Daily Papers

Segmentation of the coronary artery is an important task for the quantitative analysis of coronary computed tomography angiography (CCTA) images and is being stimulated by the field of deep learning. However, the complex structures with tiny and narrow branches of the coronary artery bring it a great challenge. Coupled with the medical image limitations of low resolution and poor contrast, fragmentations of segmented vessels frequently occur in the prediction. Therefore, a geometry-based cascaded segmentation method is proposed for the coronary artery, which has the following innovations: 1) Integrating geometric deformation networks, we design a cascaded network for segmenting the coronary artery and vectorizing results. The generated meshes of the coronary artery are continuous and accurate for twisted and sophisticated coronary artery structures, without fragmentations. 2) Different from mesh annotations generated by the traditional marching cube method from voxel-based labels, a finer vectorized mesh of the coronary artery is reconstructed with the regularized morphology. The novel mesh annotation benefits the geometry-based segmentation network, avoiding bifurcation adhesion and point cloud dispersion in intricate branches. 3) A dataset named CCA-200 is collected, consisting of 200 CCTA images with coronary artery disease. The ground truths of 200 cases are coronary internal diameter annotations by professional radiologists. Extensive experiments verify our method on our collected dataset CCA-200 and public ASOCA dataset, with a Dice of 0.778 on CCA-200 and 0.895 on ASOCA, showing superior results. Especially, our geometry-based model generates an accurate, intact and smooth coronary artery, devoid of any fragmentations of segmented vessels.

DDEBIFTOOL is a collection of Matlab routines for numerical bifurcation analysis of systems of delay differential equations with discrete constant and state-dependent delays. The package supports continuation and stability analysis of steady state solutions and periodic solutions. Further one can compute and continue several local and global bifurcations: fold and Hopf bifurcations of steady states; folds, period doublings and torus bifurcations of periodic orbits; and connecting orbits between equilibria. To analyse the stability of steady state solutions, approximations are computed to the rightmost, stability-determining roots of the characteristic equation which can subsequently be used as starting values in a Newton procedure. For periodic solutions, approximations to the Floquet multipliers are computed. The manual describes the structure of the package, its routines, and its data and method parameter structures.

We study the one-dimensional nonlocal Kirchhoff type bifurcation problem related to logistic equation of population dynamics. We establish the precise asymptotic formulas for bifurcation curve lambda = lambda(alpha) as alpha to infty in L^2-framework, where alpha:= Vert u_lambda Vert_2.

Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significant obstacle to understanding biophysical processes such as cell adhesion and migration. Here, we develop a data-driven biophysical modeling approach to learn the mechanical behavior of adherent cells. We first train neural networks to predict forces generated by adherent cells from images of cytoskeletal proteins. Strikingly, experimental images of a single focal adhesion protein, such as zyxin, are sufficient to predict forces and generalize to unseen biological regimes. This protein field alone contains enough information to yield accurate predictions even if forces themselves are generated by many interacting proteins. We next develop two approaches - one explicitly constrained by physics, the other more agnostic - that help construct data-driven continuum models of cellular forces using this single focal adhesion field. Both strategies consistently reveal that cellular forces are encoded by two different length scales in adhesion protein distributions. Beyond adherent cell mechanics, our work serves as a case study for how to integrate neural networks in the construction of predictive phenomenological models in cell biology, even when little knowledge of the underlying microscopic mechanisms exist.

We put forward the dynamical study of a novel higher-order small network of Chialvo neurons arranged in a ring-star topology, with the neurons interacting via linear diffusive couplings. This model is perceived to imitate the nonlinear dynamical properties exhibited by a realistic nervous system where the neurons transfer information through higher-order multi-body interactions. We first analyze our model using the tools from nonlinear dynamics literature: fixed point analysis, Jacobian matrix, and bifurcation patterns. We observe the coexistence of chaotic attractors, and also an intriguing route to chaos starting from a fixed point, to period-doubling, to cyclic quasiperiodic closed invariant curves, to ultimately chaos. We numerically observe the existence of codimension-1 bifurcation patterns: saddle-node, period-doubling, and Neimark Sacker. We also qualitatively study the typical phase portraits of the system and numerically quantify chaos and complexity using the 0-1 test and sample entropy measure respectively. Finally, we study the collective behavior of the neurons in terms of two synchronization measures: the cross-correlation coefficient, and the Kuramoto order parameter.

Neural networks acquire structured representations at specific moments during training, yet identifying these transitions typically relies on retrospective, label-dependent metrics. We introduce a bifurcation theory of representation dynamics to detect these moments in real time. Analyzing a passive GMM probe attached to the evolving encoder, we show the onset of structure corresponds to a supercritical pitchfork bifurcation driven by the loss Hessian. The system exhibits a theoretically predictable zero-crossing (β_c) that, compared to the network's current state (β), yields a dynamic ratio β(t)/β_c(t): a universal, label-free phase coordinate for representation dynamics, computable entirely from hidden states. We empirically validate four distinct transition regimes predicted by this coordinate across diverse settings: SAEs on language models (Pythia), SSL (CIFAR), and grokking (modular arithmetic). Crucially, under finite dissipation, macroscopic symmetry-breaking can lag the initial zero-crossing by orders of magnitude, which providing a rigorous dynamical account of the delayed escape observed in grokking. Microscopically, the bifurcation creates a shared unstable subspace, forcing collective symmetry breaking. We term this the "feature lottery" in SAE training: a feature's terminal interpretability becomes predictable remarkably early. By only 5% of training, early atom purity robustly predicts final convergence purity, with top-decile early atoms achieving over 12x the baseline purity at convergence. Beyond explaining concept emergence, β/β_c provides a practical early-warning indicator for training health, detecting the onset of usable structure, the crystallization of feature identity, and representational collapse epochs before downstream metrics react.

Biological tissues exhibit complex behaviors with their dynamics often resembling inert soft matter such as liquids, polymers, colloids, and liquid crystals. These analogies enable physics-based approaches for investigations of emergent behaviors in biological processes. A well-studied case is the spreading of cellular aggregates on solid surfaces, where they display dynamics similar to viscous droplets. In vivo, however, cells and tissues are in a confined environment with varying geometries and mechanical properties to which they need to adapt. In this work, we compressed cellular aggregates between two solid surfaces and studied their dynamics using microscopy, and computer simulations. The confined cellular aggregates transitioned from compressed spheres into dynamic living capillary bridges exhibiting bridge thinning and a convex-to-concave meniscus curvature transition. We found that the stability of the bridge is determined by the interplay between cell growth and cell spreading on the confining surfaces. This interaction leads to bridge rupture at a critical length scale determined by the distance between the plates. The force distributions, formation and stability regimes of the living capillary bridges were characterized with full 3D computer simulations that included cell division, migration and growth dynamics, directly showing how mechanical principles govern the behavior of the living bridges; cellular aggregates display jamming and stiffening analogously to granular matter, and cell division along the long axis enhances thinning. Based on our results, we propose a new class of active soft matter behavior, where cellular aggregates exhibit liquid-like adaptation to confinement, but with self-organized rupturing driven by biological activity.

All known up to now models of chemical oscillations are based exclusively on kinetic considerations. The chemical gross-process equation is split usually by elementary steps, each step is supplied by an arrow and a differential equation, joint solution to such a construction under certain, often ad hoc chosen conditions and with ad hoc numerical coefficients leads to chemical oscillations. Kinetic perception of chemical oscillations reigns without exclusions. However, as it was recently shown by the author for the laser and for the electrochemical systems, chemical oscillations follow also from solutions to the basic expressions of discrete thermodynamics of chemical equilibria. Graphically those solutions are various fork bifurcation diagrams, and, in certain types of chemical systems, oscillations are well pronounced in the bistable bifurcation areas. In this work we describe a general thermodynamic approach to chemical oscillations as opposite to kinetic models, and depict some of their new features like spontaneity and fractality. The paper doubts exclusivity of the kinetic approach to chemical oscillations, and its aim is to discuss and exemplify thermodynamically predicted chemical oscillations in closed chemical systems.

Regulatory institutions (from content moderation platforms to financial supervisors) observe, deliberate, and intervene only after a characteristic delay. We ask whether this processing lag alone can destabilize a multi-agent system that would otherwise remain stable, without exogenous shocks, coordination among agents, or malicious actors. We study this question in two stages. First, we analyze a delayed replicator equation in which autonomous agents receive a benefit from radical behavior but face punishment based on a lagged institutional alarm signal. We derive a closed-form critical delay threshold beyond which the unique interior equilibrium loses stability through a Hopf bifurcation, and prove via center manifold reduction that the bifurcation is supercritical (producing bounded oscillations, not explosive growth) for the entire sigmoid response-function family. Second, we embed N=240 agents on a network and equip them with reinforcement learning (tabular Q-learning), comparing three decision architectures in a factorial design: non-reactive agents (fixed policy), reactive agents (threshold heuristic without memory), and Q-learning agents (adaptive with cumulative value estimates). The results reveal a hierarchy opposite to the naive expectation that learning amplifies instability: non-reactive agents are immune to delay (0% runaway across all tested values), reactive agents collapse catastrophically (96% runaway by delay geq 8 steps), and Q-learning agents achieve partial resilience (66% runaway at delay = 20). The destabilizing ingredient is reactivity to delayed signals: agents that immediately exploit low-alarm windows trigger oscillatory feedback loops. Learning buffers this through implicit punishment memory encoded in Q-values

A scuba diver holding constant depth balances on an unstable equilibrium: the gas carried in the suit and buoyancy compensator compresses with depth, so the buoyant force falls as the diver sinks and rises as the diver ascends. We represent the diver as a proportional-derivative controller that regulates this compressible-buoyancy saddle after a finite reaction delay, and we derive the governing delay differential equation from the vertical force balance and the isothermal gas law, reducing it to a damping ratio, two control gains, and a dimensionless delay. The characteristic spectrum, obtained by pseudospectral collocation of the semigroup generator and checked against a direct Newton solution of the characteristic equation, locates the Hopf boundary that separates stable hovering from sustained porpoising; for the baseline diver the critical reaction delay is 3.36 s and the onset period is 28.8 s. The bifurcation is supercritical, and because the saturating force is the quadratic hydrodynamic drag, the limit-cycle amplitude grows in proportion to the delay excess rather than as its square root. The safe-operating envelope shows that runaway ascent is triggered by saturation of the compensator, not by loss of linear stability, so a stable and an unstable diver can share the same escape threshold. As onset is approached, the lag-one autocorrelation and variance rise while the fitted recovery rate falls and matches the spectral abscissa, giving an eigenvalue-exact early warning of the transition.

Let (M omega) be a two dimensional symplectic manifold, phi: M to M a symplectomorphism with hyperbolic fixed point x and transversely intersecting stable and unstable manifolds W^s(phi, x) cap W^u(phi, x)=:H(phi, x). The intersection points are called homoclinic points, and the stable and unstable manifold are in this situation Lagrangian submanifolds. For this Lagrangian intersection problem with its infinite number of intersection points and wild oscillation behavior, we first define a Floer homology generated by finite sets of so-called contractible homoclinic points. This generalizes very significantly the Floer homologies generated by (semi)primary points defined by us in earlier works. Nevertheless these Floer homologies only consider quite `local' aspects of W^s(phi, x) cap W^u(phi, x) since their generator sets are finite, but the number of all contractible homoclinic points is infinite. To overcome this issue, we construct a direct limit of these `local' homoclinic Floer homologies over suitable index sets. These direct limits thus accumulate the information gathered by the finitely generated local' homoclinic Floer homologies.

We present a numerical framework to treat infinite time horizon spatially distributed optimal control problems via the associated canonical system derived by Pontryagin's Maximum Principle. The basic idea is to consider the canonical system in two steps. First we perform a bifurcation analysis of canonical steady states using the continuation and bifurcation package pde2path, yielding a number of so called flat and patterned canonical steady states. In a second step we link pde2path to the two point boundary value problem solver TOM to study time dependent canonical paths to steady states having the so called saddle point property. As an example we consider a shallow lake model with diffusion.

This project focuses on a method to extract a frequency comb in mechanical means, for general interest and numerous practical applications in MEMS. The method of execution is the implementation of a beam that is exhibiting non-linear dynamics that is perturbed and analyzed for its transverse vibrations. The perturbation is an external harmonic driver with a chosen small amplitude and frequency (which is slightly detuned from the beam eigenfrequency), that when engaged with the unperturbed beam oscillations, causes it reach a state of "injection pulling" - an effect that occurs when one harmonic oscillator is coupled with a second one and causes it to oscillate in a frequency near its own. This causes the beam to reach SNIC bifurcation, rendering a frequency comb as desired. Theoretical analysis showed that the problem can be modelled using a non-linear equation of the beam, that translates to a form of the non-linear Duffing equation. While a solution to the dynamics function of the beam is hard to obtain in practice due to mathematical difficulties, a slow evolution model is suggested that is composed of functions of a amplitude and phase. Using several additional mathematical assumptions, the amplitude is seen to be related to the phase, while the phase equation solution is seen to be of the form of Adler's equation. These assumptions ultimately reduce the entire behaviour of the beam to a relatively simple solution to the Adler equation, which has a known analytical solution. Computerized numerical simulations are run on it to check the results and compare them to the theory and desired outcome. The results agreed with the theory and produce the expected frequency comb, showing the assumptions to be valid in extracting the comb.

We analyze a class of cell-bulk coupled PDE-ODE models, motivated by quorum and diffusion sensing phenomena in microbial systems, that characterize communication between localized spatially segregated dynamically active signaling compartments that have a permeable boundary. Each cell secretes a signaling chemical into the bulk region at a constant rate and receives a feedback of the bulk chemical from the entire collection of cells. This global feedback, which activates signaling pathways within the cells, modifies the intracellular dynamics according to the external environment. The cell secretion and global feedback are regulated by permeability parameters across the cell membrane. For arbitrary reaction-kinetics within each cell, the method of matched asymptotic expansions is used in the limit of small cell radius to construct steady-state solutions of the PDE-ODE model, and to derive a globally coupled nonlinear matrix eigenvalue problem (GCEP) that characterizes the linear stability properties of the steady-states. In the limit of large bulk diffusivity an asymptotic analysis of the PDE-ODE model leads to a limiting ODE system for the spatial average of the concentration in the bulk region that is coupled to the intracellular dynamics within the cells. Results from the linear stability theory and ODE dynamics are illustrated for Sel'kov reaction-kinetics, where the kinetic parameters are chosen so that each cell is quiescent when uncoupled from the bulk medium. For various specific spatial configurations of cells, the linear stability theory is used to construct phase diagrams in parameter space characterizing where a switch-like emergence of intracellular oscillations can occur through a Hopf bifurcation.

The transition of an impulsively excited kink oscillation of a solar coronal loop to an oscillation with a stationary amplitude, i.e., the damping pattern, is determined using the low-dimensional self-oscillation model. In the model, the decayless kink oscillations are sustained by the interaction of the oscillating loop with an external quasi-steady flow. The analytical solution is based on the assumption that the combined effect of the effective dissipation, for example, by resonant absorption, and interaction with an external flow, is weak. The effect is characterised by a dimensionless coupling parameter. The damping pattern is found to depend upon the initial amplitude and the coupling parameter. The approximate expression shows a good agreement with a numerical solution of the self-oscillation equation. The plausibility of the established damping pattern is demonstrated by an observational example. Notably, the damping pattern is not exponential, and the characteristic decay time is different from the time determined by the traditionally used exponential damping fit. Implications of this finding for seismology of the solar coronal plasmas are discussed. In particular, it is suggested that a very rapid, in less than the oscillation period, decay of the oscillation to the stationary level, achieved for larger values of the coupling parameter, can explain the relative rareness of the kink oscillation events.

We establish the existence of compactly supported solutions of the inviscid incompressible 2D Boussinesq equation with C^{1,frac{4{3}}-1-varepsilon}cap L^{2} force that develop a singularity in finite time. Importantly, the force preserves this regularity at the blow-up time. Moreover, the forces in the vorticity and density equations have compact support. The mechanism behind the blow-up is an accumulated hysteresis effect on the vorticity caused by an infinite chain of "degenerate" pendula and flickering density.

The proposed method aims to approximate a solution of a fluid-fluid interaction problem in case of low viscosities. The nonlinear interface condition on the joint boundary allows for this problem to be viewed as a simplified version of the atmosphere-ocean coupling. Thus, the proposed method should be viewed as potentially applicable to air-sea coupled flows in turbulent regime. The method consists of two key ingredients. The geometric averaging approach is used for efficient and stable decoupling of the problem, which would allow for the usage of preexisting codes for the air and sea domain separately, as "black boxes". This is combined with the variational multiscale stabilization technique for treating flows at high Reynolds numbers. We prove the stability and accuracy of the method and provide several numerical tests to assess both the quantitative and qualitative features of the computed solution.

Autonomous wire harness assembly requires robots to manipulate complex branched cables with high precision and reliability. A key challenge in automating this process is predicting how these flexible and branched structures behave under manipulation. Without accurate predictions, it is difficult for robots to reliably plan or execute assembly operations. While existing research has made progress in modeling single-threaded Deformable Linear Objects (DLOs), extending these approaches to Branched Deformable Linear Objects (BDLOs) presents fundamental challenges. The junction points in BDLOs create complex force interactions and strain propagation patterns that cannot be adequately captured by simply connecting multiple single-DLO models. To address these challenges, this paper presents Differentiable discrete branched Elastic rods for modeling Furcated DLOs in real-Time (DEFT), a novel framework that combines a differentiable physics-based model with a learning framework to: 1) accurately model BDLO dynamics, including dynamic propagation at junction points and grasping in the middle of a BDLO, 2) achieve efficient computation for real-time inference, and 3) enable planning to demonstrate dexterous BDLO manipulation. A comprehensive series of real-world experiments demonstrates DEFT's efficacy in terms of accuracy, computational speed, and generalizability compared to state-of-the-art alternatives. Project page:https://roahmlab.github.io/DEFT/.