Instrumentation and Detectors
Application of sequence learning for predicting radiation damage of the CMS electromagnetic calorimeter
Mario Ivan Gallegos Torres, Leonid Serkin and Guy Paic
In this paper we use machine learning methods to predict radiation damage in the lead tungstate
crystals of the CMS electromagnetic calorimeter at the Large
Hadron Collider. We analyze LHC Open Data collected from 2016 to 2018 and study the time
evolution of the
crystal optical transparency. We apply deep neural network models to predict its behavior over different future time intervals, and find that encoder-decoder sequence-to-sequence architectures can effectively describe
crystal aging.
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Optics · Cross-listed from quant-ph
Modal input-output theory for quantum nanophotonics from the first-order Maxwell operator
Ankit Kundu, Ishita Agarwal, Adhyyan S. Mansukhani et al. (+1 more)
We develop a
quantum input-output theory for open photonic systems based on macroscopic
quantum electrodynamics using the first-order electromagnetic Green's function.
Quantum fields enter and leave the photonic system through waveguide ports, while the electromagnetic Green's function propagates the fields through the arbitrary interior of the photonic system, which may be dispersive and absorbing. The resulting relation contains a port-to-port scattering
matrix and a Langevin-noise contribution from material absorption that together preserve the bosonic output commutation relations. For embedded emitters, the low-saturation and single-excitation scattering response is determined by Green's functions connecting the ports and emitters while retaining the non-Markovianity of the photonic environment. Using finite-difference time-domain simulation, we calculate the emitter-modified transmission for a nanophotonic cavity and inverse-designed coupler, providing a direct route from computed electromagnetic response to a
quantum input-output model.
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All authors Ankit Kundu, Ishita Agarwal, Adhyyan S. Mansukhani, Jonathan D. Hood
Fluid Dynamics
Unveiling the stress field in a flowing complex fluid with velocity and microstructure imaging
Ashinth Mangesh, Manish Kumar, Matthew E. Helgeson et al. (+1 more)
The stress in a flowing complex fluid such as a solution of
polymers, surfactants and/or colloidal particles is a fundamental dynamic property of the material. It reflects the
evolution of the fluid microstructure under deformation and determines the motion of the fluid. While spatially resolved measurements of flow (via velocimetry) and microstructure (e.g.~via scattering) can be made, neither of these individually can uniquely determine the stress. In particular, due to the degenerate nature of the relationship between the stress tensor and the net force exerted by the microstructure on the fluid, the stress tensor is hidden from direct observation. We show that integrating velocity and microstructure measurements with principles of continuum mechanics can break this degeneracy, unveiling the stress tensor. The approach has two stages. In the first, velocity information is used along with the momentum and mass conservation equations to infer the force density exerted by the microstructure on the fluid using a data assimilation framework. In the second, the equation relating force density to stress is solved. This equation has a nontrivial nullspace, introducing a homogeneous solution whose structure must be found to uniquely determine the stress. We do so by using microstructural data and a general model between microstructure and stress, the parameters of which are determined, along with the nullspace solution, by solving a least-squares problem. The approach is illustrated using synthetic velocity and microstructural data from simulation of a flowing
polymer solution, demonstrating its validity and robustness.
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All authors Ashinth Mangesh, Manish Kumar, Matthew E. Helgeson, Michael D. Graham
Applied Physics · Cross-listed from quant-ph
Accelerated search for global extrema in structured quantum signals
Sachin S. Bharadwaj and Katepalli R. Sreenivasan
Extreme values of a physical system are rare by definition, yet they can govern some of its most consequential and anomalous behavior. Their sparsity makes them particularly costly to identify in large data sets.
Quantum computation offers a potential way to reduce this cost. The challenge is that
quantum amplitudes cannot simply be read, copied, compared, or marked using conventional search oracles. Here we introduce an
algorithm for searching amplitude-encoded
quantum signals that exploits their underlying structure. Through a nonlinear amplitude transformation, the
algorithm identifies and certifies a global extremum while exponentially reducing the effective search space for structured signals. We establish a polylogarithmic query complexity in the data size $N$, together with global completeness, efficient classical verification, and a measurable criterion for quantifying exploitable structure. We demonstrate the framework using computational
turbulence data. Applied to line cuts of velocity gradients from a $1024^3$ simulation containing more than one billion grid points, the
algorithm consistently isolates the extreme tail and reduces the median search space to $O(\log N)$. The clustered structure characteristic of
turbulence further accelerates the search. These results establish a direct connection between physical structure and
quantum advantage in extreme-value search. For accessibility, the main text emphasizes the central ideas and results, while the theoretical derivations are provided in the Appendices.
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Physics and Society
Verification of the Outer Space Treaty with active interrogation
Patrick Huber
We present an analysis of active interrogation in space with the goal to verify the absence of nuclear weapons hidden in a large constellation of satellites. We propose a 16 MeV
photon beam generated by advanced
laser wakefield accelerators and the detection of fission
neutrons using segmented organic scintillators. We use Starlink as a real-world example for the constellation and solve the inspector routing problem against this set of 7,852 satellites over a 5-year mission period. We perform detailed simulation of the nuclear and orbit physics: signal generation and detection with GEANT4 against an orbit-resolved
neutron and gamma background, routes flown with Orekit including the effects from the Earth's oblateness, and detection decided by a likelihood ratio test. We identify different encounter types and fleet designs based on a range of inspector platforms. The radiation dose to target satellites from the beam can be kept to about 1% or less of the 5-year space environment dose. We find that a small number of inspection platforms, 20-70 depending on the accelerator assumptions, can serve inspections to the full constellation with a detection probability of 90% against a single deployed warhead. A 10% random sample of the whole fleet can be inspected by 2-20 platforms providing a 37% detection probability against 5 deployed warheads.
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Instrumentation and Detectors · Cross-listed from cond-mat.str-el
ToF-PAX-RIXS: A Time-of-Flight Spectrometer for combined ARPES and RIXS
Chafic Fawaz, Tom Lacmannn, Yaryna Lytvynenko et al. (+24 more)
We present ToF-PAX-RIXS, a compact instrument that combines time-of-flight momentum-microscopy angle-resolved photoemission spectroscopy (ARPES) with resonant inelastic X-ray scattering (RIXS). The latter is based on photoelectron spectrometry for analysis of X-rays (PAX). The two techniques are implemented with a single multimode electron-optical column, allowing measurements to be performed sequentially on the same sample under identical experimental conditions. In ARPES mode, the instrument records the photoemission intensity as a function of kinetic energy and two in-plane momentum components. In PAX-RIXS mode, scattered soft X-ray
photons are absorbed in a thin metallic converter, and the generated photoelectrons are analyzed in energy and position of emission on the converter. The electron kinetic energy retains the spectral information of the scattered
photons, while the position is related to the scattering angle and therefore to the momentum transfer, enabling simultaneous access to a finite momentum-transfer interval. We describe the mechanical design, converter assembly, scattering geometry, and multimode electron optics of the instrument. Its PAX-RIXS performance is benchmarked at the Cu $L_3$ edge using CaCuO$_2$, with Au, Ag, and Pt converters. The measured spectra reproduce the principal features obtained with a conventional grating RIXS spectrometer, and deconvolution yields an effective reconstructed energy resolution better than $120$~meV under the present conditions. Finally, combined ARPES and PAX-RIXS measurements on the same Ca-doped YBa$_2$Cu$_3$O$_{6.45}$ sample demonstrate the capability of the instrument to correlate electronic structure and collective excitations within a common compact platform.
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All authors Chafic Fawaz, Tom Lacmannn, Yaryna Lytvynenko, Sergii Chernov, Olena Tkach, Siegmar Roth, Jan O. Schunck, Amon Lanz, Jakob Dilling, Lukas Bruckmeier, Markus Scholz, Frank Scholz, Arne Meyer, Dirk Fuchs, Lara Schmieder, Yiran Liu, Matteo Minola, Bernhard Keimer, Dmytro Kutnyakhov, Kai Rossnagel, Olena Fedchenko, Angela Wittmann, Moritz Hoesch, Gerd Schönhense, Matthieu Le Tacon, Hans-Joachim Elmers, Martin Beye
Computational Physics · Cross-listed from cond-mat.mtrl-sci
Equivariant generative diffusion learns and generalizes the structural ensemble of amorphous oxides
Jun Jiang, Ian Berry, James N. Fry et al. (+1 more)
Amorphous materials are statistical ensembles rather than definitive structures, and conventional density-functional (DFT) and machine-learned-potential simulations sample only a small part of that ensemble. We present an $SE(3)$-equivariant denoising-
diffusion model that learns the configurational distribution of amorphous oxides, so the model itself is the structure database. The learning is data efficient. A model trained on $1{,}781$ DFT configurations suffices to reproduce partial radial distribution functions, coordination statistics and bond-angle distributions, and to generate models of over $3\times10^{5}$ atoms at a cost comparable to that of the cheapest classical pair potentials. The trained model can propose amorphous atomic structures for first-principles relaxation to explore the configuration space. For example, it locates an amorphous Zr-Ta-O structure $36$ meV/atom below the previously known minimum. Generation can also extend beyond trained conditions to non-stoichiometric compositions, other mass densities, interfaces, and doping. First-principles verification confirms that generation can be steered to a requested energy, and shows that the denoising training loss does not rank generative quality, because the two measure different things.
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All authors Jun Jiang, Ian Berry, James N. Fry, Hai-Ping Cheng
Atomic Physics · Cross-listed from quant-ph
Rydberg-mediated microwave-to-optical transduction with tunable bandwidth
Iason Tsiamis, David Petrosyan and Anders S. Sørensen
Coherent microwave-to-optical transduction is essential for hybrid
quantum networks. Typical transducers, however, have bandwidths set by fixed device parameters and face efficiency-bandwidth tradeoffs. We propose a cavity-based microwave-to-optical transducer mediated by a collective Rydberg excitation, where external driving fields tune the conversion bandwidth in situ from narrowband, spectrally selective operation to broadband operation without modifying cavity parameters. Under impedance-matching conditions, the system operates as a continuous-wave phase-preserving linear transducer, maintaining both near-unit efficiency and
quantum-limited added noise throughout the tunable bandwidth range.
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Biological Physics
A Clinical–Metabolic Approach to Determining Calcium Requirements: Interplay of the Glucose Axis, PTH–Vitamin D Signalling and Bone Mineral Density
Alex Velez Cruz, Oscar Dam and Jairo Rondon
Calcium homeostasis is maintained by an endocrine network comprising parathyroid hormone (PTH), calcitriol and calcitonin, which defends serum calcium at the expense of skeletal reserves. Serum calcium is therefore an unreliable indicator of nutritional calcium status, and empirical supplementation remains common. This narrative review proposes a clinical–metabolic approach to estimating individual calcium requirements that integrates bone mineral density (BMD), vitamin D status and the compensatory PTH response. We make three contributions. First, we present a sigmoidal phosphate–PTH model in which a glucose-dependent gain term ($\Delta k_{\mathrm{gluc}}$) captures the heightened parathyroid sensitivity associated with dysglycaemia, and we illustrate it with simulated values for healthy adults, women and individuals with gluco-osteoporosis. Second, we translate the model into a four-step decision
algorithm that frames the intake gap as a net balance of intestinal absorption, renal excretion and bone turnover. Third, we incorporate the osteocyte–osteoblast bioenergetic axis (sclerostin/Wnt signalling, GLUT1-mediated glucose uptake, aerobic glycolysis and osteocalcin–insulin crosstalk) to explain why calcium supplementation may be ineffective when cellular energy supply or insulin sensitivity is impaired. The framework aims to prevent secondary hyperparathyroidism, avoid over supplementation and preserve skeletal integrity. The model values are simulated and require prospective clinical validation.
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Biological Physics
Dynamics of microvesicle formation driven by glycocalyx
Ke Xiao and Chen-Xu Wu
Microvesicles (MVs), a type of
cell-secreted extracellular vesicle (EV), are essential for various biological processes such as local and long-distance intercellular communication and the disposal of unwanted materials. Recent evidence suggests that overexpression of MUC1 glycoproteins facilitates MV formation on the
cell membrane, but the mechanism underlying this nonequilibrium process remains unknown. Here, the kinetics of glycocalyx-driven MV formation is studied in the framework of Onsager's variational principle. Using this deterministic theory, we first show that the process of MV formation is accelerated for the denser and thicker glycocalyx-grafted
cell membrane and can be improved by reducing the ionic strength or enhancing the degree of glycocalyx ionization. Intriguingly, we further discover that there exists an optimal glycocalyx coverage for the fastest formation of MVs. We then investigated the process of MV formation using a
stochastic approach. Our results suggest that the transition rate is not constant, leading to the prediction of a shorter formation time compared to the deterministic approach. These findings provide valuable insights into the regulation of membrane morphology and MV secretion by the glycocalyx, with implications for both understanding and modulating these processes.
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Applied Physics
A Novel Iterative-Fitting Approach for the Thermal Characterization of Thin Fibers
William Spirnock, Alison Hake, Dihui Wang et al. (+3 more)
The transient electrothermal technique (TET) is widely used to measure the thermal properties of thin fibers and films, but its accuracy declines when radiative heat losses are significant and surface emissivity is unknown. These conditions are difficult to avoid at the microscale, while conventional analyses either neglect them or rely on separate measurements that introduce sequential errors. We present a TET implementation that determines multiple thermal properties and effective surface emissivity from only two transient measurements. An analytical model incorporating thermal radiation and variable heat generation supports sensitivity-guided, multiparameter fitting. Two forms of the temperature solution yield thermal conductivity and diffusivity, and thermal conductivity and volumetric heat capacity, respectively. An iterative fitting procedure then recovers intrinsic properties corrected for environmental effects while reducing the required sample count and measurement time. Measurements of amorphous silicon dioxide (SiO2) optical fiber and Hi-Nicalon Type S silicon carbide (SiC) fiber agreed with literature values to within an average error of approximately 10% across all samples. Experimental and numerical uncertainty analyses quantify measurement variability and relate it to sample geometry. This method simultaneously resolves multiple intrinsic thermal properties, corrects radiative-loss errors, and provides quantitative guidance for sample geometry selection.
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All authors William Spirnock, Alison Hake, Dihui Wang, Timothy Sullivan, Dana He, Heng Ban
Atmospheric and Oceanic Physics
A Multivariable Approach to the Regional Calibration of the Galvez Davison Index across Mexico Climate Regimes
Mauricio López-Reyes, Carlos Calvo-Sancho, Angel Meulenert et al. (+5 more)
The Gálvez Davison Index (GDI) is a thermodynamic diagnostic designed to summarize convective favorability in the tropical regions, yet its transferability across complex terrain and heterogeneous hydroclimates remains uncertain. Here we assess the climatological behavior and precipitation relevance of the GDI over Mexico using ERA5 hourly fields and CHIRPS daily precipitation for 1981 to 2024. We characterize the seasonal cycle and spatial contrasts of GDI and evaluate its association with rainfall using grid point and regional Pearson and Spearman correlations between daily maximum GDI and daily precipitation. To introduce an independent convective proxy, we also quantify the relationship between hourly GDI and ERA5 outgoing longwave radiation (OLR). Event level discrimination skill is assessed with receiver operating characteristic (ROC) curves and area under the curve (AUC) across regions and months. While GDI precipitation correlations are moderate and region dependent, GDI OLR coupling is consistently stronger, partly because OLR approaches a lower bound once deep convection develops, supporting its use as an intermediate proxy between thermodynamic favorability and rainfall. However, GDI values are systematically lower over elevated terrain because of the pressure level formulation of the index, which should be considered when interpreting the GDI over mountainous regions. ROC results indicate skill above random chance in nearly all region month combinations, with AUC frequently exceeding 0.75 during the core convective season. Building on these diagnostics, we propose a regionally calibrated GDI convective regime scale for May to October, adapted from the original GDI framework but recalibrated for Mexico using event conditioned distributions defined from OLR and precipitation and quantified with bootstrap uncertainty.
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All authors Mauricio López-Reyes, Carlos Calvo-Sancho, Angel Meulenert, José Francisco León-Cruz, Jose Manuel Gálvez, Javier Díaz Fernandez, Juan Jesús González-Alemán, María Luisa Martín Pérez
Accelerator Physics
Quarter-wave shift for an extra pass in an energy recovery linac
Julien Michaud and Alex Fomin
Energy Recovery Linacs (ERLs) are advanced particle accelerators that recover the kinetic energy of the beam after interaction, significantly improving efficiency. In this paper we discuss an alternative operation mode for multi-pass ERLs with an extra pass at top energy, allowing a doubled beam current at the expense of an increased energy spread. We explain the theoretical concept behind this approach, detailing how the phase shift enables an extra acceleration pass without requiring additional hardware. Preliminary simulations on a
lattice similar to the PERLE one explore the feasibility of this method. The results are discussed in the context of ERL performance optimization, and potential applications for future accelerator designs are explored.
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Atomic Physics
Electrical and optical dipole polarizabilities of two lowest triplet states of the beryllium atom
Tymoteusz Mrozek and Krzysztof Strasburger
High-accuracy static and dynamic polarizabilities of the $2^3P_u$ and $^{3}S_{g}$ states of the neutral beryllium atom are reported. The calculations employed explicitly correlated Gaussian (ECG) basis sets, and first-order wave functions were obtained by minimization of the Hylleraas functional. The final basis sets used for the response-property calculations contained c.a. 7000-8000 functions, depending on the polarizability component and the chosen
symmetry. The results cover frequencies from the static limit, \(\omega = 0\), up to the third resonance for the \(2^{3}P_{u}\) state and up to the second resonance for the \(3^{3}S_{g}\) state. To the best of our knowledge, these are the first calculations of dynamic and static polarizabilities for these excited states of the beryllium atom using explicitly correlated basis sets.
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Computational Physics · Cross-listed from cond-mat.str-el
The ALPS project release 3.0: open source software for strongly correlated systems
F. Alet, T. Chen, A. Feiguin et al. (+16 more)
We present release 3.0 of the ALPS (
Algorithms and Libraries for Physics Simulations) project, an open-source software project to develop libraries and application programs for the simulation of strongly correlated
quantum lattice models such as
quantum magnets,
lattice bosons, and strongly correlated
fermion systems. As in previous releases, development is centered on common data formats, on libraries to simplify and speed up code development, and on full-featured simulation programs that let non-experts carry out serial or parallel numerical simulations using the important
algorithms for
quantum lattice models: classical and
quantum Monte Carlo (QMC) using non-local updates, extended-ensemble simulations, exact and full diagonalization (ED), the density
matrix renormalization group (DMRG), and continuous-time QMC solvers for dynamical mean-field theory (DMFT). Major changes in release 3.0 include distribution of the pyalps binary through the Python Package Index (pip install pyalps) and through Spack for HPC systems; migration of development to GitHub with continuous integration and automated testing; relicensing of the package under the permissive MIT license; a rebuilt documentation and tutorial website, including a set of Jupyter-notebook tutorials and localized content; a broad modernization of the C++ codebase (C++17 compliance, Boost and NumPy 2.0 compatibility, and warning and dead-code cleanup) together with a major DMRG update and associated reliability and build-compatibility fixes; the removal of legacy components (the VisTrails provenance integration and the TEBD, MPS, and directed-worm-
algorithm application codes); archival of release 3.0.0 with a Zenodo DOI; and a formal governance and sustainability model developed under the US National Science Foundation (NSF) POSE program. The software is available at https://alps.comp-phys.org.
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All authors F. Alet, T. Chen, A. Feiguin, E. Gull, S. Iskakov, J. P. F. LeBlanc, F. Lin, A. Mirmira, G. Möller, L. Pollet, M. Rosales, V. W. Scarola, H. Shinaoka, H. Terletska, S. Todo, M. Troyer, M. Wallerberger, P. Werner, T. M. R. Wolf
Physics Education
Adapting Public Exams for Introductory Physics: A Mixed-Methods Investigation of Student Outcomes
Binisha Marahatta and Matthew D. Sievert
Public Exams are an assessment system designed in the context of Biology Education Research to increase student engagement in the exam design process. Students are shown incomplete versions of test questions ahead of time, with the format of the question revealed but some details withheld. Students are also given the chance to provide feedback on the questions, refining them for clarity before the actual exam. In this study, we examined the impact of Public Exams on the experiences and outcomes of N = 42 students in an introductory physics course at New Mexico State University. Using a combination of online numerical surveys, open-ended written responses, and student grade data, we conducted a mixed-methods analysis of the impact of Public Exams on students in this class. We also applied our method to re-analyze the publicly available data of Wiggins et al. Students reported various benefits of Public Exams, including reduced test anxiety and directing to core concepts, and we observed a significant positive correlation between the participation rate of students in editing public exam questions and their average exam grade. But students also expressed dissatisfaction with the incomplete information provided on problems, and they had a less positive response rate than the control sample. In other qualitative responses, students also consistently highlighted the applications of procedural knowledge as most helpful to their learning and a recommendation for the future. Our findings suggest that physics students at NMSU do benefit from Public Exams through reduced anxiety and directing to core concepts, but that the Public Exam system, as previously described, is not optimized for use in physics. We attribute this to the particular emphasis in physics on applying procedural knowledge and suggest modifications of the Public Exam system to better tailor it to a physics context.
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Optics · Cross-listed from hep-th
Comment on ”Chiral electromagnetic surface waves on Chern-Simons interfaces” Phys.Rev.D114(2026)L051903 and on arXiv:2606.12513 by N. Kaloper
Igor Bandos and Bohdan Zvorskyi
We demonstrate that Maxwell electrodynamics interacting with a planar Chern-Simons interface does not have plane wave solutions localized on the interface. We re-examine the derivation of such waves presented by N. Kaloper in [Phys.Rev.D114(2026)L051903] and show that at an intermediate step certain terms were missed in an equation therein. Taking these terms into account changes the final conclusion of [Phys.Rev.D114(2026)L051903]. We also show that the method used in [arXiv:2606.12513 [hep-th]] to reproduce the same result is not consistent.
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Physics and Society
Cooperation thrives when moral judgment matches moral conduct
Jorge Peña, Julian Garcia and Toby Handfield
A leading explanation for why humans cooperate with strangers is indirect reciprocity: when conduct is observed, individuals earn good reputations by cooperating with the deserving. Previous research has identified many "moral systems" that sustain cooperation through indirect reciprocity - each pairing a strategy for how to act with a norm for how to judge others - yet what makes them succeed, and whether that success generalizes beyond the donation game, has remained unclear. Here we evaluate all 1,048,576 moral systems whose norms condition on both players' reputations and actions, across every two-player social dilemma. We find that every highly stable, cooperative system pairs a "discriminating" strategy - one that cooperates with the good and defects against the bad when in good standing - with a "consistent" norm that deems good exactly those who act as the strategy prescribes. Such systems "practice what they preach" and preach what they practice. In the limit of small errors, only one strategy paired with a consistent norm remains stable across all social dilemmas: the "contrite discriminator", which cooperates to make amends when its standing is bad. Our results unify decades of research on indirect reciprocity, revealing moral consistency as the common ingredient of every stable, cooperative moral system.
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Chemical Physics · Cross-listed from cond-mat.mtrl-sci
Space Charge Layer and Facile Halide Rearrangement Enable Fast Lithium-Ion Transport at Halide Solid Electrolyte Interfaces
Md Salman Rabbi Limon, Matthew Beltran, Boyu Wang et al. (+2 more)
Halide solid electrolytes are promising candidates for energy-dense all-solid-state batteries because they combine high-voltage stability, facile processing, and fast Li-ion conduction. A recent study showed that physically mixing two halide solid electrolytes, Li$_2$ZrCl$_6$ (LZC) and Li$_3$YCl$_6$ (LYC), raises the Li-ion conductivity by 46% and 58% relative to LZC and LYC, respectively, suggesting that halide heterointerfaces offer a new route to faster ion transport; however, the origin of this enhancement remains unknown. Here, we combine density functional theory calculations, defect thermodynamics, machine-learning-driven molecular dynamics, and vibrational and Raman spectroscopy to elucidate Li-ion transport in LZC, LYC, and their heterointerface. Using low-energy ordered supercells that represent the configurational disorder of these halides, we find that Li and Cl interstitials are the dominant charged defects in both materials. Forming an LZC|LYC interface favors the generation of interfacial Li Frenkel pairs, producing Li interstitials in LZC and Li vacancies in LYC, thereby increasing the charge-carrier concentration near the interface. By analyzing the angular orientations of Cl around the metal cations in molecular dynamics trajectories of a coherent interface, we show that the interface creates new stable Cl configurations that accommodate the framework rearrangement accompanying Li hops. Simulated vibrational power spectra and measured Raman spectra indicate
lattice softening and octahedral distortion at the interface, consistent with the formation of these Cl configurations. These results support a cooperative mechanism in which space charge layer formation and a dynamically flexible interfacial halide framework enhance Li-ion conduction, providing atomistic design principles for superionic halide
heterostructures and multicomponent solid electrolytes.
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All authors Md Salman Rabbi Limon, Matthew Beltran, Boyu Wang, Laisuo Su, Zeeshan Ahmad
Biological Physics · Cross-listed from cs.LG
RNADyn: A Benchmark for Generating and Understanding RNA Dynamics
Yiming Huang, Lennart Bastian, Hanqun Cao et al. (+2 more)
Ribonucleic acid (RNA) functions through conformational changes that are not fully captured by static structures. However, large-scale standardized RNA dynamics data remain limited, and existing approaches typically treat trajectory generation and dynamics understanding as separate objectives. Here, we introduce RNADynBench, a standardized RNA molecular dynamics (MD)
benchmark with 2585 quality-controlled 100-ns all-atom trajectories and leakage-controlled splits. Building on RNADynBench, we develop RNADynNet, a unified model for RNA dynamics learning that uses a shared backbone for both trajectory generation and dynamics fingerprint extraction from a single conformer. It combines coordinate denoising, single-frame-to-trajectory
alignment, and physical grounding to connect all-atom trajectory generation with dynamics representation learning. Physical grounding improves both generated dynamics and the physical information recoverable from these fingerprints. Across both test sets, including the high-flexibility challenge set, the generated trajectories achieve RMSF correlations of 0.875 and 0.766, while single-conformer predictions show comparable agreement with MD-derived dynamics. RNADynBench and RNADynNet together establish a
benchmark and unified modeling framework for generating and understanding RNA dynamics.
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All authors Yiming Huang, Lennart Bastian, Hanqun Cao, Luis Vollmers, Tolga Birdal
Instrumentation and Detectors · Cross-listed from cs.AI
NeutronGym: Physics-Graded Neutron Instrument Design for LLM Agents
Lijie Ding and Changwoo Do
Designing a scientific instrument tests whether
language-model
agents can do physics rather than recall it, provided the grading cannot be argued with. We introduce NeutronGym, to our knowledge the first executable environment for
neutron instrument design:
agents build instruments through validating tools, McStas ray-traces what they build, and a level-resolved ladder grades syntax, runtime, structure and science with no LLM judge. Procedural families supply unlimited instances of a fixed layout whose design parameters the
agent must set, with held-out parameter regimes; a curated slice, McStasBench, adds 16 tasks from published instruments behind memorization probes and a sandbox. Seven models reproduce at most 7 of the 16, none retrieves a reference, and none meets an improvement target. The environment also trains. Reinforcement learning on its reward takes Qwen3-8B from 11% to 77% of held-out instances of a family whose targets come from a hidden design (69% at a second seed), past an untrained Qwen3-32B, and the recipe holds, at one seed each, on three further gated families. The analysis says what that gain is. Without the ladder's partial credit it collapses by 60 points. From reward alone the trained model reaches what a classical optimizer reaches, at the
agent's simulation budget, only when handed the closed-form physics (77% against 81%, a gap that does not separate at this size), while frontier models still solve 98-99%. Getting a trustworthy result meant failing four task designs that no-model baselines could solve, and we release the probes that found them.
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Biological Physics
Cost convexity controls the architecture of resistance-optimal networks
Hugo Tovar, Genaro Vázquez-Victorio, Enrique Hernández-Lemus et al. (+2 more)
A conducting network improves access to its interior only by spending material, so architectures compare only at equal budget. We redistribute conductance under a power-law resource law $\C_{\alpha}=\sum_e a_e w_e^{\alpha}$ and measure access by the reciprocal of the mean pairwise effective resistance. When the cost is strictly convex the allocation is unique and every admissible edge keeps positive conductance; at $\alpha=1$ uniqueness survives but an edge can be priced out. The marginal worth of an edge is then its squared biharmonic distance, a Murray-type balance whose balanced quantity is global rather than junction-local. The same optimum scores any weighted network at its own budget, separating an allocation factor from a topological one. Under concave cost the marginal price of an incipient channel diverges, the feasible set is nonconvex, and conductance condenses onto sparse backbones. The uniform
star and the uniform complete graph cross at $\alpha_c(n)=\log(n/2)/\log(n-1)$, near which intermediate states beat both. Up to $n=64$ the best states found grow approximately linearly in $n$, so channels per node change much less than the active fraction does. Loops are governed instead by a collapse exponent $\alpha^{*}(n)$, resolved to $0.005$ at every size: it rises from $0.555$ at $n=8$ to $0.675$ at $n=64$, and the collapse across it is abrupt, the support at $n=64$ falling from $133$ active edges to the $63$ of a spanning tree. A fixed exponent therefore changes character with size by crossing this boundary. One prescribed source and sink instead gives a loopless optimum.
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All authors Hugo Tovar, Genaro Vázquez-Victorio, Enrique Hernández-Lemus, Alejandra Cervera, Daniel Pérez-Calixto
Chemical Physics · Cross-listed from cond-mat.soft
Surface Charge–Potential Relation for Spherical Particles in Electrolyte Solutions
Olga I. Vinogradova and Elena F. Silkina
Predicting the relationship between surface charge density and electrostatic potential for spherical particles remains a fundamental challenge in colloid science. Because the governing non-linear Poisson–Boltzmann equation lacks a general exact analytical solution, researchers typically rely on numerical calculations or various semi-empirical approximations. In this paper, we overcome these limitations by developing a dual-asymptotic framework that provides explicit, closed-form expressions for this surface charge–potential relationship across the entire spectrum of particle
curvature. For weakly curved systems, where the Debye length $\lambda_D$ is much smaller than the particle radius $R$ ($\lambda_D/R \ll 1$), a formal mathematical derivation rigorously establishes the Ohshima–Healy–White formula as an exact regular perturbation expansion. Conversely, for highly curved spheres ($R/\lambda_D \ll 1$), we employ singular perturbation analysis using the scaled particle radius as the small parameter. This approach provides a first-principles mathematical justification for the spherical Debye–Hückel theory, proving that its leading-order expansion remains asymptotically exact within the full non-linear Poisson–Boltzmann framework due to the
geometric deactivation of non-linearity. Crucially, we map the exact limits of this
geometric regulation, demonstrating how non-linear screening re-emerges as the particle radius increases, with the breakdown threshold governed by the interplay between
curvature and surface charge density.
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Instrumentation and Detectors · Cross-listed from quant-ph
The QICK Box: A Modular RF Front-End System for Quantum Control and Readout
L. Arnaldi, D. Martin, S. Sussman et al. (+11 more)
The QICK (
Quantum Instrumentation Control Kit), first introduced in 2022, is a standalone open source control system for
quantum information science. Since then, QICK has been migrated to new hardware platforms, expanded its functionality for applications with different types of
qubits (superconducting, atomic, ion-trapped, and
spin defects), as well as
quantum sensors, and
quantum networks. QICK is a highly optimized control kit, with a library of functions that can be used for more than one application. In particular, the software and firmware are customized to minimize latency and maximize control performance and throughput. In this white paper, we describe hardware details and performance of the QICK Box. The QICK Box features up to 16 outputs, up to 8 inputs, and 8 20-bit DC biases. Modular output and input daughtercards give the choice of signal chains optimized for fast DC-coupled signals or RF signals up to 10 GHz. Power levels, step attenuation, and bandpass filtering are controlled by software. We demonstrate the system's performance through single-shot readout measurements of a six-transmon device at the
Quantum Underground Instrumentation Experimental Testbed (QUIET) at Fermilab, achieving (91.7 +/- 0.4)% readout fidelity limited by T1 decay during the readout. The single shot readout signal-to-noise ratio (SNR) is 4.4 +/- 0.1 without a
quantum amplifier, confirming that the QICK Box is suitable for high-fidelity
quantum control and measurement applications. Advances in firmware and software will be described in a separate paper.
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All authors L. Arnaldi, D. Martin, S. Sussman, S. Uemura, K. Treptow, N. Wilcer, A. Colón Cesaní, O. Seidel, K. Anyang, G. Bratrud, F. Abouzahr, J. Christiansen-Salameh, D. Baxter, G. Cancelo
Fluid Dynamics
Flow regime determines whether larval settlement hydrodynamics are governed by swimming speed or shape
Daniel Gysbers, Mark A. Levenstein and Gabriel Juarez
Larval dispersal and settlement govern the replenishment of sessile marine populations and the assembly of benthic communities, yet how larval traits interact with near-surface flow structures to direct settlement remains unclear. We used coupled hydrodynamic and larval-scale simulations to resolve how swimming speed and body shape, from circular to elongated, influence settlement in oscillatory flow over ridged substrates. Settlement success differed by up to an order of magnitude across trait combinations. Near-surface flow acted as a trait filter by differentially regulating transport to, retention near, and encounters with the substrate. The trait that mattered most depended on the local flow structure. Where rapid flow restricted access to settlement surfaces, swimming speed was most important. Where flow recirculated between substrate ridges, shape-dependent
alignment controlled transport and retention. These results link larval traits to flow-mediated settlement mechanisms and provide a physical framework for understanding how recruitment varies across complex benthic habitats.
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Chemical Physics
CIS(2): a state-specific, size-intensive perturbative correction to configuration interaction singles
Takashi Tsuchimochi
We present a state-specific second-order perturbation theory based on a configuration interaction singles (CIS) reference and its generalized Fock operator. Starting from a fully internally contracted construction, we retain the complete doubles space and internally contracted triples in the first-order wave function. We consider two partitions, Canonical and Block-diagonal, with reference excitation energies given by the Fock excitation gap $\omega^{(0)}$ and the CIS excitation energy $\omega_{\rm CIS}$, respectively. Our analysis establishes that strict size-intensivity is preserved when the contracted-triples denominators use bare Fock gaps and the occupied–virtual Fock block is projected to remove residual spectator coupling. Based on this observation, combining Canonical triples with Block-diagonal doubles yields a size-intensive Hybrid partition. These properties are verified for water with non-interacting helium atoms. Our formulation enables $O(o^3v^2)$ cost per
matrix–vector product in a semicanonical basis. On the QUEST\#1
benchmark, Canonical and Block-diagonal show opposite systematic biases, whereas Hybrid gives the best overall accuracy among the three partitions. Its mean absolute errors for singlets and triplets are 0.24 and 0.15~eV, compared with 0.28 and 0.22~eV for CIS(D). The improvement is largest for Rydberg excitations, although CIS(D) remains more accurate for valence singlets.
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Physics and Society
Disentangling epidemics and percolation
Takayuki Hiraoka and Jari Saramäki
Non-recurrent epidemics on complex networks, such as the paradigmatic susceptible-infected-recovered (SIR) model, are often studied by mapping the model to bond percolation. However, the conditions under which this identification is justified have not been fully understood, except in specific cases. Here, we systematically determine when this mapping can be applied, starting from minimal assumptions on the epidemic model and the underlying network. Specifically, we discuss the conditions for three different forms of equivalence between a general non-recurrent epidemic model and Bernoulli bond percolation: isomorphism, equality of marginal infection probabilities, and equality of expected epidemic size. We numerically demonstrate the validity of our findings and examine how epidemiological outcomes are affected when these equivalences are not upheld. Our results establish the methodological basis and limitations of a common tool for analyzing epidemic processes on networks.
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Optics
Beyond the PT-Broken Phase: Constant-Frequency Oscillation from Floquet Hybridization
Xiaoke Gao, Xiaoyin Sha, Xunyan Sun et al. (+3 more)
Constant-frequency oscillation is usually tied to the broken phase of a spatially coupled PT-symmetric dimer, where the eigenfrequencies form a complex-conjugate pair with a fixed real part. This work shows that an analogous locking can instead come from Floquet hybridization in a synthetic frequency dimension. Periodic gain–loss modulation folds the spectrum into replicas spaced by the drive frequency $\Omega$. Coupling between neighboring replicas opens an additional real-part degeneracy at the edge of the Floquet Brillouin zone. The hybridized Floquet mode at $\omega_0\pm\Omega/2$ requires the minimum gain and is therefore selected for the self-oscillation. A Floquet PT-symmetric
circuit with a JFET time-varying negative resistance confirms the prediction. The observed constant-frequency oscillation contains two frequency components of comparable amplitude, separated by the modulation frequency, which identifies its origin from Floquet hybridization rather than ordinary PT-
symmetry breaking or dispersion flattening. More broadly, once a suitably
symmetry-constrained spectral degeneracy is established, self-sustained frequency pinning can arise beyond the conventional spatial PT-broken phase.
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All authors Xiaoke Gao, Xiaoyin Sha, Xunyan Sun, Xianglin Hao, Huaiqing Zhang, Tianyu Dong
Plasma Physics
X-ray spectroscopy of hot dense plasmas using LLNL's upgraded Titan 2$\omega$ short-pulse laser
A. J. Fairchild, D. T. Bishel, T. Cordova et al. (+10 more)
We are developing an experimental platform at Lawrence Livermore National Laboratory's Jupiter
Laser Facility to characterize X-ray emission from highly charged ions in the high-density ($n_e > 10^{23}$ cm$^{-3}$), high-temperature ($T_e \sim 1$ keV) regime, leveraging the recently upgraded frequency-doubled short-pulse Titan
laser. These measurements will provide experimental
benchmarks for high electron density effects on atomic structure, including Stark broadening, ionization potential depression, density-dependent line shifts, and suppression of dielectronic recombination, effects that are relevant to spectral modeling packages used by both the high-energy-density and astrophysics communities. Here, we describe the current status of the platform and present results from first experiments using the upgraded frequency-doubling capability, including calibrated K-shell spectra acquired from five time-integrated X-ray channels. Comparisons with MERL line shape calculations and with spectra recorded at AWE's Orion
Laser Facility indicate that the upgraded Titan
laser reliably produces the necessary
plasma conditions, establishing a foundation for systematic benchmarking of high-density atomic physics in future campaigns.
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All authors A. J. Fairchild, D. T. Bishel, T. Cordova, H. Flores-Alimboyoguen, M. F. Gu, P. Hamilton, N. Hell, M. J. MacDonald, E. W. Magee, R. C. Mancini, E. V. Marley, R. Shepherd, G. V. Brown
Biological Physics
Migrating cell clusters as active droplets with asymmetric shape and contact angles
Hanno I. Hennighausen, Jaime A. Espina, Elias H. Barriga et al. (+1 more)
During embryonic development and cancer progression, clusters of
cells migrate collectively following external cues. Such migrating
cell clusters have been modeled as active droplets wetting a substrate. So far, this active wetting model assumed the cluster to take the symmetric shape of a spherical cap. Here, in contrast, we experimentally show that migrating clusters of frog neural crest
cells have asymmetric height profiles, with a lower contact angle at the front than at the rear. We then extend the active wetting model by deriving an equation for the cluster shape, which becomes part of the solution rather than an assumption. Our model shows that shape asymmetry can arise from the asymmetric tractions that drive cluster migration: They generate a pressure gradient across the tissue which, via the Young-Laplace equation, leads to a
curvature gradient on the cluster's upper surface. Finally, by fitting the theoretical predictions to the measured height profile, we estimate the tissue viscosity. Overall, our results provide a general mechanism for the emergence of asymmetric shapes in migrating
cell clusters, understood as active droplets on a wettability gradient.
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All authors Hanno I. Hennighausen, Jaime A. Espina, Elias H. Barriga, Ricard Alert