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Physics Physics

physics Watch Physics

Wednesday 2 September

Optics · Cross-listed from quant-ph

Single-Shot Fidelity Reveals Hard and Soft Limits: A Universal Yardstick for Photon-Number-Resolving Detectors

Tetsuya Tsuruta, Akio Yoshizawa and Daiji Fukuda

Photon-number-resolving (PNR) detectors are essential for photonic quantum computing, where a single measurement outcome must reliably herald a specific quantum state. However, detector fidelity is conventionally evaluated using ensemble-averaged statistics obtained from many measurements, which can remain high even when individual photon-number assignments are frequently misidentified. Here we introduce a universal single-shot fidelity that directly quantifies the probability of correctly identifying a photon number in a single measurement. The framework combines an efficiency-based POVM with a resolution-driven confusion matrix derived from the detector response, allowing photon loss and photon-number misidentification to be treated separately and then recombined into a single operational metric. This distinction reveals two fundamentally different limitations. Detection-efficiency loss represents an unrecoverable hardware constraint, whereas resolution-driven misidentification can be reduced by introducing a rejection region, trading generation rate for confidence. Because the metric is defined independently of detector architecture, it enables direct comparison between energy-resolving detectors such as transition-edge sensors and multiplexed click-based detectors on the same footing. Applying the framework to calibration data from three distinct detector architectures, we demonstrate quantitative comparison across photon-number regimes relevant to both discrete-variable and continuous-variable photonic quantum computing. The resulting benchmark provides a common operational metric for evaluating photon-number-resolving detectors and connecting detector performance to photonic quantum-computing requirements.
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Computational Physics · Cross-listed from cs.CE

A meshfree solver for coupled bulk-surface problems with self-organizing surface geometry

Lennart J. Schulze, Alejandra Foggia and Ivo F. Sbalzarini

In many systems, the interaction between a deformable surface or interface and the surrounding bulk fluid is coupled with intrinsic spatiotemporal dynamics within the moving surface. Examples include tumor growth, biological tissue morphogenesis, cardiac mechanics, multi-phase surfactant chemistry, additive manufacturing, clothing wear-and-tear, and reactive combustion flows. Solving such problems requires both geometric computing algorithms to track and resolve the surface and numerical methods to solve the coupled governing equations in the surface and the surrounding bulk phase. Here, we present a fully meshfree numerical solver for such coupled bulk-surface problems with deformable interfaces. The presented solver tracks the surface implicitly, solving for the dynamic surface geometry based on stress balance coupled to surrounding fluid phases. We show convergence for a mass-conserving case on a growing sphere and solve bulk-surface problems with incompressible Navier-Stokes fluids coupled to in-surface nonlinear reaction-diffusion dynamics. Finally, we show a model of biological morphogenesis, solving simultaneously for the dynamic surface shape and the fields on the curved surface with two-way coupling.
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Optics · Cross-listed from cond-mat.str-el

Prominent Dimensional Effects on High-order Harmonic Generation in Strongly Correlated Electron Systems

Kento Uchida, Shintaro Takayoshi, Yuta Murakami et al. (+6 more)

Dimensionality strongly affects elementary excitations in correlated quantum materials, yet its impact on extreme nonlinear optical responses remains largely unexplored. Here, we combine high-harmonic generation (HHG) experiments on quasi-one-dimensional SrCuO$_2$ and quasi-two-dimensional Pr$_2$CuO$_4$ with nonequilibrium simulations of Hubbard models. We find a pronounced dimensional contrast: SrCuO$_2$ exhibits a robust plateau-like high-harmonic spectrum with weak temperature dependence, whereas Pr$_2$CuO$_4$ shows a monotonic decrease in harmonic yield and strong thermal suppression, especially at higher harmonics. The simulations qualitatively reproduce these trends and identify dimensionality-dependent doublon–holon dephasing, governed by spin–charge coupling, as their microscopic origin. These results establish dimensionality and spin–charge coupling as key control parameters for extreme nonlinear optical responses in correlated insulators.
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All authors Kento Uchida, Shintaro Takayoshi, Yuta Murakami, Dongjoon Song, Alannah M. Hallas, Masayuki Watanabe, Takashi Konishi, Aiko Nakano, Koichiro Tanaka

Atomic Physics · Cross-listed from quant-ph

Accurate theoretical methods for photoionization of H$_2$ molecules

Hakon Volkmann, Jannis Schürmann and Alejandro Saenz

Single-photon ionization cross sections of molecular hydrogen in the electric dipole limit are numerically computed by employing three independent methods. Both time-dependent and -independent approaches within the clamped-nuclei approximation at equilibrium internuclear distance are used, featuring the explicit time-propagation of the time-dependent Schrödinger equation and newly developed multi-channel configuration-interaction free-boundary as well as complex-scaling methods using an explicitly correlated geminal basis set. The found results show convincing mutual agreement despite their entirely different fundamental formulations. They further highlight the challenges in bringing together different theoretical predictions from literature with the experimental data at high photon energies. Overall, the novel CI-based approach demonstrates fast and controllable convergence while being able to provide full channel-resolved information, indicating the need for more accurate experimental data.
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Physics Education

Student responses to a modified Force Concept Inventory: The Newtonian Mechanics Quiz

Ashutosh Kumar Pathak, Mark A. J. Parker, Andrew J. A. James et al. (+2 more)

Even in the era of modern physics, understanding and applying Newton's classical Laws of Motion are key skills for physicists and form a core component of instructional programmes. Students arrive in the classroom with intuitive ideas about force and motion that are often misaligned with Newtonian thinking. Prior research has shown that these incorrect intuitive ideas are remarkably persistent, and can stay with students throughout their education and beyond. Reliable instruments, that can accurately evaluate student understanding of Newtonian mechanics, are required to track student progress and evaluate the efficacy of instructional programmes. The Force Concept Inventory (FCI), a conceptual quiz composed of multiple-choice questions, is a well-established instrument, developed to address these challenges. The FCI, and how students respond to its questions, has been widely investigated and discussed in the literature. Notably, research has shown that: correct responses to questions do not always correspond to correct application of Newtonian concepts; and the limited response options given for multiple-choice questions often do not capture the full range of student thinking. There is therefore a burgeoning need to develop new instruments that probe students' understanding at a deeper level, by interrogating conceptual understanding from multiple perspectives and incorporating different question formats that require students to construct and consider their responses. We introduce the Newtonian Mechanics Quiz (NMQ), a modified version of the FCI that incorporates follow-up questions in a variety of formats, each with different diagnostic functions. This article describes the development and validation of the NMQ instrument, and illustrates several novel analyses enabled by the student response dataset that can offer deep insight into students' conceptual understanding of Newton's Laws.
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All authors Ashutosh Kumar Pathak, Mark A. J. Parker, Andrew J. A. James, Sally E. Jordan, Jonathan Nylk

Biological Physics · Cross-listed from q-bio.CB

3D hybrid cellular Potts model with a discrete deformable fiber network: modeling cell contraction and extracellular matrix remodeling

Koen A.E. Keijzer and Roeland M.H. Merks

The extracellular matrix (ECM) is a fibrous and dynamic network that plays a critical role in development, homeostasis, and disease. Cells both respond to and remodel the ECM, engaging in a mechanical reciprocity that shapes tissues. To study these interactions, computational models have been developed that simulate either ECM mechanics or cell behavior. The Cellular Potts Model (CPM) is a flexible cell-based framework that has been extended to many biological processes, including coupling to a discrete deformable fiber network. So far, however, this extension has only been applied in two dimensions, even though a three-dimensional setting is biologically more relevant. Here, we present a 3D hybrid framework that couples the CPM with a discrete and deformable representation of the ECM. This model enables explicit simulation of cell-induced ECM remodeling, including fiber reorientation and matrix densification. By incorporating contractile forces through static adhesion points, the model captures how ECM elasticity and fiber stiffness influences cell shape. The simulations show that ECM stiffness, controlled by fiber crosslinking, resists contraction and reaches equilibrium, while crosslink density modulates fiber alignment and local matrix accumulation. This framework provides a versatile platform for studying cell-ECM mechanics and supports future studies of multicellular behavior in realistic 3D environments.
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Optics

Static and breathing dynamics of optical bullets in nonlinear GRIN fibers

Sonali Maity, Tiyas Das, Anuj P. Lara et al. (+2 more)

We explore the properties of spatiotemporal solitons within nonlinear graded-index (GRIN) optical fibers, specifically addressing their formation, stability, and breathing dynamics. We solve the (3+1)-dimensional nonlinear Schrödinger equation employing a semi-analytical variational approach, which leads to a set of reduced coupled ordinary differential equations describing the bistable bullet dynamics. The stability of these states is assessed using the Vakhitov-Kolokolov criterion and linear stability analysis within the Kantorovich optimization framework. The breathing dynamics of the optical bullets are investigated adopting the potential formalism, revealing an oscillatory behavior and self-imaging dynamics in GRIN fibers. The analytical results demonstrate strong agreement with full numerical simulations, validating the robustness of our theoretical model. Our research enhances the understanding of stabilizing self-repeated 3D optical structures, which is beneficial for the development of advanced photonic technologies.
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All authors Sonali Maity, Tiyas Das, Anuj P. Lara, Ashis Paul, Samudra Roy

Biological Physics · Cross-listed from cond-mat.soft

Collective Cell Fluidity Controls Active Prestress Transmission in Cell-Extracellular-Matrix Tissues

Liyang Wang, J. M. Schwarz and Tao Zhang

Tissues are active composites in which multicellular collectives and extracellular matrices mechanically reorganize one another. We develop a three-dimensional micromechanical model that couples deformable, rearranging cell clusters to a disordered network of semiflexible fibers through a dynamic, force-generating interface. Cell clusters are represented as solid-like or fluid-like vertex-model spheroids and coupled to the matrix by passive or contractile linkers renewed as the cluster boundary reorganizes. Matched intact, voided, and passive-linker controls separate cavity formation, interfacial tethering, and active loading. At small strain, passive tethering provides modest reinforcement, whereas active contraction prestresses and strongly stiffens the matrix. Solid-like clusters preserve coherent force transmission and exhibit an excess modulus scaling approximately as $|\sigma|^{1.4}$ across changes in activity, cluster size, and cluster number. Fluid-like clusters undergo greater interfacial renewal, producing weaker and nonmonotonic coupling between prestress and stiffness. Increasing cluster number produces collective stiffening when prestressed regions become connected through sufficiently persistent interfaces. At large strain, both solid-like and fluid-like systems approach the corresponding voided-network response as the residual fiber backbone becomes mechanically dominant. Thus, cell-generated prestress controls macroscopic stiffness only together with the organization and persistence of its transmission across the cell-matrix interface.
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Chemical Physics · Cross-listed from cond-mat.stat-mech

Effect of reactive targets on diffusive transport with intermittent restarts

Samali Ghosh, Suvam Pal, Dibakar Ghosh et al. (+1 more)

We study search processes in a complex environment using the strategy of stochastic resetting. A common occurrence in these environments is targets with finite reactivity. Stochastic resetting has emerged as a powerful mechanism for optimizing search processes by curtailing long, unproductive excursions inherent to diffusive dynamics. Most theoretical studies, however, assume perfectly absorbing targets – an idealization that overlooks the finite reactivity commonly encountered in realistic chemical and biological systems. In this work, we investigate the interplay between stochastic resetting and finite-target reactivity in reaction - diffusion processes. Considering a one-dimensional system with multiple reactive targets, we demonstrated that the target reactivity modifies the optimization landscape. We uncover distinct regimes in which resetting enhances transport efficiency towards specific targets based on their chemical kinetics. As a consequence, the optimal resetting rate becomes intrinsically reactivity dependent. Our results identify target reactivity as a crucial control parameter governing stochastic transport and provide insights into reaction-diffusion processes in complex media.
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All authors Samali Ghosh, Suvam Pal, Dibakar Ghosh, P. S. Pal

Instrumentation and Detectors

Toward High-Resolution Detection of Target Fragmentation: TEA-Sensitized NIT for Proton Therapy Applications

V. Boccia, T. Asada, A. Alexandrov et al. (+96 more)

Nano Imaging Trackers (NIT) are fine-grained nuclear emulsions capable of tracking charged particles with sub-micrometric spatial resolution. The DAMON (Direct Measurement of Target Fragmentation) experiment recently employed NIT to detect target-fragmentation events relevant to proton therapy in direct kinematics. These measurements showed that the small crystal size, while providing high spatial resolution, limits the reconstruction efficiency for primary proton tracks and high-energy secondary protons. This work reports an enhancement of NIT sensitivity achieved through alternative chemical sensitization methods, namely gold-plus-sulfur (Au-S) and triethanolamine (TEA), together with the use of the GR-1 developer. The detector response was evaluated with gamma-ray, carbon-ion and proton exposures, including clinically relevant proton energies.
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All authors V. Boccia, T. Asada, A. Alexandrov, G. Ambrosi, S. Argirò, M. Barbanera, N. Bartosik, G. Battistoni, A. Bigot, M. G. Bisogni, G. Butella, F. Cavanna, P. Cerello, E. Ciarrocchi, N. D'Ambrosio, G. De Lellis, A. Di Crescenzo, B. Di Ruzza, M. Dondi, M. Donetti, Y. Dong, M. Durante, R. Faccini, V. Ferrero, C. Finck, E. Fiorina, M. Francesconi, M. Franchini, G. Franciosini, L. Galli, A. Iuliano, K. Kanxheri, B. Kharpuse, M. Kimura, S. Kodaira, A. C. Kraan, A. Lauria, E. Lopez Torres, T. Maggipinto, M. Magi, A. Manna, M. Marafini, S. Masci, M. Massa, C. Massimi, I. Mattei, S. Mazzolani, A. Mengarelli, A. Mereghetti, R. Mirabelli, A. Moggi, M. C. Montesi, M. C. Morone, M. Morrocchi, S. Muraro, T. Naka, N. Pastrone, V. Patera, F. Pennazio, C. Pisanti, P. Placidi, M. Pullia, F. Quattrini, S. Rabaglia, L. Ramello, C. A. Reidel, R. Ridolfi, L. Rocchetti, L. Sabatini, L. Salvi, C. Sanelli, A. Sarti, O. Sato, S. Savazzi, A. Schiavi, C. Schuy, E. Scifoni, L. Servoli, G. Silvestre, M. Sitta, K. Someya, B. Spadavecchia, R. Spighi, E. Spiriti, L. Testa, V. Tioukov, S. Tomassini, F. Tommasino, M. Toppi, G. Traini, A. Trigilio, G. Ubaldi, S. Valentinetti, M. Vanstalle, M. Villa, U. Weber, R. Zarrella, A. Zoccoli, G. Galati

Optics

Dispersion-engineered meta-coverslip for multimodal synthetic imaging

Yuchen Ma, Danlin Xu, Xinwei Wang et al. (+2 more)

Multimodal optical imaging provides comprehensive sample characterization but has traditionally been hindered by complex and bulky instrumentation. Here, we propose a dispersion-engineered meta-coverslip to seamlessly integrate bright-field, differential, fluorescence, and holographic imaging modalities within a standard microscope architecture, requiring no hardware modification or realignment. The meta-coverslip utilizes a scalable subwavelength multilayer film to engineer spatio-temporal dispersion for a customized high-dimensional transfer function. As an example, we demonstrate flexible switching among the four imaging modalities by simply tuning the illumination wavelengths. Lastly, we demonstrate that the synthesis of multimodal images can provide spatially registered structural and molecular information for more comprehensive biological analysis. Our approach provides an accessible, scalable, and flexible solution for advanced imaging and is extensible to other multiplexed optical systems in sensing and computing.
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All authors Yuchen Ma, Danlin Xu, Xinwei Wang, Guangwei Hu, Liangcai Cao

Plasma Physics

Chirped-Pulse Forward Raman Amplification in Nonuniform Plasmas

Zhi-Yu Lei, Zheng-Ming Sheng, Su-Ming Weng et al. (+2 more)

Light amplification via Raman scattering in plasma has been severely constrained by stringent phase matching conditions and the need for plasma uniformity. To overcome these limitations, we propose a forward Raman amplification scheme that employs a positively chirped seed pulse co-propagating with a pump pulse in a nonuniform plasma with an upramp density profile. We demonstrate that the phase detuning induced by plasma nonuniformity can be dynamically compensated, enabling broadband amplification across the entire spectral bandwidth of the seed pulse. Concurrently, the chirped pulse duration undergoes continuous compression as a result of the spatially varying dispersion of the plasma. Our theoretical model, incorporating the detuning term and supported by particle-in-cell simulations, elucidates the compensation mechanism. It is shown that a chirped seed pulse with an initial bandwidth ~10% can be directly amplified by a factor of 1e7 to an intensity exceeding 1e17W/cm2 within a picosecond timescale in a steep density ramp. This scheme establishes a new foundation for advancing plasma-based light amplification toward practical applications.
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All authors Zhi-Yu Lei, Zheng-Ming Sheng, Su-Ming Weng, Min Chen, Jie Zhang

Fluid Dynamics

Improved uncertainty representation for reducing artificial energy production in structured input-output stability analysis

Ofek Frank-Shapir and Igal Gluzman

This work employs a new form of fixed structured uncertainty within the structured small-gain theorem approach proposed by Frank-Shapir & Gluzman (J. Fluid Mech., vol. 1030, 2026, pp A8) for the stability analysis of incompressible shear flows subject to finite-magnitude disturbances. Within this framework, the nonlinear advection term in the Navier-Stokes equations is replaced by a structured feedback uncertainty interconnection with the linearized dynamics to account for the impact of nonlinear feedback. Herein, a new uncertainty representation is derived via linear transformations of the input and output channels, transforming the feedback loop such that the resulting structured uncertainty has a repeated-diagonal structure. This structure aims to preserve the component-wise pathways of the nonlinear advection term while keeping the structured singular value computation tractable. We apply the method to two canonical base flows: Couette and plane Poiseuille flows. The resulting thresholds on disturbance magnitude to preserve stability are less conservative and more accurate. We compare the novel methodology presented here with previously proposed repeated and non-repeated block approximations of the uncertainty structure, where our stability threshold provided the closest agreement with previous numerical and experimental studies. We show that repeated and non-repeated block structures that were proposed in past studies result in an artificial energy-production term arising from using constant structured uncertainty in the structured input-output formulation, violating the divergencefree assumption. This energy-production term is smallest when using the methodology presented in this work, providing a more faithful representation of the impact of nonlinear feedback interconnection with the linearized dynamics of the Navier-Stokes system.
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Fluid Dynamics

Mechanism-Resolved Interface Momentum Transfer in Immersed-Boundary Lattice Boltzmann Simulations

Hongju Jo

Immersed-boundary lattice Boltzmann (IB-LBM) simulations of cylinder and particle flows are usually compared by ranking boundary-enforcement schemes, kernels, and collision models. Such comparisons can obscure the mechanism that controls each response. Here, canonical fixed-cylinder, oscillating-cylinder, and sedimenting-particle cases are used as controlled probes of Eulerian-Lagrangian interface momentum transfer. For prescribed bodies, differences among direct forcing (DF), multi-direct forcing (MDF), and distribution-function correction (DFC) are most clearly discriminated by local no-slip fidelity rather than by a universal drag ranking. For DFC, the kernel-dependent drag-coefficient ranking reversal between the hat and Peskin 4-point kernels is associated with the spatial redistribution of the marker-resolved correction and the resulting near-boundary slip and pressure deviation, rather than the total correction magnitude alone. For sedimenting particles, single-particle settling provides a moving-body baseline, whereas two-particle differential-density wake-interaction sedimentation shows the wake-exposed light particle to be comparatively more sensitive to the explicit internal-mass correction in the force evaluation, a configuration-dependent, finite-window moving-boundary closure response. Targeted two-relaxation-time (TRT) and central-moment multiple-relaxation-time (CM-MRT) collision controls remain secondary to the boundary and closure mechanisms within the tested regimes (prescribed-body comparisons at Re <= 200, two-dimensional, and the reported moving-particle cases). The resulting picture replaces a universal scheme ranking with a mechanism-resolved interpretation of IB-LBM interface momentum transfer.
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Fluid Dynamics

Ventilated Cavitation around a sphere through surface air injection at Re = 10,000

Soundararajan R and Anikesh Pal

We perform DNS of ventilated cavitation over a sphere at subcritical (Re=10,000). The flow is modeled as a homogeneous mixture of water and air, with the interface tracked using the volume-of-fluid method. Unlike previous numerical investigations, surface tension is explicitly included. Air is injected through a circular strip on the sphere at three locations selected based on the bulk flow dynamics: front (FR025, (18^\circ\leq\theta\leq63^\circ)), mid (MD025, MD050, (75^\circ\leq\theta\leq104^\circ)), and back (BK025, (120^\circ\leq\theta\leq180^\circ)), with (C_q=0.2) and (0.4). The injection location strongly governs cavity inception and stability and alters flow separation in the front- and mid-injection cases. Front injection produces an unsteady bubbly cavity due to vigorous puffing, which fragments the injected air and increases drag by (\sim56%) relative to the single-phase case. In contrast, mid- and back-injection produce stable cavities with distinct leading-edge dynamics. In the mid-injection cases, puffing dominates and, despite delayed flow separation, the cavity detaches from the leading edge of the injection patch. For back injection, the cavity detaches upstream of the injection patch owing to the adverse pressure gradient induced by cavity formation. Kelvin–Helmholtz instabilities and divot formation characterize the back-injection cavity. Stable cavities exhibit strong air entrainment and close through a re-entrant jet. The mid-injection cases achieve (35%) and (25%) drag reduction at (C_q=0.2) and (0.4), respectively, while back injection yields a maximum drag reduction of (46%) relative to the single-phase case.
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Fluid Dynamics · Cross-listed from math-ph

Heat transfer problem of a dense gas described by the Enskog equation with a modification of the Enskog factor

Shigeru Takata, Soma Sakata and Masanari Hattori

Heat transfer in a dense gas between two parallel plates is studied for assessing the quantitative difference of two variants of the Enskog equation, i.e., the original Enskog equation and the Enskog equation with a modified Enskog factor recently proposed in Phys. Rev. E 111, 065108 (2025). The main advantage of the latter is that the H theorem, which the former lacks, has been established. The influence of the modification is assessed by comparing the macroscopic quantities in detail. It is found that the impact of this modification is quite limited and the two variants reasonably agree as a whole.
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Plasma Physics

Instabilities in Cylindrical Geometry Using the Minimalist Approach: Formalism and Rotational Instabilities

Nektarios Vlahakis

The minimalist approach for linear stability analysis is applied to fluids and magnetized ideal plasmas in cylindrical geometry. In this approach, the dispersion relation is obtained by integrating a single first-order differential equation - referred to as the principal equation - subject to appropriate boundary conditions. We first derive the principal equation for a general unperturbed state with radially varying density and pressure, axial and azimuthal components of both the velocity and magnetic field, and a radially directed gravitational field. We then use this formulation to analyze rotating flows with axial magnetic fields, addressing both wall-bounded and interface-driven axisymmetric instabilities. In addition to exact results for selected unperturbed states, we obtain approximate dispersion relations using the WKBJ method in the incompressible and compressible limits. The analysis encompasses centrifugal, magnetorotational, and buoyancy-driven instabilities as special cases, and it clarifies how compressibility modifies their stability properties.
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Optics · Cross-listed from quant-ph

A proposal for a hybrid free-space optical quantum communication network with hexagonal boron nitride-based single photon sources

Julien Chénedé, Mostafa Abasifard, Tjorben Matthes et al. (+2 more)

Hexagonal boron nitride (hBN) is known as a promising solid-state platform to host room temperature quantum emitters that produce high purity single photons. The bright and spectrally adaptable hBN emitters are space-compatible, making hBN well-suited for satellite-based free-space optical (FSO) quantum key distribution (QKD) at wavelengths where the atmospheric background is naturally suppressed. This paper presents a pathway to develop hBN emitters operating near the Ca-II Fraunhofer line (at 854 nm), enabling daylight FSO operation. Moreover, due to its compatibility with the first telecommunication window at 850 nm, it is possible to interface with optical fibers to bridge the `last mile' in a scenario where multiple end-users connect through a single optical ground station to a QKD satellite. We therefore introduce a concept that combines continuous operation of a quantum network, hybrid links to minimize deployment costs, and high data rates due to the use of realistic single photon sources. The realization would be an important milestone for the development of the quantum internet.
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All authors Julien Chénedé, Mostafa Abasifard, Tjorben Matthes, Asl{\i} Çakan, Tobias Vogl

Chemical Physics

Prototype-guided transfer of sparse literature knowledge for electrolyte additive discovery

Weixiang Hong, Hongting Du, Jiayue Tang et al. (+4 more)

Electrolyte additive discovery remains challenging because experimentally validated molecules are sparse, whereas accessible chemical spaces are vast and largely unlabeled. This challenge is amplified in lithium-ion batteries, where additive performance arises from coupled interfacial reactions rather than a single molecular property. Here, we develop a prototype-guided molecular intelligence, ProtoMI, a literature-driven framework that learns transferable structural priors from reported electrolyte additives and uses them to prioritize candidates in unlabeled chemical space. For boron-containing additives, ProtoMI combines 126 literature-reported molecules with 179,977 unlabeled candidates. Graph contrastive learning identifies seven chemically interpretable prototypes from the reported additives, and prototype guided semi-supervised contrastive learning adapts these prototypes to the candidate space under source-target distribution mismatch. In retrospective temporal validation, ProtoMI achieves enrichment factors of 9.2-45.6 while screening less than 2% of the candidate space. A subsequent translation step identifies four commercially accessible candidates. One representative candidate, 4,4,5,5-Tetramethyl-2-[10-(1naphthyl)anthracen-9-yl]-1,3,2-dioxaborolane (TNDB), improves high-temperature LiFePO4||graphite cycling at 55 {\deg}C by 34.93% relative to the baseline electrolyte. An arsenal of characterizations and operando optical fiber Fourier transform infrared spectroscopy suggest that TNDB forms B-containing, F/P/O-modified inorganic interphases, suppresses solvent decomposition and reduces Fe deposition on graphite. This case study shows how sparse literature knowledge can guide experimentally efficient molecular discovery in data-scarce battery-additive spaces.
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All authors Weixiang Hong, Hongting Du, Jiayue Tang, Ruifeng Tan, Yangjian Quan, Jia Li, Jiaqiang Huang

Biological Physics

Trypanosome motility in blood and particle suspensions

Florian A. Overberg, Marie Kater, Timothy Krüger et al. (+3 more)

Motile microorganisms often navigate crowded and structurally complex environments, where surrounding obstacles can strongly influence locomotion. The bloodstream form of the flagellate parasite Trypanosoma brucei circulates in blood, a dense suspension of red blood cells (RBCs), yet the physical mechanisms governing its locomotion under such conditions remain poorly understood because direct experimental observations are challenging. Here, we combine numerical simulations with in vitro experiments to investigate trypanosome motility in concentrated RBC suspensions and in suspensions of spherical colloidal particles. Simulations reveal that the parasite swimming speed increases by up to $50\%$ at RBC volume fractions comparable to those in blood. To identify the origin of this enhancement, we perform controlled studies in colloidal suspensions with particles of different sizes. We find that suspended particles substantially increase the anisotropy between the perpendicular and parallel friction coefficients acting on the beating flagellum, thereby enhancing propulsion. This effect is most pronounced when the suspended particles are comparable to or smaller than the characteristic wavelength of the flagellar beat. Experiments with microparticle suspensions confirm an increase in trypanosome propulsion with increasing particle concentration, in qualitative agreement with the simulations. Our results uncover a general physical mechanism by which concentrated particle suspensions can enhance flagellar-beat-driven locomotion and suggest that the densely crowded, particulate environment of blood may facilitate trypanosome propulsion. These findings provide new insight into trypanosome motility in the bloodstream and may apply broadly to other flagellated microswimmers in complex suspensions.
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All authors Florian A. Overberg, Marie Kater, Timothy Krüger, Gerhard Gompper, Markus Engstler, Dmitry A. Fedosov

Optics · Cross-listed from quant-ph

Observation of Hong-Ou-Mandel interference between photon and polariton

Yun-Ru Fan, Ying-Ao Su, Kai Guo et al. (+11 more)

Light-matter interactions underlie many quantum technologies, yet whether quasiparticles formed from such interactions preserve the full quantum state of light remains unresolved. Surface plasmon polaritons (SPPs), a class of polaritons formed by interacting photons with free-electron oscillations at metal-dielectric interfaces, are prime candidates to explore this question. Here we demonstrate quantum interference between single photons and SPPs using an Au-SiN$_{\mathrm{x}}$ integrated photonic-plasmonic device. Our results reveal that SPPs retain the indistinguishability of their excitation photons, establishing SPP as a viable quantum information carrier and opening a potential route toward photonic-plasmonic quantum circuitry.
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All authors Yun-Ru Fan, Ying-Ao Su, Kai Guo, Bo-Yu Fan, Yao-Qing Zhang, Hai-Zhi Song, Hao Li, Yong Geng, Kun Chen, Deng-Ke Zhang, Li-Xing You, Yan-Yu Wei, Guang-Can Guo, Qiang Zhou

Biological Physics · Cross-listed from cs.NE

Memory as an Energy Landscape—Hopfield

Nima Dehghani

This chapter reconstructs the Hopfield network as a physical theory of memory rather than merely an early neural-network algorithm. It begins with the problem as it stood before 1982-threshold logic, Hebbian association, correlation memories, and recurrent binary networks-and isolates what Hopfield's synthesis added: a dynamical definition of content-addressable memory, a symmetric recurrent architecture with a Lyapunov function, a Hebbian embedding of patterns in its couplings, and a physical account of basins, robustness, and graceful degradation. The binary and graded-response energy functions are derived in full, together with the signal-crosstalk decomposition governing pattern stability, the mean-field theory of retrieval at extensive load, and the zero-temperature retrieval spinodal at (alpha 0.138) established by Amit, Gutfreund, and Sompolinsky. The energy-based program is then followed through analog optimization networks, polynomial dense associative memories, exponential interactions, and modern continuous Hopfield updates, including the precise conditions under which the update becomes scaled dot-product attention. Throughout, capacity claims are tied to their disorder ensemble, scaling limit, and success criterion, showing why numerically different storage limits need not conflict. A closing assessment distinguishes established results from surviving principles, assumption-bound limitations, and open problems, treating the Hopfield network as an effective theory whose symmetry, locality, and point-neuron assumptions delimit its biological reach. Fixed-seed numerical experiments expose the mechanisms discussed but do not substitute for analytical results.
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Biological Physics · Cross-listed from q-bio.NC

Neural Logic, Invariance, and the Retina—McCulloch and Pitts

Nima Dehghani

This chapter reconstructs the McCulloch-Pitts program as a physics of neural computation rather than the familiar cartoon of a binary neuron. The 1943 logical calculus is developed in both directions: given a net, characterize the propositions realized by its activity; given an admissible logical expression, construct a net that realizes it. We recover the original distinction between thresholded excitatory summation and absolute inhibitory veto-one the weighted-threshold form cannot preserve for arbitrarily large excitatory inputs-and read unit-time delay as the physical realization of logical depth. Recurrence is treated exactly: an autonomous, deterministic network of finitely many binary units has a finite state space, so every trajectory eventually enters a periodic orbit-a fact about finite-state dynamics, not unbounded Turing computation. A single threshold element realizes only linearly separable Boolean functions, whereas finite feedforward networks of them synthesize any Boolean function on a finite domain. We then follows McCulloch and Pitts beyond threshold logic. The 1945 heterarchy paper turns cyclic preference into an obstruction to representation by a scalar utility. The 1947 work on universals asks how a physical network can identify inputs related by nuisance transformations, developed here via group averaging and feedback canonicalization. The 1959 frog-retina study makes the adequate-stimulus question experimental, revealing parallel invariant operations before the brain proper. Spike-triggered analysis shows how a nonlinearly driven neuron can have a vanishing first-order average while second-order statistics recover its hidden selectivity: methodological failure can masquerade as physiological absence. Modern mathematical tools are used without projecting their notation onto the historical papers, and limitations of the idealization are stated explicitly.
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Plasma Physics

A Hybrid Simulation Code for Hall Thrusters and its Sensitivity to Numerical Parameters

Xingdong Che, Hong Li, Xin Guo et al. (+3 more)

Hybrid methods offer an attractive balance between computational efficiency and physical accuracy, playing an important guiding role in the design and optimization of Hall thrusters. In this work, a hybrid simulation code, named HYSCH, is developed, utilizing a 1D-MFAM as the mesh framework for the electron submodel. HYSCH enables decoupling of the two submodel meshes, providing a higher degree of flexibility in spatial resolution settings. The sensitivity of the simulated results to numerical parameters is analyzed to validate the model's numerical robustness and physical consistency. The analysis shows that the temporal resolution of the heavy-species submodel and the spatial resolution of the electron submodel exert a more pronounced influence in the agreement with measurements than the heavy-species macroparticle weight and spatial resolution, confirming that the decoupled formulation enables more efficient resource allocation than coupled discretizations.
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All authors Xingdong Che, Hong Li, Xin Guo, Zhaoyu Wang, Xifeng Cao, Daren Yu

Optics

Multidimensional Light Detection with Symmetry-engineered Heterojunctions

Yucai Lin, Yaoqiang Zhou, Ruijuan Tian et al. (+11 more)

Miniaturised multidimensional light detection, encompassing full-Stokes polarimetry and spectroscopy in ultracompact footprints, is attracting growing interest for its potential to capture a comprehensive set of light properties in portable platforms. Although significant progress has been made in miniaturised schemes for independent polarisation and spectral detection, achieving simultaneous high-dimensional light detection remains an outstanding challenge that limits their development toward full integration. We overcome this limitation by breaking the rotational and inversion symmetries in a symmetry-engineered van der Waals heterojunction to realise an ultracompact multidimensional photodetector. The dual symmetry breaking gives rise to non-trivial quantum geometric and topological features, enabling simultaneous broadband polarisation- and spectrum-resolved light detection, in contrast to previous van der Waals material-based devices, which could detect only one of these modalities. Our device, with an effective area of only 10 micron x 10 micron, reconstructs full-Stokes polarisation with overall root-mean-square errors below 0.05 and resolves spectral peaks separated by 0.4 nm, capabilities not previously achieved in single-pixel detectors. By unifying high-fidelity polarimetry and sub-nanometre spectroscopy in a single electrically tunable junction, our work eliminates the need for cascaded detection architectures and establishes a foundation for multidimensional detector arrays for integrated photonics, quantum information processing, and precision imaging.
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All authors Yucai Lin, Yaoqiang Zhou, Ruijuan Tian, Faisal Ahmed, Andreas C. Liapis, Youqiang Huang, Yawei Dai, Yuwei Chen, Weiwei Cai, Zongyin Yang, Weida Hu, Tawfique Hasan, Luojun Du, Zhipei Sun

Plasma Physics · Cross-listed from astro-ph.SR

Electron acceleration by turbulent reconnection in solar flares

Zining Ren, Xin Cheng, Yulei Wang et al. (+1 more)

Solar flares can release magnetic energy explosively in the corona and produce high-energy particles on short timescales. However, how and where these particles are accelerated remains an open question. Here, we investigate the acceleration and transport of electrons during self-developed three-dimensional turbulent reconnection of solar flares by solving Parker's transport equation in the framework of high-resolution MHD simulations. We find that thermal electrons at both the flare current sheet and loop top are rapidly accelerated up to ~90keV, with energy spectra exhibiting a power-law feature. Although the population of accelerated electrons at the flare loop top is larger than that at the current sheet, their spectral indices are similar, close to the values usually observed. More importantly, the acceleration is achieved by turbulence-driven compression structures of various scales rather than the supposed termination shock, particularly at the flare loop top. A portion of compression structures even forms shocks. These results highlight the critical role of turbulent reconnection in accelerating electrons, thereby shedding new light on the acceleration and transport of particles in other high-energy phenomena.
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All authors Zining Ren, Xin Cheng, Yulei Wang, Mingde Ding

Fluid Dynamics

Bridging the local and the global: a physically constrained buoyancy–drag model for unified prediction of Rayleigh–Taylor and Richtmyer–Meshkov mixing widths across density ratios

You-Sheng Zhang, Ya-Feng Li, Meng-Juan Xiao et al. (+1 more)

Accurate prediction of the macroscopic width of Rayleigh–Taylor (RT) and Richtmyer–Meshkov (RM) turbulent mixing layers is central to inertial confinement fusion and supernova dynamics. However, bubble–spike asymmetry, density-ratio dependence and unsteady forcing pose a persistent closure challenge: existing low-order buoyancy–drag models struggle to describe different mixing problems accurately with one model and coefficient set. We combine local front dynamics with global mass conservation in separate buoyancy–drag equations for the bubble and spike fronts. Rather than imposing shared or fixed empirical coefficients, the model retains separate inertia, buoyancy and drag coefficients on the two sides and allows them to vary independently with density ratio. Given the bubble-side state scalings, RT/RM similarity relations, a mean-composition profile and endpoint asymptotics jointly constrain all six effective coefficients without case-by-case fitting. A profile-shape parameter $c$ labels distinct internal composition states and is selected a priori from RT spike scaling measured in linear-electric-motor experiments. The model then cross-predicts the RM spike exponent without recalibration to RM spike data and, by construction, recovers low-Atwood-number bubble–spike symmetry and the high-density-ratio free-fall RT-spike and ballistic RM-spike limits. Tests against constant- and variable-acceleration RT mixing, post-impulse RM evolution and Nova laser deceleration show that one closure describes mixing-width evolution across density ratios and acceleration histories without case-specific retuning, while reducing excessive spike growth at high density ratio. This physically interpretable, asymptotically consistent framework enables cross-problem prediction of wide-density-ratio RT and post-impulse RM mixing.
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All authors You-Sheng Zhang, Ya-Feng Li, Meng-Juan Xiao, Yu-Hui Wang

Fluid Dynamics

Reynolds-number evolution of wall-pressure statistics beneath canonical turbulent boundary layers

Rahul Deshpande, Balaraman Panneerselvam, Vijaya R. R. Gudla et al. (+2 more)

This study investigates the Reynolds-number (Re_\tau) evolution of wall-pressure statistics beneath zero-pressure-gradient TBLs, and links their logarithmic variation to the increasingly energetic large-scale motions in the logarithmic region. The wall-pressure skewness is found to become more negative with increasing Re_\tau, owing to increasing contributions from large-scale wall-pressure fluctuations (that are negatively skewed) and their nonlinear interaction with the statistically invariant inner-scale fluctuations (that are positively skewed). The analysis draws on new, well-resolved simultaneous measurements of wall pressure and streamwise velocity spanning 5000 < Re_\tau < 11300 in the Melbourne tunnel, atmospheric surface-layer measurements at Re_\tau = O(10^6) and a published simulation dataset at Re_\tau = O(10^3). Particular attention is paid to the principal experimental limitations affecting wall-pressure statistics: spatial resolution, Helmholtz resonance, facility noise and statistical convergence. Helmholtz resonance is shown to contaminate inner-scale wall-pressure contributions even after conventional corrections, and reliable estimation of skewness is found to require acquisition durations of O(10^5) eddy-turnover times or longer. The inner-scaled wall pressure spectrum is Reynolds-number invariant over the small-scale regime, in contrast to turbulent channel and pipe flows, whereas at intermediate and large scales it grows substantially with Re_\tau, consistent with these internal flows. Linear and quadratic velocity–wall-pressure coherence link these intermediate- and large-scale contributions to two dynamically distinct coherent structures: the self-similar attached-eddy hierarchy and turbulent superstructures, respectively. These analyses establish the connection between the inertial region and the log variation of wall-pressure variance and skewness with Re_\tau
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All authors Rahul Deshpande, Balaraman Panneerselvam, Vijaya R. R. Gudla, Joe Klewicki, Ivan Marusic

Chemical Physics · Cross-listed from quant-ph

Logarithmic-scale variational quantum eigensolver for off-lattice protein structure prediction in continuous torsional angle space

Fabio Cumbo, Bryan Raubenolt, Varun Puram et al. (+3 more)

Classical and current quantum approaches to protein structure prediction (QPSP) face limitations, notably massive qubit requirements restricting near-term models to simplistic on-lattice simulations. We propose a logarithmic-scale variational quantum eigensolver (VQE) that reduces qubit requirements for N torsional degrees of freedom to O(log2N), enabling off-lattice, all-atom simulations. Our architecture extracts molecular torsions from relative phases in statevector simulations. On quantum hardware, a decoder maps the empirical cumulative distribution function (CDF) from basis-state probabilities to bounded torsional variables. These feed a classical algorithm to build heavy-atom coordinates. We use an EfficientSU2 ansatz and multi-stage relaxation to mitigate barren plateaus. Structures are evaluated via a custom hybrid quantum-classical Hamiltonian, alongside Rosetta and OpenMM benchmarks. Evaluation on chignolin and Trp-cage yielded native-like conformations. Chignolin reached a 0.623 Å C{\alpha} RMSD in retained snapshots and 1.199 Å in final models; Trp-cage achieved a 2.501 Å RMSD among snapshots (3.512 Å in final models). Execution on IBM processors (ibm_cleveland, ibm_miami) successfully recovered native-like structures with a best RMSD of 1.758 Å. The custom energy function performed best overall, though energy-ranking imbalances persisted across sampled landscapes for all functions. This introduces the first all-atom, continuous-space quantum algorithm for QPSP. By converting physical qubit constraints into circuit depth constraints, it proves high-resolution prediction is feasible with exponentially fewer qubits. Despite current limits like computational overhead and energy function sensitivity, it establishes a scalable foundation for hybrid quantum biophysics.
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All authors Fabio Cumbo, Bryan Raubenolt, Varun Puram, Natalie Katzenmeyer, Jayadev Joshi, Daniel Blankenberg

Optics

Laser-induced phase shift of swift electrons

Christian Dwyer and David M. Paganin

We revisit the calculation of the phase shift experienced by swift electrons on passing through the electromagnetic field of a laser. Such phase shifts are now utilized in the form of `laser phase plates' in transmission electron microscopes (TEMs), for example. We calculate the phase shift using three different methods, namely, perturbation theory applied to the Dirac equation, the Volkov solution to the Klein-Gordon equation, and the relativistic Hamilton-Jacobi equation. We find that all three methods are in agreement, and that the calculated phase shift is independent of the relative orientation of the electron and laser beams. The agreement between the quantum and classical theories is explained. The duality between the phase shifts experienced by electrons, photons and neutrons is described. Our Lorentz invariant result for the phase shift differs from certain results published in the literature.
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