings pave the way for reconfigurable, on-chip
magnetic nanopore platforms capable of selective trapping and high-throughput single-particle detection. KEYWORDS: Nanopores,
magnetic tweezers, fluorescence microscopy,
vortex state, active control,
magnetic nanoparticles
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All authors Nageswar Reddy Sanamreddy, Jeanne Maunier, Malavika Kayyil Veedu, Anastasiia Sapunova, Nicolò Maccaferri, Denis Garoli, Jérôme Wenger, Paolo Vavassori
Data Analysis and Statistics · Cross-listed from econ.GN
The Phase Structure of Metallic Money: An MPTT Framework for the Spanish Price Revolution
Ran Huang
The Spanish Price Revolution is usually treated as a classic case in which American bullion inflows expanded the money supply and generated inflation. This view captures the first phase of the episode but fails to explain why the same monetary expansion did not continue to produce proportional price growth after 1600. We develop a two-phase Money Phase Transition Theory (MPTT) model in which the classical monetary relation is recovered before a transition point, while a second-phase correction term modifies the money-price transmission coefficient after the transition. Using annual Spanish CPI and reconstructed money-supply data, we show that 1500-1600 was a high-transmission metallic inflationary phase: CPI increased approximately 3.35-fold while money supply increased approximately 3.73-fold. After 1600, money supply continued to rise, increasing approximately 1.82-fold during 1600-1650, while CPI rose only approximately 1.22-fold. A classical one-phase model fitted on 1500-1600, therefore, overpredicts post-1600 prices when extrapolated forward. The MPTT two-phase model with transition point tau=1600 estimates beta_1=0.949, gamma=-0.812, and beta_2=beta_1+gamma=0.137, indicating a sharp post-transition weakening of monetary transmission. An unrestricted break scan identifies a deeper BIC-minimizing break around 1636. These results suggest that the Spanish Price Revolution was not a single monotonic bullion-inflation process but the rise and exhaustion of high-transmission metallic money inflation.
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Biological Physics · Cross-listed from cond-mat.soft
Concentration-Dependent Membrane Destabilization in DPPC Bilayers: Distinct Insertion Mechanisms and Stress Redistribution by Chloroform and Alkanols
Anirban Polley
How do solute concentration and molecular chemistry govern the transition from membrane saturation to destabilization? We address this using microsecond-scale molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC)
bilayers with chloroform (CHCl$_3$) and a homologous series of alkanols (methanol, ethanol, octanol) over $0-50\%$ concentrations. Although complete membrane melting is not observed within $1000\, ns$, all systems exhibit clear precursors of destabilization, including enhanced thickness fluctuations, reduced lipid order, and mechanical softening. Chloroform induces pronounced thinning and large fluctuations, consistent with deep, transient insertion. Methanol perturbs primarily the headgroup region, while ethanol shows intermediate behavior with partial insertion. Octanol preserves
bilayer thickness at high concentrations due to lipid-like insertion but significantly increases fluctuations and interdigitation. Across all systems, increasing concentration decreases the area compressibility modulus and deuterium order parameter, accompanied by smoothing of lateral pressure profiles, indicating stress redistribution. Free energy analysis reveals increased membrane partitioning and reduced translocation barriers with concentration, strongest for octanol and weakest for methanol. These results demonstrate that membrane destabilization is governed by the interplay of insertion depth, interfacial crowding, and lipid packing disruption.
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Optics
Magnetoplasmonic Nanopore Lensing for Enhanced Optical Readout and Controlled Translocation
Nageswar Reddy Sanamreddy and Paolo Vavassori
Plasmonic nanopores hold a significant promise for molecular sequencing, but their sensitivity and temporal resolution are constrained by limited signal strength and rapid translocation of molecules through the pore. Here we report an experimentally developed hybrid magnetoplasmonic nanopore platform based on bull's-eye geometry that concentrates surface plasmon polaritons into the pore, resulting in significant electric-field enhancement and improved signal readout. The addition of a
ferromagnetic layer allows for
magnetic tweezing of magneto-plasmonic nanoparticle-tagged molecules, providing active control over their translocation dynamics. Simulations reveal a further boost in enhancement arising from mirror-on-mirror plasmonic coupling between the nanopore and wall-aligned tagged nanoparticles. Together, experimental realization and simulation-guided insights establish a magnetically configurable, plasmonically enhanced nanopore platform that combines signal amplification with controlled translocation for advanced single-molecule sensing and sequencing. KEYWORDS: Nanopores, plasmonics, single-molecule sequencing, magneto-plasmonics, active control,
magnetic tweezing.
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Applied Physics
Time-Controlled Resonances in 2-D Metasurfaces via Equivalent Circuits
J. Rafael Sánchez-Martínez, Mario Pérez-Escribano, Antonio Alex-Amor et al. (+2 more)
This work introduces a semi-analytical frequency-domain framework for the analysis of two-dimensional, time-modulated (2+1)-D metasurfaces controlled by PIN diodes. The formulation focuses on the unit-
cell level, modeled as a waveguide discontinuity problem, where the space-time periodicity of the structure enables the representation of scattered fields via Floquet expansions. After appropriate mathematical treatment, these expansions lead to an equivalent
circuit description of the metasurface, providing physical insight into its spatiotemporal scattering behavior and facilitating the design of reconfigurable electromagnetic devices. The model is employed to explore key phenomena present in space-time systems, such as frequency mixing and spatiotemporal scattering. In addition, dynamic tuning is explored in resonant metasurfaces, where time becomes an additional degree of freedom for the design. The dynamic control of resonances opens a new way to explore multi-band and wideband behaviors from very thin metasurfaces under temporal coupling.
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All authors J. Rafael Sánchez-Martínez, Mario Pérez-Escribano, Antonio Alex-Amor, Juan F. Valenzuela-Valdés, Carlos Molero
Medical Physics
Automated Optical Density Normalization for Myelin Quantification: Cross-Modal Validation with 7T Ex Vivo MRI
Zahra Khodakarami, Sheina Emrani, Pulkit Khandelwal et al. (+21 more)
White matter hyperintensities (WMH) are bright regions on T2-weighted
magnetic resonance imaging (MRI) scans and are associated with cerebrovascular pathology and neurodegeneration, including myelin loss. While Luxol Fast Blue histopathology provides visualization of myelin integrity, quantitative analysis requires measuring Optical Density as a proxy for myelin concentration. However, differences in laboratory protocols and tissue processing introduce staining variability that acts as systematic noise, obscuring the biological signal and preventing consistent comparison across histology runs. To address this, we developed an automated pipeline that identifies reference (non-pathologic) regions in whole-slide images to compute normalized Optical Density heatmaps. We validated this approach through two complementary evaluations: (1) comparison against expert ratings of myelin loss severity, and (2) cross-modal spatial comparison with co-registered 7T ex vivo MRI for voxel-wise evaluation within white matter regions. The pipeline's reference selection showed strong concordance with expert-identified reference regions, and normalized Optical Density demonstrated a substantially stronger correlation with MRI signal intensity than raw measurements. This correlation persisted within WMH, confirming that the pipeline captures continuous myelin pathology rather than merely the presence or absence of myelin loss contrast. By mitigating staining artifacts, this pipeline provides a robust, validated framework for quantitative cross-modal comparison, establishing a critical methodological foundation for future translation to in vivo myelin mapping and biomarker discovery.
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All authors Zahra Khodakarami, Sheina Emrani, Pulkit Khandelwal, Chinmayee Athalye, Amanda Denning, Winifred Trotman, Lisa M Levorse, Eric Teunissen-Bermeo, Hamsanandini Radhakrishnan, Daniel Ohm, Christophe Olm, Noah Capp, Ranjit Ittyerah, Karthik Prabhakaran, John A. Detre, Sandhitsu R. Das, David A. Wolk, Corey T McMillan, Gabor Mizsei, M. Dylan Tisdall, David J Irwin, John L. Robinson, Edward B Lee, Paul A. Yushkevich
Chemical Physics
Detection Defines Dephasing in Two-Dimensional Electronic Spectroscopy of Materials: Coherent Field Emission versus Incoherent Population Observables
Simón Paiva-Ortega, Hao Li, Eric R. Bittner et al. (+1 more)
The homogeneous spectral linewidth associated with light-matter interactions is a fundamental descriptor of the optical properties of materials, governed by the
quantum dynamics of the condensed-matter system. We discuss here that the homogeneous linewidth measured by means of two-dimensional electronic spectroscopy depends not only on the intrinsic microscopic dynamics of the material, but also on the observable through which those dynamics are projected onto the measurement. In this Perspective, we develop a unified framework showing that identical microscopic dynamics can yield different experimentally inferred dephasing times because different detection operators project different sectors of the nonequilibrium dynamics. For coherent emitted-field measurements, the observed linewidth largely retains its conventional connection to the optical coherence time $T_2$. By contrast, in population-detected modalities such as photoluminescence, photocurrent, and other action-detected two-dimensional spectroscopies, the apparent linewidth can additionally encode excited-state population redistribution dynamics, leading naturally to an effective coherence time $T_{2,\mathrm{eff}}$. Using a coupled-mode model propagated under a common Liouvillian, we show that identical microscopic dynamics yield distinct apparent dephasing times when projected onto coherent-emission and population-derived observables. The detection observable is therefore not merely part of the experimental implementation, but determines what dynamical information remains experimentally observable and how homogeneous linewidths should be interpreted as materials descriptors.
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All authors Simón Paiva-Ortega, Hao Li, Eric R. Bittner, Carlos Silva-Acuña
Atmospheric and Oceanic Physics · Cross-listed from cs.LG
METBRA25Y: Brazil Surface Meteorology Archive with Harmonized Variables and Quality Control
Matheus Lima Castro, William Dantas Vichete and Leopoldo Lusquino Filho
This data paper describes METBRA25Y, a harmonized archive of hourly surface meteorological observations from Brazil derived from public historical records of the Instituto Nacional de Meteorologia (INMET). The
dataset was designed to support reproducible environmental, climatological, hydrological, agricultural, urban-risk, and machine-learning studies that require station-level meteorological time series with standardized variable names and explicit quality-control metadata. The processing workflow ingests annual INMET archives, parses station metadata from raw file headers, normalizes heterogeneous Portuguese column names into a canonical schema, constructs hourly timestamps, consolidates observations by city and station, and exports compressed CSV files together with station manifests, per-station quality flags, daily precipitation aggregates, variable-level failure summaries, and missing-data audits. The quality-control protocol follows a two-stage strategy: first, physically implausible values are converted to missing values and flagged; second, temporal and cross-variable consistency checks generate diagnostic flags without necessarily overwriting the original measurements. The resulting package covers observations between 2000 and 2025, with stationspecific temporal coverage, and includes key meteorological variables such as precipitation, air temperature, dew point, relative humidity, atmospheric pressure, wind speed, wind gust, wind direction, and global
solar radiation. Based on the summary files included in the current release snapshot, the archive contains 616 unique station codes across variable summaries, of which 605 have coordinates within a broad Brazil plausibility envelope. This paper documents the
dataset provenance, file organization, harmonized schema, quality-control rules, technical validation outputs, limitations, and recommended usage practices.
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