Fluid Dynamics · Cross-listed from cs.LG
Geometry-free prediction of inertial lift forces in microfluidic devices using deep learning
Jesse Ward-Bond, Ali Mashadian, Timothy C. Y. Chan et al. (+1 more)
Inertial microfluidic devices (IMDs) offer low-cost, high-throughput alternative techniques for many traditional particle- (or
cell-) manipulation tasks, but simulating them requires being able to predict particle migration, and thus particle lift forces, under a variety of possible channel geometries. Recent work has demonstrated that machine learning models can be used to drastically speed up these numerical simulations, but doing so required training individual models for every unique channel cross-section type (e.g., rectangular, triangular) – shifting the burden from the simulation step to the training step. In this paper, we develop a novel approach for predicting particle lift forces that contains no explicit
geometric parameters. We train a neural network model using a new parameter set and show that while it performs comparably to existing models on channel geometries in the training set, it is able to generalize to unseen channel geometries far more effectively. We show that the lift force model developed herein can be easily transferred to particle tracing simulation software, where it is capable of predicting particle migration patterns consistent with the literature across a variety of channel designs.
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All authors Jesse Ward-Bond, Ali Mashadian, Timothy C. Y. Chan, Edmond W. K. Young
Optics · Cross-listed from cond-mat.str-el
Opto-criticality in Drude metals near the plasma frequency
Bikram Keshari Behera, Rhitabrata Bhattacharyya and Shyamal Biswas
Within a simple unified framework of classical electrodynamics that incorporates background bound charges and currents, we have analytically determined the attenuation constant, phase constant, and reflectivity of Drude metals across the full frequency spectrum ($0 < \omega < \infty$).Our result for reflectivity agrees well with existing experimental data for both
plasmas and seawater. Notably, for highly conductive Drude metals ($\omega_p \tau \gg 1$), the attenuation constant simplifies to $k_- \simeq \sqrt{\frac{\mu \epsilon}{2}} \sqrt{\omega_p^2 - \omega^2 + \vert{}\omega_p^2 - \omega^2\vert{}}$ across a broad high-frequency range spanning the
plasma frequency $\omega_p$. The branch-point singularity at $\omega=\omega_p$ in this relation reveals opto-critical behavior near $\omega=\omega_p$ in properties such as the attenuation constant, group velocity, and complex dielectric constant, for which we have determined the corresponding opto-critical exponents. Furthermore, we have incorporated
quantum corrections into these optical properties via the Drude-Sommerfeld model with Thomas-
Fermi screening.
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Computational Physics
On Reconstructing Conservative and Primitive Variables: An Eigenvector Analysis on Curvilinear Grids
Amareshwara Sainadh Chamarthi
In wall-modelled large-eddy simulations of hypersonic boundary-layer transition, Hoffmann, Chamarthi and Frankel reported that characteristic reconstruction based on conservative-variable eigenvectors produced markedly better results than the corresponding primitive-variable implementation. The observation was empirical. A subsequent wave-appropriate conservative reconstruction (WA-CR)
algorithm used a rank-one
entropy correction based on the premise that contact-discontinuity error lies in a single conservative
entropy/contact direction. This note gives the algebraic foundation for both observations. For the standard conservative curvilinear eigenvectors, the density row of the right-eigenvector
matrix contains exact, metric-free zeros in the shear columns, so shear waves carry no density perturbation and a contact discontinuity is represented by the conservative
entropy eigenvector alone. The conservative left eigenvectors provide the dual projection property: the
entropy amplitude is obtained with a metric-independent left eigenvector and has unit contact scaling, while total-energy perturbations have zero projection onto the shear amplitudes. In the standard primitive curvilinear eigenvectors, by contrast, shear right eigenvectors contain metric-dependent density components and the primitive
entropy left eigenvector contains metric-weighted tangential-velocity terms. Thus the conservative formulation supplies the two algebraic requirements for an exact, sufficient, metric-invariant, rank-one
entropy correction: metric-independent
entropy projection and a metric-independent
entropy update direction. Curvilinear metrics make the distinction explicit, but the conservative state-space contact direction is already the natural direction underlying WA-CR even on Cartesian grids.
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General Physics
Electron-impact ionization rates for neutral He, Li, and Be in the Tsallis framework
Abdelmalek Boumali
The single-ionization rate coefficient of a
plasma neutral depends both on the microscopic electron-impact cross section and on the macroscopic shape of the electron energy distribution function (EEDF). We present a reproducible
benchmark and sensitivity study – not a new theory – of these two effects for the three lightest neutrals He, Li, and Be, combining the recommended Bell~et~al.\ (1983) cross sections with a properly normalized two-temperature Tsallis $q$-generalized EEDF and varying $q$ on both sides of the Maxwellian limit and the hot-electron fraction $f_{\mathrm{hot}}$ at $T_{\mathrm{hot}}=10\,T_{\mathrm{bulk}}$. The calculation cleanly separates two independent uncertainty axes – cross-section model (Bell vs.\ Lotz) and EEDF shape (Maxwellian vs.\ Tsallis). The Bell–Lotz spread on $\tau_M$ is small for He (within about $7\%$), moderate for Be ($\lesssim 17\%$), and largest for Li (up to $+95\%$ at $T=1$~keV); sub-extensive distributions ($q<1$) suppress ionization through a hard tail cut-off, while super-extensive distributions ($q>1$) enhance low-temperature ionization through a $\kappa$-like power-law tail with $\kappa=1/(q-1)$. The quantitatively safest non-Maxwellian cases are $q=1$ and $q=1.2$ ($\kappa=5$), which lie inside the finite-mean-energy regime; the cases $q=1.4$ and $q=1.6$ are retained as heavy-tail stress tests and should be read as qualitative trends rather than as quantitatively reliable predictions. Both EEDF effects scale with $I_p/k_BT$, so He responds most strongly and Li least. The full numerical pipeline is released as a persistent reproducibility package, intended as a drop-in non-Maxwellian ionization module for collisional-radiative and ionization-balance modelling of light-neutral
plasmas.
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Plasma Physics
Quasilinear flux model consistent with gyrokinetic ordering
O. Yamagishi and G. Watanabe
We propose a quasilinear (QL) flux model in which the saturation amplitude is uniquely determined using multiscale gyrokinetic ordering relations. The model is fully self-contained within a linear framework and does not rely on calibration against nonlinear simulations or mixing-length estimates. The wavenumber-dependent flux is given in ion gyro-Bohm units with a weighting factor of $|k_\theta \rho_i|$, such that its area integral in the log-linear scale yields the total flux, as employed in multiscale simulations. In systems with comparable ion and electron temperature gradients, the QL ion energy flux reproduces nonlinear simulation results in both its wavenumber dependence and absolute magnitude. In contrast, the QL electron flux is predominantly generated at electron scales, indicating that the shift of electron-scale transport toward ion scales observed in nonlinear Gsimulations is not captured within the present linear framework. We argue that the relation $Q_i\sim Q_e$, obtained as a closed conclusion of the QL model, may be predictive of simulation results if the area-integrated flux is conserved in nonlinear energy cascade process.
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Biological Physics · Cross-listed from q-bio.MN
Learning biophysical models of gene regulation with probability flow matching
Suryanarayana Maddu, Victor Chardès and Michael J. Shelley
Cellular differentiation is governed by gene regulatory networks, the high-dimensional
stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although single-
cell RNA sequencing provides quantitative snapshots of the transcriptome, current methods for inferring gene-regulatory dynamics often lack mechanistic interpretability and fail to generalize to unseen conditions. Here we introduce Probability Flow Matching (PFM), a scalable framework for learning biophysically consistent
stochastic processes directly from time-resolved single-
cell measurements. Applying PFM to three hematopoiesis
datasets, we show that models with similar interpolation accuracy can encode fundamentally different dynamics, with only biophysically consistent formulations accurately capturing mechanisms of lineage transitions, fate specification, and gene perturbation responses. We further demonstrate that PFM accommodates unbalanced populations, enabling simultaneous inference of cellular proliferation and death dynamics. Together, these results establish PFM as a flexible, scalable framework for integrating mechanistic modeling with single-
cell omics.
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Chemical Physics · Cross-listed from cond-mat.stat-mech
Statistical mechanics in continuous space with tensor network methods
Gunhee Park, Tomislav Begušić, Si-Jing Du et al. (+2 more)
Tensor network (TN) methods are well established for computing partition functions in statistical mechanics, though this use has traditionally been limited to
lattice models. We extend the scope of TN methodology to interacting particle systems in continuous space. Through a real-space discretization combined with a
cell-based coarse-graining scheme, we formulate an effective
lattice model that explicitly preserves spatial locality. The partition function of this model is represented as a TN, and the thermodynamic quantities are computed via boundary contraction. We apply this framework to the two-dimensional hard-disk problem and demonstrate the strengths of the TN formulation compared to existing Monte Carlo simulations.
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All authors Gunhee Park, Tomislav Begušić, Si-Jing Du, Johnnie Gray, Garnet Kin-Lic Chan
Chemical Physics
Thermal conductivity of aligned polymers with kinks
Igor V. Parshin, Igor V. Rubtsov and Alexander L. Burin
Thermal conductivity of aligned
polymer molecules can be exceptionally high along the
alignment direction due to energy transport through strong covalent bonds. At the same time, it is highly sensitive to molecular conformation, varying by orders of magnitude as a result of gauche kinks. Here, we theoretically investigate
phonon transport in kinked
polymers by numerically evaluating thermal conductivity and interpreting the results in terms of
phonon scattering from randomly distributed kinks. For strongly aligned
polymers with restricted deviations from a linear backbone, we find that heat transport becomes superdiffusive at long lengths, with thermal conductivity scaling as $\kappa \propto L^{1/3}$. At shorter lengths, thermal conductivity exhibits non-monotonic behavior: it increases at very short scales due to ballistic transport of almost all
phonons, then decreases at intermediate lengths due to the Anderson localization of most
phonon modes. These results are consistent with experiments and molecular dynamics simulations, and they elucidate the microscopic mechanisms governing heat transport in
polymers.
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Atmospheric and Oceanic Physics · Cross-listed from nlin.CD
Lagrangian Rotating Contracting Structures
F.J. Beron-Vera
We identify materially defined regions in unsteady two-dimensional flows that combine finite-time contraction with elevated accumulated intrinsic rotation along trajectories, which we term Lagrangian rotating contracting structures (LRCS). These regions are detected using existing objective diagnostics – the Lagrangian-averaged vorticity deviation (LAVD) together with direct tests of material contraction – without relying on the geometry of LAVD level sets. In strongly deforming flows, LAVD maxima need not correspond to vortical regions or be enclosed by regular level sets, rendering geometry-based identification unreliable. Nevertheless, regions exhibiting inward spiraling motion and contraction can be extracted by combining LAVD with a contraction criterion. Applications to atmospheric and oceanic flows show that such behavior arises both in twisted LAVD fields generated at submesoscales and in mesoscale flows where it is enhanced by inertial effects, with finite-time contraction providing the dynamical constraint that isolates materially organized regions with elevated intrinsic rotation.
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Space Physics
Solar Energetic Particle Reflection by Precursor ICMEs: Multi-spacecraft Observations of Bi-Directional Electron Beams at 1 AU
Lucas Liuzzo, Wenwen Wei, Andrew R. Poppe et al. (+2 more)
We present case studies of two impulsive
solar energetic electron (SEE) events during which particles at energies from 1-600 keV were detected by THEMIS-ARTEMIS orbiting the Moon, Wind at Earth's first Lagrange point, and (for one event) STEREO-A located at 1 AU, off the Sun-Earth line. The SEEs were initially highly anisotropic, traveling outward along the
magnetic field with distinct energy-time dispersion. For one event, the spectra contained inverse velocity dispersion (IVD) signatures, whereby electrons at intermediate energies arrived to the spacecraft before those at higher energies. Similar features were recently discovered within 1 AU for energetic
protons; this represents the first IVD detection for energetic electrons at Earth's orbital distance. During both events, a second beam of counter-streaming electrons was detected after a short time. Based on the time-delay in the detections at various energies, the path traveled by these counter-streaming electrons was on the order of 1-2 AU. We show that an interplanetary coronal mass ejection (ICME) passed the spacecraft a few days prior to the onset of each event and was located beyond 1 AU when the SEEs were detected, suggesting that the electrons were part of the same population, but reflected off the shock front of these precursor ICMEs. In the context of
solar system exploration, this represents an unidentified hazard for astronaut safety beyond low-Earth orbit: although the initial phase of impulsive SEE events typically stream anti-Sunward, ICMEs located beyond Earth provide a mechanism for hazardous particles to travel Sunward during extreme events.
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All authors Lucas Liuzzo, Wenwen Wei, Andrew R. Poppe, Christina O. Lee, Vassilis Angelopoulos
Optics
Hidden optical nonlinearities in linear spectra of quantum emitter arrays
Sricharan Raghavan-Chitra, Arghadip Koner and Joel Yuen-Zhou
Classical optical frameworks such as the discrete dipole approximation (DDA) assume that the linear spectrum of coupled
quantum emitters can be computed solely from the linear susceptibilities of individual constituents. However, recent polariton studies show that cavity linear response can encode nonlinear optical susceptibilities. Here, we demonstrate that this phenomenon is more general: emitter-emitter interactions allow nonlinearities of individual emitters to emerge in the linear response of arrays, without cavities or permutational
symmetry. To illustrate this phenomenon, we show linear spectra for coupled heterodimers and linear chains, and demonstrate that Raman features of individual monomers show up as vibrational sidebands of collective resonances. Moreover, tuning Raman-type anharmonicities enables systematic control of spectral features, establishing a genuine
quantum optical effect in molecular aggregates and
quantum emitter arrays, which goes beyond mean-field descriptions in light-matter interactions.
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Physics and Society
Relocation without preference: A destination-agnostic Schelling-type metapopulation model
Fei Cao and Roberto Cortez
In this work, we propose and analyze a novel Schelling-type metapopulation model that examines how random relocations of families between neighborhoods can lead to segregation. The model consists of a large number of houses organized into $N$ neighborhoods with $L$ houses each, without any spatial structure. Houses can be occupied by either a blue or a red family, and families relocate – to an empty house selected uniformly at random – at a rate that depends only on the number of families of the other type within the same neighborhood. We study two mean-field regimes: the large $N$ limit with fixed $L$, and the large $L$ limit with fixed $N$. The associated mean-field systems of ODEs are derived, and their long-time behavior is investigated. As is often the case with Schelling-type models, we find a rich interplay between the model parameters and the social structure of the
equilibrium distribution, which exhibits segregation in some parameter ranges. Our work demonstrates that segregation patterns can emerge even when the relocation mechanism is destination-agnostic.
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Physics Education
Bridging the Quantum Divide: A Learning-Centric Quantum Hackathon for Underrepresented Students (Extended Version)
Fahimeh Bayeh, Linh Dinh, Dongho Lee et al. (+1 more)
This paper describes the design and implementation of a two-day
quantum hackathon for underrepresented high school students in Nova Scotia, Canada. The first day of the hackathon is spent introducing students to
quantum computing through hands-on activities, whereas the second day teaches students to apply this knowledge through guided challenges. Both days are informed by the theory of mastery learning and specification grading, with the full curriculum being crafted within the Integrated Course Design framework. This requires identifying situational factors unique to our target demographics, from which we develop learning outcomes, and then work backwards to a full curriculum with educative assessments. A novel aspect of our hackathon is that all
circuit simulations are performed within Quirk: a decision based on best practices in computer science education. Based on feedback from students, we conclude that our hackathon successfully introduced students to the basics of
quantum computing, and was able to reach most of our target demographics.
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All authors Fahimeh Bayeh, Linh Dinh, Dongho Lee, Scott Wesley
Plasma Physics
Knudsen number as a non-thermal parameter: possible origin of skewness in space plasma distributions
Iván Gallo-Méndez, Adolfo F. Viñas and Pablo S. Moya
Non-Maxwellian distributions and their origins in space
plasma have attracted significant
attention due to their prevalence and impact on various astrophysical and space-related phenomena. This paper presents a theoretical study of the consequences of incorporating a Skew-Kappa distribution to describe the non-thermal electron distribution in the
solar wind. By introducing a Krook-like term into the Boltzmann equation to represent collision effects, we investigate the dependence of the skewness parameter on
plasma macro-dynamics. Our analysis focuses on understanding the departure from thermal
equilibrium and the statistical behavior of the
plasma under the influence of collisional processes. By analyzing the Boltzmann transport equation adapted to space
plasma, we derive expressions for the skewness parameter as a function of
plasma parameters and the collision effect. Our results provide valuable information on the relationship between skewness, collisional dynamics, and the statistical properties of space
plasmas, namely $\delta \sim K_N$, the relationship between the skewness parameter and the effective Knudsen number. This study contributes to a deeper understanding of non-Maxwellian distributions and their role in astrophysical and space
plasma phenomena.
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Fluid Dynamics
Effects of temperature-dependent material properties in coldwater Rayleigh-Bénard convection
Gustavo Estay, Daisuke Noto and Hugo N. Ulloa
Water exhibits an anomalous nonlinear density equation of state (EOS) as it approaches freezing, along with an increase in viscosity ($\mu$) and a decrease in thermal conductivity ($k$). Here we ask: how do these temperature-dependent material properties affect thermal convection in coldwater? We examine these effects within the canonical Rayleigh-Bénard convection (RBC) system, performing direct numerical simulations with coldwater between $0^{\circ}$C and the temperature of maximum density $3.98^{\circ}$C. To disentangle the effects of these properties, we consider two main cases: RBC with a quadratic EOS and constant $\mu$ and $k$; and RBC with a quadratic EOS and temperature-dependent $\mu(T)$ and $k(T)$. We show that the most significant consequence is a shift in the mean fluid temperature relative to `standard RBC'. The nonlinear EOS and the temperature-dependent $\mu$ and $k$ drive this shift in opposite directions, with the former dominating and producing a net decrease in the mean temperature. This decrease varies with the Rayleigh number $Ra$, reaching up to $0.08^{\circ}$C at $Ra=10^{8}$. Additionally, the onset of convection is affected, but the influence from the EOS and $\mu(T)$ and $k(T)$ compensate, resulting in a negligible net effect. Despite these changes, the Nusselt and the Reynolds numbers follow classical scalings in all cases. Our results establish how the anomalous material properties of coldwater affect local and global features of convection, evidencing the implications of model selection for studies of cryospheric water bodies.
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Applied Physics · Cross-listed from cond-mat.soft
Entropic Trapping of Hard Spheres in Spherical Confinement
Praveen K. Bommineni, Junwei Wang, Nicolas Vogel et al. (+1 more)
Monodisperse spherical colloidal particles confined within emulsion droplets can crystallize into icosahedral clusters. Experimentally it was observed that a few large colloidal particles added as defects preferentially migrate to the vertices of the icoshedral clusters. To understand this structure formation phenomenon, we simulate the confined self-assembly of hard spheres in the presence of a small number of larger particles. The results demonstrate that large spheres are significantly influenced by concentric shells of small spheres near the crystallization transition. Entropic forces drive the large spheres to the cluster surface, where they settle into free energy minima at the icosahedron vertices. Notably, the addition of twelve large spheres results in the formation of a perfect icosahedral frame. Free energy calculations via umbrella sampling are used to quantify this process and show that both the migration to the cluster surface and the trapping at the vertices with trapping strength of multiple $k_\text{B}T$ results from free energy minimization. Moreover, our study reveals that the crystallization pathway and dynamics of large spheres are consistent across different systems, suggesting robustness of entropic trapping.
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All authors Praveen K. Bommineni, Junwei Wang, Nicolas Vogel, Michael Engel