Biological Physics
Optimal Discretization in Hour-Glass Molecular Clocks Driven by Oscillating Free Energy
Zhuangcheng Zhen, Kaiyue Shi, Qi Ouyang et al. (+1 more)
Hour-glass clocks do not free-run; they keep time by riding an external rhythm. Motivated by the
primordial KaiBC system in cyanobacteria, we study a driven, finite-state molecular clock that advances through a small number of biochemical states under an intrinsic driving energy and a rotating energy landscape set by day-night metabolism. In the continuum limit, coherence is maximized at a resonant operating point where the intrinsic drift matches the driving frequency. In realistic clocks with a finite number of states, discreteness matters: as the rotating landscape sweeps over a
lattice of states, it generates a small and high frequency vibration of the collective phase that makes timing inaccurate. Combining the resonant cost with this discreteness penalty yields a trade-off in the number of states: few states are energetically cheap but noisy; many states are precise but costly. The optimum lies at moderate discretization (typically five to fifteen states) and an environmental coupling that is strong enough for responsiveness yet weak enough to avoid large discrete-state vibrations. These design rules rationalize why KaiC's hexameric architecture falls near the predicted optimum and suggest a general principle for hour-glass clocks across organisms.
Read the full abstract ▾
All authors Zhuangcheng Zhen, Kaiyue Shi, Qi Ouyang, Yuansheng Cao
Computational Physics
ChemXDyn: Dynamics-informed species and reaction detection methodology from atomistic simulations
Raj Maddipati, Dhruthi Boddapati, Elangannan Arunan et al. (+2 more)
Accurate identification of chemical species and reaction pathways from molecular dynamics (MD) trajectories is a prerequisite for deriving predictive chemical-kinetic models and for mechanistic discovery in reactive systems. However, state-of-the-art trajectory analysis methods infer bonding from instantaneous distance thresholds, which can misclassify transient, nonreactive encounters as bonds and thereby introduce spurious intermediates, distorted reaction networks, and biased rate estimates. Here, we introduce ChemXDyn, a dynamics-aware computational methodology that leverages time-resolved interatomic distance signatures as a core principle to robustly identify chemically consistent bonded interactions and, consequently, extract meaningful reaction pathways. In particular, ChemXDyn propagates molecular connectivity through time while enforcing atomic valence and coordination constraints to distinguish genuine bond-breaking and bond-forming events from transient, nonreactive encounters. We evaluate ChemXDyn on ReaxFF MD simulations of hydrogen and ammonia oxidation and on neural-network potential MD simulations of methane oxidation, and
benchmark its performance against widely used trajectory analysis methods. Across these cases, ChemXDyn suppresses unphysical species prevalent in static analyses, recovers experimentally consistent reaction pathways, and improves the fidelity of rate constant estimation. In ammonia oxidation, ChemXDyn removes unphysical intermediates and resolves key NOx- and N2O-forming and -consuming routes. In methane oxidation, it reconstructs the canonical progression from CH4 to CO2. By linking atomistic dynamics to chemically consistent reaction identification, ChemXDyn provides a transferable foundation for MD-derived reaction networks and kinetics, with potential utility spanning combustion, catalysis,
plasma chemistry, and electrochemical environments.
Read the full abstract ▾
All authors Raj Maddipati, Dhruthi Boddapati, Elangannan Arunan, Phani Motamarri, Konduri Aditya
Plasma Physics
Electric field-driven Rayleigh-Taylor-like instability in binary complex plasma
Priya Deshwal and Hitendra K. Malik
This study uses two-dimensional molecular dynamics simulations to explore Rayleigh-Taylor-like instability in a strongly coupled binary complex
plasma, when heavier
dust particles are positioned above the lighter ones, having the same charge-to-mass ratio, in a planar configuration. Langevin dynamics simulations are used to study the
evolution of perturbations at the interface between these two distinct species of charged
dust particles, subject to an externally applied electric field and an
equilibrium charge density gradient. We have performed analytical calculations to determine the growth rate of instability under both strongly coupled and weakly coupled dusty
plasma regimes. These theoretical predictions are subsequently validated through molecular dynamics simulations, enabling the reproduction of the instability in a strongly coupled binary complex
plasma. The instability in these cases ultimately causes mixing among the charged species. The study comprehensively analyzes the growth rate as a function of various system parameters, and it offers deeper insight into the underlying physical mechanisms.
Read the full abstract ▾
Optics
Measuring Nanoscale Torques with Cylindrical-Polarization-based Interferometric Scattering Microscopy
Milan Vala, Ivan Kopal, Lauren Takiguchi et al. (+5 more)
The ability to observe rotational dynamics and measure underlying torques is a crucial component in understanding the function and mechanics of nanoscale systems. Yet, direct observation of rotational dynamics at the single-molecule level in
liquids remains challenging due to the trade-off between optical detectability and hydrodynamic responsiveness. Labels that are bright enough for rapid readout typically introduce excessive drag, while minimally perturbing probes are difficult to detect at high speed. This limits access to fast rotational dynamics required for direct torque measurements. Here, we introduce cylindrical-polarization-based interferometric scattering microscopy (cypiSCAT), a method encoding the orientation of anisotropic scatterers directly into a single interferometric point spread function, while intrinsically suppressing the isotropic background. We achieve rotational tracking of low-drag orientation labels based on DNA origami-attached gold nanorods with sub-degree angular precision and microsecond temporal resolution, allowing quantitative characterization of nanoscale rotational dynamics. This capability provides direct access to torque metrology at the single-molecule level, here demonstrated through the extraction of optically induced torques as small as ~1 pN nm. Relying on elastic scattering, cypiSCAT combines ultrafast temporal resolution with long observation times, making it well-suited for capturing rapid and rare rotational events and reaction steps in nanoscale biomolecular systems.
Read the full abstract ▾
All authors Milan Vala, Ivan Kopal, Lauren Takiguchi, Yevhenii Shaidiuk, Vítězslav Lužný, Łukasz Bujak, Pallav Kosuri, Marek Piliarik
Optics · Cross-listed from quant-ph
Verification of continuous variable entanglement with undetected photons
Sanjukta Kundu, Balakrishnan Viswanathan, Pawel Szczypkowski et al. (+3 more)
We verify transverse spatial
entanglement of
photon-pairs generated in spontaneous parametric down conversion using a nonlinear interferometric technique without relying on any coincidence detection. We experimentally demonstrate the violation of the Einstein-Podolsky-Rosen criterion and of the Mancini-Giovannetti-Vitali-Tombesi criterion using single
photon interference of one of the
photons of the pairs. We also provide a comprehensive theoretical analysis. The experimental results that we have obtained show good agreement with the theoretical values. Our method performs well under experimental losses and can be applied to highly non-degenerate sources, where there are no suitable detectors for one of the
photons in the
quantum state and our method could also be extended to the discrete degrees of freedom to certify high-dimensional (OAM)
entanglement.
Read the full abstract ▾
All authors Sanjukta Kundu, Balakrishnan Viswanathan, Pawel Szczypkowski, Gabriela Barreto Lemos, Mayukh Lahiri, Radek Lapkiewicz
Geophysics
Large earthquakes follow highly unequal ones
Sudip Sarkar and Soumyajyoti Biswas
It was conjectured for a long time that the tectonic plates are in a self-organised state of criticality and that the Gutenberg-Richter law is a manifestation of that. It was recently shown that for a system near criticality, the inequality of their responses due to external driving would sharply rise and show universal behavior that could indicate the proximity of the system to a critical point. As a result, measures such as the Gini and Kolkata indices that quantify inequality can also serve as indicators of imminent criticality and those of diverging (system-spanning) responses. In the context of earthquakes, such a large response would correspond to events of high magnitudes. In this work, we show with numerical simulations and seismic data analysis that large earthquake events have a tendency to follow events that are highly unequal, similar to the case of a system near a critical point. Even though this is not a proof of tectonic plate systems being near-critical, a continuous monitoring of the inequality indices of the earthquake time series could be an useful tool for hazard estimates. We have applied this framework to models of earthquakes as well as to the earthquake time series from various seismically active regions, such as North America, Southern Japan, parts of Southeast Asia and Indonesia. The findings indicate that the SOC picture of tectonic plates is consistent with the increase in size inequality of earthquakes, even though this cannot be treated as a rigorous proof.
Read the full abstract ▾
Classical Physics
Adiabatic Lamb modes in 3D tapered waveguides: Cut-off effects and ZGV resonances
Alexandre Yoshitaka Charau, Jérôme Laurent and Tony Valier-Brasier
This paper aims to enhance our understanding of the physical behavior of adiabatic modes in inhomogeneous elastic plates, particularly their remarkable capacity to adapt to gradual perturbations. The study investigates the propagation characteristics of higher-order adiabatic Lamb modes in waveguides with linearly varying thickness, with a focus on the influence of critical thicknesses on their propagation. This is achieved by leveraging the broadband excitation capabilities of a pulsed
laser generating higher order Lamb modes to reveal various critical thicknesses, such as the cut-off and Zero-Group Velocity (ZGV) thicknesses. Remarkably, ZGV resonances can be induced at locations well beyond the
laser source. Moreover, the mode's behavior is strongly influenced by thickness variations in all directions, imparting the plate an anisotropic-like behavior. Additionally, based on the observed effects, our experimental approach enables precise reconstruction of elastic waveguide profiles in additively manufactured aluminum plates with such thickness variations. The reconstructed profiles show a strong correlation with reference measurements across the scanned area.
Read the full abstract ▾
Plasma Physics
Velocity-Space Signatures of Energy Transfer for Ion-Acoustic Instabilities
Mahmoud Saad Afify, Kristopher G. Klein, Mihailo M. Martinović et al. (+1 more)
Context. Observations by Parker
Solar Probe (PSP) of electrostatic waves suggest that electrostatic instabilities, including the ion-ion-acoustic instability (IIAI) frequently observed in the inner heliosphere, play an important role in
plasma heating and particle acceleration. Aims. Our aim is to explore the application of single spacecraft diagnostics to the IIAI, in anticipation of application to the current missions operating in the inner heliosphere, e.g. PSP and
Solar Orbiter. Methods. We apply the field-particle correlation (FPC) technique to fully kinetic simulations of IIAI. We characterize the conversion of energy between the electric field and particle species, allowing the differentiation between oscillatory and secular energy transfer to and from the particles and highlighting the role of resonant energy exchange. We then identify the characteristic IIAI signatures for the
proton and electron distributions, and relate them to our previous knowledge of IIAI onset and energy exchange mechanisms. Results. Applying the FPC technique to our simulations run in parameters regime compatible with
solar wind conditions, we have identified IIAI signatures that would enable efficient recognition of IIAI in observations. This task is left for future missions, since the time scale over which IIAI signatures develop is too fast for the sampling rates of current missions.
Read the full abstract ▾
All authors Mahmoud Saad Afify, Kristopher G. Klein, Mihailo M. Martinović, Maria Elena Innocenti
Plasma Physics
Interstellar Medium Modulation of Nonlinear Kinetic Alfvén Morphology in Structured Galactic Environments
Manpreet Singh, Siming Liu and N. S. Saini
We present a spatially dependent framework for the existence and propagation of nonlinear kinetic Alfvén (KA) structures in the interstellar medium (ISM). Using a multi-component analytical model that incorporates the diffuse warm ionized medium together with localized H II regions,
supernova remnants (SNR), and
stellar-wind bubbles (SWB), we derive location-dependent coefficients governing KA dispersion and nonlinearity. The reductive perturbation method is applied to obtain Korteweg-de Vries (KdV) equations, enabling the characterization of
solitons under realistic astrophysical conditions. Numerical analysis demonstrates how superthermality,
plasma $\beta$, temperature, and density gradients modulate
soliton amplitude, width, and stability. Our results reveal distinct exclusion zones (EZs) for KA
solitons in high-$\beta$ HII regions and SWB/SNR interiors, as well as ultra low-$\beta$ regions near central
pulsar wind nebulae. While H II regions exhibit simple Gaussian-driven depletions, the complex “hole-and-shell" morphologies of SWBs and SNRs imprint sharp spatial variations and discontinuities on
soliton properties. This study establishes a direct link between macroscopic ISM morphology, ion-kinetic scale dissipation, and the emergence of coherent Alfvénic activity, with implications for
radio scattering,
pulsar scintillation, and fine-scale signatures in astrophysical observations.
Read the full abstract ▾
Chemical Physics · Cross-listed from cond-mat.soft
A microscopic origin for the breakdown of the Stokes Einstein relation in ion transport
Zhenyu Wei, Mu Chen, Jun Ren et al. (+9 more)
Ion transport underlies the operation of biological ion channels and governs the performance of electrochemical energy-storage devices. A long-standing anomaly is that smaller alkali metal ions, such as Li$^+$, migrate more slowly in water than larger ions, in apparent violation of the Stokes-Einstein relation. This breakdown is conventionally attributed to dielectric friction, a collective drag force arising from electrostatic interactions between a drifting ion and its surrounding solvent. Here, combining nanopore transport measurements over electric fields spanning several orders of magnitude with molecular dynamics simulations, we show that the time-averaged electrostatic force on a migrating ion is not a drag force but a net driving force. By contrasting charged ions with neutral particles, we reveal that ionic charge introduces additional Lorentzian peaks in the frequency-dependent friction coefficient. These peaks originate predominantly from short-range Lennard-Jones (LJ) interactions within the first hydration layer and represent additional channels for energy dissipation, strongest for Li$^+$ and progressively weaker for Na$^+$ and K$^+$. Our results demonstrate that electrostatic interactions primarily act to tighten the local hydration structure, thereby amplifying short-range LJ interactions rather than directly opposing ion motion. This microscopic mechanism provides a unified physical explanation for the breakdown of the Stokes-Einstein relation in aqueous ion transport.
Read the full abstract ▾
All authors Zhenyu Wei, Mu Chen, Jun Ren, Pinyao He, Wei Xu, Wei Liu, Fei Zheng, Yin Zhang, Wei Si, Jinjie Sha, Zhonghua Ni, Yunfei Chen
Applied Physics
Ultra-low-frequency reflection mode conversion from compressional to shear waves enabled by periodic inclined slits
Kaifei Feng and Pai Peng
A periodically patterned free surface with inclined slits can convert an incident compressional wave into a reflected shear wave with nearly complete efficiency at very low frequency. The system is described by two-dimensional in-plane linear elasticity, and the slits are treated as voids. The conversion is quantified by the ratio between the reflected shear-wave energy and the incident compressional-wave energy, obtained from mode decomposition and energy-flux evaluation below the surface. The results indicate that the inclined geometry introduces strong coupling between normal and tangential motions at the boundary, enabling suppression of the ordinary compressional reflection while redirecting the reflected energy into the shear channel. This simple, geometry-controlled mechanism provides a compact route for low-frequency elastic-wave polarization control.
Read the full abstract ▾
Applied Physics
Through the bottle authentication of red wine using near-IR fluorescence spectroscopy
Ané Kritzinger, Ralf Mouthaan, Graham D. Bruce et al. (+2 more)
A major unaddressed challenge for food science remains the accurate characterisation of contents in sealed containers with a non-invasive method. This issue is particularly pressing for tackling fraud in the red wine industry, valued at billions of dollars globally, where product authenticity, brand reputation, and consumer trust are paramount. Whilst many techniques exist for authenticating wine externally, to date performing accurate classification of the contents within unopened bottles remains elusive. Using only a single near-infrared optical excitation source operating at a wavelength of 785 nm, in combination with a bespoke geometry to circumvent the confounding signal of the glass, we demonstrate that through-bottle fluorescence spectra can distinguish between twenty different red wines in their original, intact bottles. All twenty wine bottles were correctly classified with linear discriminant analysis (LDA) and principal component analysis (PCA) revealed strong varietal grouping. This non-invasive and rapid technique has the potential to enable on-site, routine wine authentication to combat the growing issue of wine fraud. The geometry itself is applicable across multiple fields for the analysis of other high-value products through their packaging, where authenticity verification is critical.
Read the full abstract ▾
All authors Ané Kritzinger, Ralf Mouthaan, Graham D. Bruce, Eric Wilkes, Kishan Dholakia
Fluid Dynamics
Connecting the Hydrodynamics of Polymeric Fluids and Active Nematics
Vedad Dzanic, Sumesh P. Thampi, Rahil N. Valani et al. (+1 more)
We establish a correspondence between the continuum descriptions of
polymer solutions and active nematics, two seemingly disparate but well-studied complex fluids. Through a mapping of the governing equations, we demonstrate that polymeric fluids can be interpreted as deformable, contractile, high-temperature active nematics, with an effective activity controlled by
polymer extension. Using numerical simulations under Kolmogorov flow, we construct a phase diagram connecting the nematic and
polymer limits, highlighting how their one- and two-dimensional instabilities depend on deformability. This encompasses both a flow-suppressed regime, in which active stresses oppose the imposed flow, and a transverse instability that generates secondary flows and leads towards elastic
turbulence. The transverse instability is facilitated by spatial gradients in activity, which arise naturally in extensible
polymers through variations in chain extension. We further show that the transition into the well-known traveling arrowhead structures in elastic
turbulence is marked by the emergence of charge $\pm 1/2$ topological defects in the
polymer director field, indicating emergent nematic ordering of stretched
polymers. Our results establish a unified framework connecting
polymer and active matter hydrodynamics, with implications for low-Reynolds-number
turbulence, active
polymer systems, and the mechanics of deformable living matter.
Read the full abstract ▾
All authors Vedad Dzanic, Sumesh P. Thampi, Rahil N. Valani, Julia M. Yeomans
Optics
Perturbation theory for phase correlations of a light wave propagating in a turbulent medium
I.V. Kolokolov and V.V. Lebedev
We theoretically investigate the correlation functions of the phase of a light wave propagating through a turbulent medium. We use an equation for the logarithm of a wave packet envelope, which includes a second-order nonlinear term. Based on this equation, we develop a diagrammatic technique to calculate corrections to the correlation function obtained in the linear approximation. We calculate the first corrections determined by one-loop diagrams and find its asymptotic behaviors. Some non-perturbative conclusions are made using the
symmetry properties of the equation. These results allow us to conclude that the applicability condition for the perturbation theory is the smallness of the Rytov dispersion, $\sigma_R^2$, and this condition holds uniformly over the distances between observation points.
Read the full abstract ▾
Optics
Correlations of the phase gradients of the light wave propagating in a turbulent medium in the regime of weak scintillations
V.A.Bogachev, I.V. Kolokolov, V.V. Lebedev et al. (+2 more)
We investigate numerically correlation functions of the phase of light waves that propagate through turbulent media. Special
attention is paid to the off-diagonal component of the correlation function of the phase gradients which is insensitive to the outer scale of
turbulence. The results of our simulations are in a good agreement with the analytical expressions obtained in Ref. \cite{KLS25}. Thus, we numerically confirm expectations based on uniformity of the perturbation theory for the logarithm of the envelope.
Read the full abstract ▾
All authors V.A.Bogachev, I.V. Kolokolov, V.V. Lebedev, A.V.Nemtseva, F.A.Starikov
Computational Physics · Cross-listed from q-bio.QM
An open-source computational framework for immersed fluid-structure interaction modeling using FEBio and MFEM
Ryan T. Black, Steve A. Maas, Wensi Wu et al. (+4 more)
Fluid-structure interaction (FSI) simulation of biological systems presents significant computational challenges, particularly for applications involving large structural deformations and contact mechanics, such as heart valve dynamics. Traditional ALE methods encounter fundamental difficulties with such problems due to mesh distortion, motivating immersed techniques. This work presents a novel open-source immersed FSI framework that strategically couples two mature finite element libraries: MFEM, a GPU-ready and scalable library with state-of-the-art parallel performance developed at LLNL, and FEBio, a nonlinear finite element solver with sophisticated solid mechanics capabilities designed for biomechanics applications developed at the University of Utah and Columbia University. This coupling creates a unique synergy wherein the fluid solver leverages MFEM's distributed-
memory parallelization and pathway to GPU acceleration, while the immersed solid exploits FEBio's comprehensive suite of hyperelastic and viscoelastic constitutive models and advanced solid mechanics modeling targeted for biomechanics applications. FSI coupling is achieved using a fictitious domain methodology with variational multiscale stabilization for enhanced accuracy on under-resolved grids expected with unfitted meshes used in immersed FSI. A fully implicit, monolithic scheme provides robust coupling for strongly coupled FSI characteristic of cardiovascular applications. The framework's modular architecture facilitates straightforward extension to additional physics and element technologies. Several test problems are considered to demonstrate the capabilities of the proposed framework, including a 3D semilunar heart valve simulation. This platform addresses a critical need for open-source immersed FSI software combining advanced biomechanics modeling with high-performance computing infrastructure.
Read the full abstract ▾
All authors Ryan T. Black, Steve A. Maas, Wensi Wu, Jalaj Maheshwari, Tzanio Kolev, Jeffrey A. Weiss, Matthew A. Jolley
Applied Physics
Slit-Induced Reflection Mode Conversion Between Fundamental Lamb Modes in Elastic Plates with Low-Frequency and Broadband Response
Kaifei Feng and Pai Peng
We present a compact slit-based interface that enables reflection mode conversion in an elastic plate by transforming an incident lowest-order antisymmetric Lamb mode into a reflected lowest-order symmetric Lamb mode. The interface is realized by introducing inclined
vacuum slits along the lateral sides of the plate. This geometry intentionally breaks
symmetry and produces a strongly localized,
vortex-like deformation near the slit tips, which provides an efficient coupling pathway from the antisymmetric incident response to a symmetric reflected component. The conversion is quantified in a consistent, field-based manner by extracting the reflected antisymmetric level from the standing-wave envelope on a probe line placed sufficiently far from the slits, and then inferring the converted symmetric energy under a lossless assumption with only two reflected propagating channels. The proposed design delivers strong low-frequency conversion and sustains broadband half-power operation, while parametric studies confirm that the performance is tunable and robust over a wide range of slit angles and widths.
Read the full abstract ▾
Optics
Terahertz Communications Using Effective-Medium-Slot Waveguides
Nguyen H. Ngo, Weijie Gao, Guillaume Ducournau et al. (+8 more)
All-dielectric effective-medium-clad waveguides have been widely exploited in terahertz communications owing to their extremely low loss, low dispersion, and broad bandwidth. In this work, we propose a substrateless effective-medium-slot waveguide. Additionally, we introduce a taper-free interface that allows terahertz waves to directly couple from a metallic hollow waveguide without requiring dielectric insertion. By engineering slot couplers with an effectivemedium channel for impedance and modal matching, the waveguide achieves a fractional 3-dB bandwidth of 40% with a maximum coupling efficiency of 90% in the WR-2.2 band (330-500 GHz). By employing a broadband uni-traveling-carrier photodiode transmitter and sub-harmonic mixer receivers, we achieve an aggregated data rate of 0.8 Tbit/s with quadrature amplitude modulation schemes across 14 channels from 330-600 GHz. The effective-medium-slot waveguide platform yields robust broadband coupling with enhanced mechanical protection, offering reliable interconnects for ultra-high-speed terahertz integrated systems.
Read the full abstract ▾
All authors Nguyen H. Ngo, Weijie Gao, Guillaume Ducournau, Hadjer Nihel Khelil, Rita Younes, Pascal Szriftgiser, Hidemasa Yamane, Yoshiharu Yamada, Shuichi Murakami, Withawat Withayachumnankul, Masayuki Fujita
Atomic Physics
The 1/3 Geometric Constant: Scale Invariance and the Origin of 'Missing Energy' in 3D Quantum Fragmentation
Jinzhen Zhu
We report the discovery of a universal
geometric constraint on the detection of kinetic energy release (KER) in three-dimensional
quantum fragmentation. By analyzing the dissociation of localized wavepackets, we demonstrate that the $4\pi r^2$ radial volume element acts as a topological filter that inherently masks a significant portion of a system's energy budget, imposing a fundamental peak-to-mean bound of $R_E < 0.5$. We introduce an invariant scaling law, $\alpha = MQ/\zeta$, and prove that the resulting energy detection ratio is scale-invariant across twelve orders of magnitude, bridging attosecond molecular science and
nuclear physics. We identify a universal
geometric landmark at $R_E \approx 0.33$, which precisely replicates the 7~eV discrepancy in $H_2^+$ fragmentation. Furthermore, we show that the population of excited-state
manifolds and the increase in
nuclear localization ($\zeta$) provide a definitive
geometric mechanism for the spectral broadening observed across atomic and subatomic scales. Remarkably, the spectral morphology derived from our scaling law aligns with the universal 1/3 energy landmark of historical beta decay, while the high-mass limit naturally accounts for the sharpening of alpha spectra. Our results suggest that “missing energy” is often a topological artifact of 3D geometry rather than an exclusive signature of undetected particles. This work establishes a universal master curve for energy reconstruction and identifies a “detection crisis” in highly localized systems, where the true interaction energy becomes effectively invisible to peak-centric calorimetry.
Read the full abstract ▾
Biological Physics · Cross-listed from cond-mat.soft
Designing topological edge states in bacterial active matter
Yoshihito Uchida, Daiki Nishiguchi and Kazumasa A. Takeuchi
Topology provides a unifying framework for understanding robust transport through protected edge states arising from nontrivial wavenumber
topology. Extending these concepts to active matter, however, remains largely unexplored experimentally, with realizations limited to systems composed of
chiral active particles. Here, we realize topological edge states in dense bacterial suspension, which represents a prototypical active matter system, using microfabricated geometrical structures with nontrivial wavenumber
topology. Inspired by previous theoretical studies, we constructed a directional kagome network composed of ratchet-shaped channels that induce unidirectional bacterial flow. In this network, we found clear edge localization of bacterial density. A steady-state analysis based on the bacterial transport model and experimentally measured velocity field reveals how the characteristic collective flow generates edge localization. The model also uncovers the topological origin of the observed edge states. By tuning the geometry of the microfabricated networks, we identified directional channel design and network chirality as the key design features essential for the emergence of the edge state. Our results pave the way for establishing a control and design principle of topological transport in such active matter systems.
Read the full abstract ▾
Fluid Dynamics · Cross-listed from math.AP
Phase-Textured Complex Viscosity in Linear Viscous Flows: Non-Normality Without Advection, Corner Defects, and 3D Mode Coupling
Lillian St. Kleess
We consider time-harmonic incompressible flow with a spatially resolved complex viscosity field $\mu^*(\mathbf{x},\omega)$ and, at fixed forcing frequency $\omega>0$, its constitutive phase texture $\varphi(\mathbf{x})=\arg\mu^*(\mathbf{x},\omega)$. In three-dimensional domains periodic in a spanwise direction $z$, $z$-dependence of $\mu^*$ converts coefficient multiplication into convolution in spanwise
Fourier index, yielding an operator-valued Toeplitz/Laurent coupling of modes. Consequently, even spanwise-uniform forcing generically produces $\kappa\neq 0$ sidebands in the harmonic response as a linear, constitutive effect. We place $\mu^*$ at the closure level $\hat{\boldsymbol{\tau}}=2\,\mu^*(\mathbf{x},\omega)\mathbf{D}(\hat{\mathbf{v}})$, as the boundary value of the Laplace transform of a causal stress-
memory kernel. Under the passivity condition $\Re\mu^*(\mathbf{x},\omega)\ge \mu_{\min}>0$, the oscillatory Stokes/Oseen operators are realized as m-sectorial operators associated with coercive sectorial forms on bounded Lipschitz (including cornered) domains, yielding existence, uniqueness, and frequency-dependent stability bounds. Spatial variation of $\varphi$ renders the viscous operator intrinsically non-normal even in the absence of advection, so amplification is governed by resolvent geometry (and associated pseudospectra), not by
eigenvalues alone. In the pure-phase class $\mu^*(\mathbf{x},\omega)=\mu_0(\omega)e^{i\varphi(\mathbf{x})}$, the texture strength is quantified by $\mu_0(\omega)\|\nabla\varphi\|_{L^\infty}$.
Read the full abstract ▾
Fluid Dynamics
Lattice Boltzmann methods for simulating non-Newtonian fluids: A comprehensive review
Vedad Dzanic, Qiuxiang Huang, Christopher S. From et al. (+1 more)
Non-Newtonian fluids encompass a large family of fluids with additional nonlinear material properties, contributing to non-trivial flow behaviour that cannot be captured through a single constant viscosity term. Common non-Newtonian characteristics include shear-thinning, shear-thickening, viscoplasticity, and viscoelasticity, commonly encountered in everyday fluids, such as ketchup, blood, toothpaste, mud, etc., as well as practical applications involving porous media, cosmetics, food processing, and pharmaceuticals. Due to the complex nature of these fluids, accurate computational fluid dynamics simulations are essential for predicting their behaviour under various flow conditions. Recent advancements have highlighted the growing trend of using the
lattice Boltzmann method to solve such complex flows, owing to its ability to handle intricate boundary conditions, ease of including additional multiphysics, and providing computationally efficient parallel simulations. Since the initial review over a decade ago [Phillips & Roberts, IMA J. Appl. Math. 76, 790-816 (2011)], significant advancements have been made to the
lattice Boltzmann method to simulate non-Newtonian fluids. Here, we present a comprehensive review of different
lattice Boltzmann techniques used to solve non-Newtonian fluid systems, specifically dealing with shear-dependent viscosity, viscoplasticity, and viscoelasticity. In addition, we discuss various
benchmark cases that validate these approaches and highlight their growing application to realistic and challenging complex flow problems. We further address outstanding issues in current
lattice Boltzmann models, as well as future directions for numerical advancement and application.
Read the full abstract ▾
All authors Vedad Dzanic, Qiuxiang Huang, Christopher S. From, Emilie Sauret
Optics
Vacuum-dressed superconductivity in NbN observed in a high-$Q$ terahertz cavity
Hongjing Xu, Andrey Baydin, Qinyan Yi et al. (+8 more)
Emerging theoretical frameworks suggest that physical properties of matter can be altered within an optical cavity by harnessing
quantum vacuum electromagnetic fluctuations, even in the total absence of external driving fields. Among the most intriguing predictions is the potential to noninvasively manipulate superconductivity. Here, we experimentally observe modified superconductivity in niobium nitride (NbN) thin films within high-quality-factor ($Q$) terahertz cavities. Using terahertz time-domain spectroscopy, we characterize the NbN response both in free space and within a high-$Q$ photonic-
crystal cavity. Our analysis reveals significant cavity-induced modifications to the optical conductivity. A theoretical model indicates that these changes originate from a substantial ($\sim13\,\%$) reduction in the superfluid density and a minor ($\sim2\,\%$) reduction in the superconducting gap, driven by cavity
vacuum fluctuations. These results demonstrate a platform for engineering ground states via
vacuum–matter coupling, opening frontiers in cavity materials science.
Read the full abstract ▾
All authors Hongjing Xu, Andrey Baydin, Qinyan Yi, I-Te Lu, Ningxu Zhu, T. Elijah Kritzell, Jacques Doumani, Dasom Kim, Fuyang Tay, Angel Rubio, Junichiro Kono
Computational Physics · Cross-listed from cond-mat.mtrl-sci
Autonomous Materials Exploration by Integrating Automated Phase Identification and AI-Assisted Human Reasoning
Ming-Chiang Chang, Maximilian Amsler, Duncan R. Sutherland et al. (+9 more)
Autonomous experimentation holds the potential to accelerate materials development by combining artificial intelligence (AI) with modular robotic platforms to explore extensive combinatorial chemical and processing spaces. Such self-driving laboratories can not only increase the throughput of repetitive experiments, but also incorporate human domain expertise to drive the search towards user-defined objectives, including improved materials performance metrics. We present an autonomous materials synthesis extension to SARA, the Scientific Autonomous
Reasoning Agent, utilizing phase information provided by an automated probabilistic phase labeling
algorithm to expedite the search for targeted phase regions. By incorporating human input into an expanded SARA-H (SARA with human-in-the-loop) framework, we enhance the efficiency of the underlying
reasoning process. Using synthetic
benchmarks, we demonstrate the efficiency of our AI implementation and show that the human input can contribute to significant improvement in sampling efficiency. We conduct experimental active learning campaigns using robotic processing of thin-film samples of several
oxide material systems, including Bi$_2$O$_3$, SnO$_x$, and Bi-Ti-O, using lateral-gradient
laser spike annealing to synthesize and kinetically trap metastable phases. We showcase the utility of human-in-the-loop autonomous experimentation for the Bi-Ti-O system, where we identify extensive processing domains that stabilize $\delta$-Bi$_2$O$_3$ and Bi$_2$Ti$_2$O$_7$, explore dwell-dependent ternary
oxide phase behavior, and provide evidence confirming predictions that cationic substitutional doping of TiO$_2$ with Bi inhibits the unfavorable transformation of the metastable anatase to the ground-state rutile phase. The autonomous methods we have developed enable the discovery of new materials and new understanding of materials synthesis and properties.
Read the full abstract ▾
All authors Ming-Chiang Chang, Maximilian Amsler, Duncan R. Sutherland, Sebastian Ament, Katie R. Gann, Lan Zhou, Louisa M. Smieska, Arthur R. Woll, John M. Gregoire, Carla P. Gomes, R. Bruce van Dover, Michael O. Thompson
Fluid Dynamics
An Investigation into the Applicability of Friction Velocity Estimation Methods for the Channel with A Deposit Body
Jing Zhang, Ruihan Qin, Zhixue Guo et al. (+3 more)
This study investigates how the deposit body influences friction characteristics by altering local flow fields, which is closely related to bed shear stress. Using generalized flume experiments, the study assesses the applicability of classical uniform flow friction models in deposit body river sections, revealing frictional changes induced by flow field non-uniformity. Initially, based on \( \frac{u_*}{\sqrt{\overline{w'^2}}} = 0.85 \sim 1.15 \) under uniform flow conditions as the judgment basis, the reliability of the classical model is verified. Four models are then applied to estimate near-bed friction velocity in deposit body sections. Results show a significant
alignment between the longitudinal velocity gradient and the peak friction velocity derived from the turbulent kinetic energy method (TKE). Dimensional analysis of friction indicators reveals that: (a) friction velocity is primarily influenced by
turbulence intensity, with constricted and narrowed sections resembling uniform flow, while the expansion section forms a peak; (b) models incorporating flow field fluctuations (TKE, Vertical
Turbulence Kinetic Energy (TKE w'), Reynolds shear stress method (RSS)) effectively capture the impact of non-uniform flow fields on friction characteristics; (c) when energy states are low or when deposit body proportions are large, the deposit body's resistance ratio increases, and peak friction velocity rises. This study provides theoretical insights into friction estimation and sediment transport in non-uniform flow fields of deposit bodies.
Read the full abstract ▾
All authors Jing Zhang, Ruihan Qin, Zhixue Guo, Huantao Xu, Jiahui Zhou, Yun Bai
Plasma Physics
The effect of surface quenching coefficients of $O_2(a^{1}{\Delta}g)$ and $O_2(b^{1}{\Sigma}g^{+})$ on capacitively coupled $Ar$/$O_2$ discharge: A global/equivalent circuit model study
Wan Dong, Yi Wang, Yi-Fan Zhang et al. (+1 more)
Capacitively coupled discharges operated in mixtures of $Ar$ and $O_2$ are extensively utilized in
plasma etching and deposition processes due to the oxidative properties and precursor functionality of the reactive species produced in the discharge. In $Ar$/$O_2$ discharges, the surface quenching coefficient of $O_2(a^{1}{\Delta}g)$ is known to affect this metastable density, which, in turn, affects the electronegativity and other important
plasma characteristics. In this work, in addition to $O_2(a^{1}{\Delta}g)$, $O_2(b^{1}{\Sigma}g^{+})$ and its associated reactions are incorporated into a global/equivalent
circuit model of an $Ar$/$O_2$ discharge. By independently adjusting the quenching coefficients of both metastable species, changes of these surface coefficients are found to significantly affect the discharge characteristics, indicating that the role of $O_2(b^{1}{\Sigma}g^{+})$ cannot be neglected. The effects of their respective surface quenching coefficients of these metastables based on various wall materials on the discharge are revealed including their effects on different particle species densities,
plasma impedance, voltage drops across the sheaths, as well as
plasma power absorption.
Read the full abstract ▾
All authors Wan Dong, Yi Wang, Yi-Fan Zhang, Yuan-Hong Song
Computational Physics · Cross-listed from quant-ph
Cost scaling of MPS and TTNS simulations for 2D and 3D systems with area-law entanglement
Thomas Barthel
Tensor network states are an indispensable tool for the simulation of strongly correlated
quantum many-body systems. In recent years, tree tensor network states (TTNS) have been successfully used for two-dimensional systems and to
benchmark quantum simulation approaches for condensed matter,
nuclear, and particle physics. In comparison to the more traditional approach based on
matrix product states (MPS), the graph distance of physical degrees of freedom can be drastically reduced in TTNS. Surprisingly, it turns out that, for large systems in $D>1$ spatial dimensions, MPS simulations of low-energy states are nevertheless more efficient than TTNS simulations. With a focus on $D=2$ and 3, the scaling of computational costs for different boundary conditions is determined under the assumption that the system obeys an
entanglement (log-)area law, implying that bond dimensions scale exponentially in the interface area of the associated subsystems.
Read the full abstract ▾
Atmospheric and Oceanic Physics · Cross-listed from cs.LG
Learning a Stochastic Differential Equation Model of Tropical Cyclone Intensification from Reanalysis and Observational Data
Kenneth Gee and Sai Ravela
Tropical cyclones are among the most consequential weather hazards, yet estimates of their risk are limited by the relatively short historical record. To extend these records, researchers often generate large ensembles of synthetic storms using simplified models of cyclone intensification. Developing such models, however, has traditionally required substantial theoretical effort. Here we explore whether equation-discovery methods, a class of data-driven techniques designed to infer governing equations, can accelerate the process of developing simplified intensification models. Using observational storm data (IBTrACS) together with environmental conditions from reanalysis (ERA5), we learn a compact
stochastic differential equation describing tropical cyclone intensity
evolution. We focus on TCs because their dynamics are well studied and a hierarchy of reduced-order models exist, enabling direct comparison of the learned model to physically-derived counterparts. We find that the learned model simulates synthetic TCs whose intensification statistics and hazard estimates are consistent with observations and competitive with a leading physics-based TC intensification model. Our model also reproduces known nonlinear dynamical behavior of tropical cyclones, including as a saddle node bifurcation as inner core ventilation is increased. This result shows that equation-discovery approaches, when applied directly to storm intensity, can recover not only realistic statistics but also physically meaningful dynamical structure. These findings highlight the potential for data-driven methods to complement existing theory and reduced-order models in the study of extreme weather.
Read the full abstract ▾
Fluid Dynamics · Cross-listed from cond-mat.soft
Spreading and absorption of silicone oil droplets on silicone elastomer films
Lauren Dutcher, Benjamin Baylis, John R. Dutcher et al. (+2 more)
When a
liquid droplet completely wets a hard substrate, its spreading dynamics follow Tanner's law, with the droplet radius growing as the one-tenth power of time. Here, we investigate how these dynamics change when silicone oil droplets spread on soft silicone elastomer and gel films supported by a rigid silicon substrate. While the droplets fully wet the elastomer surface, they also simultaneously swell the elastomer film. By varying the film thickness, we observe deviations from the classical power-law scaling, which we interpret in terms of changes to the effective stiffness and the absorption potential of the system. We describe the spreading behavior using a phenomenological model that accounts for both absorption and mechanical contributions.
Read the full abstract ▾
All authors Lauren Dutcher, Benjamin Baylis, John R. Dutcher, Elie Raphael, Kari Dalnoki-Veress
Fluid Dynamics
Physics-Informed Deep Operator Learning for Computational Hydraulics Modeling
Xiaofeng Liu and Yong G. Lai
Traditional 2D hydraulic models face significant computational challenges that limit their applications that are time-sensitive or require many model evaluations. This study presents a physics-informed Deep Operator Network (DeepONet) framework for computational hydraulics modeling that learns the solution operator of the 2D shallow water equations (SWEs) to create fast surrogate models. The framework can operate in two modes: a purely data-driven SWE-DeepONet that learns from numerical solver such as SRH-2D, and a physics-informed PI-SWE-DeepONet that additionally incorporates the continuous SWEs as constraints during training. Based on a real-world case, steady flows in a reach of the Sacramento River in California, it is demonstrated that PI-SWE-DeepONet possesses much enhanced prediction capability than SWE-DeepONet when applied to out-of-distribution scenarios. The physics-informed model is shown to exhibit slower error growth and larger breakdown distances in comparison with SWE-DeepONet. The gain of the physics-informed training, however, comes with costs, chief among which are the simulated results have slightly higher errors for in-distribution cases. It reflects the existence of a tension between the two competing training objectives: fitting the results from the traditional hydraulic model and satisfying the continuous governing equations. In this study, guidelines are developed for selecting the appropriate approach based on a real-world case: PI-SWE-DeepONet is preferred for out-of-distribution predictions, uncertain training data, or when physical consistency is a priority, while SWE-DeepONet is recommended if the modeling objective is to replicate faithfully the traditional hydraulic model results within the training distribution. Other challenges are also discussed, such as the loss weighting approach.
Read the full abstract ▾