Daily Papers

We apply the Nakajima-Zwanzig approach to open quantum systems to study steady-state transport across generic multi-level junctions coupled to bosonic or fermionic reservoirs. The method allows for a unified diagrammatic formulation in Liouville space, with diagrams being classified according to an expansion in the coupling strength between the reservoirs and the junction. Analytical, approximate expressions are provided up to fourth order for the steady-state boson transport that generalize to multi-level systems the known results for the low-temperature thermal conductance in the spin-boson model. The formalism is applied to the problem of heat transport in a qubit-resonator junction modeled by the quantum Rabi model. Nontrivial transport features emerge as a result of the interplay between the qubit-oscillator detuning and coupling strength. For quasi-degenerate spectra, nonvanishing steady-state coherences cause a suppression of the thermal conductance.

Steady-state electrothermal systems involve strongly coupled heat transfer, fluid flow, and electric-potential transport, creating severe numerical challenges for standard physics-informed neural networks (PINNs) due to stark disparities in gradient scales and residual stiffnesses across the physical fields. To resolve these multiphysics bottlenecks, we introduce a Long Short-Term Memory PINN (LSTM-PINN) framework that utilizes a depth-recursive memory mechanism to preserve long-range spatial feature dependencies and maintain strict cross-field consistency. The proposed architecture is rigorously evaluated against conventional and attention-based networks across a unified five-field formulation encompassing four complex convective and drag regimes: Boussinesq electrothermal flow, drift-potential gauge-constrained transport, strong buoyancy-coupled convection, and Brinkman--Forchheimer drift. Quantitative and visual analyses demonstrate that LSTM-PINN successfully suppresses non-physical artifacts and structural distortions, yielding the highest thermodynamic fidelity and consistently outperforming state-of-the-art baselines in global error metrics. Ultimately, this memory-enhanced approach provides a highly robust and accurate computational baseline for capturing localized boundary layers and complex energy-momentum feedback in advanced electrothermal energy systems.

Polymer membranes are typically assumed to be inert and nonresponsive to the flux and density of the permeating particles in transport processes. Here, we study theoretically the consequences of membrane responsiveness and feedback on the steady-state force--flux relations and membrane permeability using a nonlinear-feedback solution-diffusion model of transport through a slab-like membrane. Therein, the solute concentration inside the membrane depends on the bulk concentration, c_0, the driving force, f, and the polymer volume fraction, phi. In our model, solute accumulation in the membrane causes a sigmoidal volume phase transition of the polymer, changing its permeability, which, in return, affects the membrane's solute uptake. This feedback leads to nonlinear force--flux relations, j(f), which we quantify in terms of the system's differential permeability, P_sys^{Delta}mathrm{dj}/{df}. We find that the membrane feedback can increase or decrease the solute flux by orders of magnitude, triggered by a small change in the driving force, and largely tunable by attractive versus repulsive solute--membrane interactions. Moreover, controlling the input, c_0 and f, can lead to steady-state bistability of phi and hysteresis in the force--flux relations. This work advocates that the fine-tuning of the membrane's chemo-responsiveness will enhance the nonlinear transport control features, providing great potential for future (self-)regulating membrane devices.

A large-scale database of two-dimensional UEDGE simulations has been developed to study detachment physics in KSTAR and to support surrogate models for control applications. Nearly 70,000 steady-state solutions were generated, systematically scanning upstream density, input power, plasma current, impurity fraction, and anomalous transport coefficients, with magnetic and electric drifts across the magnetic field included. The database identifies robust detachment indicators, with strike-point electron temperature at detachment onset consistently Te around 3-4 eV, largely insensitive to upstream conditions. Scaling relations reveal weaker impurity sensitivity than one-dimensional models and show that heat flux widths follow Eich's scaling only for uniform, low D and Chi. Distinctive in-out divertor asymmetries are observed in KSTAR, differing qualitatively from DIII-D. Complementary time-dependent simulations quantify plasma response to gas puffing, with delays of 5-15 ms at the outer strike point and approximately 40 ms for the low-magnetic-field-side (LFS) radiation front. These dynamics are well captured by first-order-plus-dead-time (FOPDT) models and are consistent with experimentally observed detachment-control behavior in KSTAR [Gupta et al., submitted to Plasma Phys. Control. Fusion (2025)]

Active matter systems, from self-propelled colloids to motile bacteria, are characterized by the conversion of free energy into useful work at the microscopic scale. These systems generically involve physics beyond the reach of equilibrium statistical mechanics, and a persistent challenge has been to understand the nature of their nonequilibrium states. The entropy production rate and the magnitude of the steady-state probability current provide quantitative ways to do so by measuring the breakdown of time-reversal symmetry and the strength of nonequilibrium transport of measure. Yet, their efficient computation has remained elusive, as they depend on the system's unknown and high-dimensional probability density. Here, building upon recent advances in generative modeling, we develop a deep learning framework that estimates the score of this density. We show that the score, together with the microscopic equations of motion, gives direct access to the entropy production rate, the probability current, and their decomposition into local contributions from individual particles, spatial regions, and degrees of freedom. To represent the score, we introduce a novel, spatially-local transformer-based network architecture that learns high-order interactions between particles while respecting their underlying permutation symmetry. We demonstrate the broad utility and scalability of the method by applying it to several high-dimensional systems of interacting active particles undergoing motility-induced phase separation (MIPS). We show that a single instance of our network trained on a system of 4096 particles at one packing fraction can generalize to other regions of the phase diagram, including systems with as many as 32768 particles. We use this observation to quantify the spatial structure of the departure from equilibrium in MIPS as a function of the number of particles and the packing fraction.

Superconducting systems may display different types of nonequilibrium states depending on the specific constraints imposed for measurement. We probe current-voltage relations of three-dimensional superconducting films by allowing finite voltages to develop across their length. Our experiments reveal sharp features of negative differential conductance which highlight the validity of the principle of minimum entropy production at the critical current transition. We have observed dissipative states with resistances intermediate between those of superconducting and normal phases at zero applied magnetic field, indicating a phenomenon of phase coexistence under nonequilibrium conditions. The features of steady states reported here are not accessible in conventional transport experiments with current-biasing methods.

Synchrophasor technology is an emerging and developing technology for monitoring and control of wide area measurement systems (WAMS). In an elementary WAMS, two identical phasors measured at two different locations have difference in the phase angles measured since their reference waveforms are not synchronized with each other. Phasor measurement units (PMUs) measure input phasors with respect to a common reference wave based on the atomic clock pulses received from global positioning system (GPS) satellites, eliminating variation in the measured phase angles due to distant locations of the measurement nodes. This has found tremendous applications in quick fault detection, fault location analysis, accurate current, voltage, frequency and phase angle measurements in WAMS. Commercially available PMU models are often proven to be expensive for research and development as well as for grid integration projects. This research article proposes an economic PMU model optimized for accurate steadystate performance based on recursive discrete Fourier transform (DFT) and provides results and detailed analysis of the proposed PMU model as per the steady state compliance specifications of IEEE standard C37.118.1. Results accurate up to 13 digits after decimal point are obtained through the developed PMU model for both nominal and off-nominal frequency inputs in steady state.

The theory of open quantum systems lays the foundations for a substantial part of modern research in quantum science and engineering. Rooted in the dimensionality of their extended Hilbert spaces, the high computational complexity of simulating open quantum systems calls for the development of strategies to approximate their dynamics. In this paper, we present an approach for tackling open quantum system dynamics. Using an exact probabilistic formulation of quantum physics based on positive operator-valued measure (POVM), we compactly represent quantum states with autoregressive transformer neural networks; such networks bring significant algorithmic flexibility due to efficient exact sampling and tractable density. We further introduce the concept of String States to partially restore the symmetry of the autoregressive transformer neural network and improve the description of local correlations. Efficient algorithms have been developed to simulate the dynamics of the Liouvillian superoperator using a forward-backward trapezoid method and find the steady state via a variational formulation. Our approach is benchmarked on prototypical one and two-dimensional systems, finding results which closely track the exact solution and achieve higher accuracy than alternative approaches based on using Markov chain Monte Carlo to sample restricted Boltzmann machines. Our work provides general methods for understanding quantum dynamics in various contexts, as well as techniques for solving high-dimensional probabilistic differential equations in classical setups.

Massive activations are scalar values in transformer hidden states that achieve values orders of magnitude larger than typical activations and have been shown to be critical for model functionality. While prior work has characterized these phenomena in fully trained models, the temporal dynamics of their emergence during training remain poorly understood. We present the first comprehensive analysis of massive activation development throughout transformer training, using the Pythia model family as our testbed. Through systematic analysis of various model sizes across multiple training checkpoints, we demonstrate that massive activation emergence follows predictable mathematical patterns that can be accurately modeled using an exponentially-modulated logarithmic function with five key parameters. We develop a machine learning framework to predict these mathematical parameters from architectural specifications alone, achieving high accuracy for steady-state behavior and moderate accuracy for emergence timing and magnitude. These findings enable architects to predict and potentially control key aspects of massive activation emergence through design choices, with significant implications for model stability, training cycle length, interpretability, and optimization. Our findings demonstrate that the emergence of massive activations is governed by model design and can be anticipated, and potentially controlled, before training begins.

We present a continuous geometric framework that models the discrete algebraic operations of the Transformer architecture as an integro-differential equation (IDE) on a semantic fiber bundle calE = calM times R^d. Beginning from a single geometric axiom -- that the token sequence forms a discrete 1-manifold equipped with a canonical measure lattice -- we translate every core component of the modern Transformer (RMSNorm, RoPE, Softmax Attention, FFN, Residual Stream, SGD, Weight Decay) into a cohesive vocabulary of differential geometry, measure theory, and stochastic calculus. The resulting framework yields quantitative predictions spanning entropic optimal transport (Attention as a Schrödinger bridge) and non-equilibrium thermodynamics (SGD as Itô diffusion violating detailed balance). We conduct a six-part experimental campaign across five architectures (Qwen3, LLaMA\nobreakdash-3.1, Gemma\nobreakdash-3, GPT-2, Mistral) spanning 124M to 8B parameters. The empirical observables are quantitatively consistent with the geometric predictions: the ε^{-1/2} Lipschitz scaling calibration at machine precision (R^2 = 1.000), the Lie--Trotter operator-splitting torsion, the symmetric ablation instability confirming the Dual-Law of Topological Stability, the calO(1/k) thermodynamic suppression of Poincaré recurrence on the RoPE torus, the thermodynamic context-limit phase transition, and the Non-Equilibrium Steady State parameter vortex -- verified across two optimizers (AdamW and Pure SGD) to exclude momentum artifacts. The results demonstrate that analyzing Transformers through the lens of continuous stochastic differential geometry provides a predictive descriptive vocabulary for the stability limits, context bounds, and optimization dynamics of Large Language Models.

Autoregressive video diffusion models enable streaming generation but often degrade over long rollouts: static scene layouts drift, while mechanisms that improve spatial stability tend to suppress motion, causing natural flows such as water, fire, or smoke to stagnate. We study this stability-motion trade-off in fixed-camera long-horizon nature video generation, where the two failure modes can be more clearly separated than in moving-camera settings. We propose Steady-Forcing, a memory and training framework combining a persistent visual anchor (V-Sink), an exponential moving-average motion memory (EMA-Sink), block-relative temporal encoding, periodic cache purification, and distillation from a Wan2.1-14B teacher with motion-rewarded priors under task-focused configurations. Together, these components are designed to preserve background identity while sustaining visually plausible fluid dynamics over multi-minute autoregressive rollouts. Evaluations across seven baselines show that Steady-Forcing improves long horizon background consistency and imaging quality, while a blind user study indicates stronger perceived stability and motion continuity. The benchmark evaluation further suggest that generic VBench aggregate scores under-penalize fixed-camera artifacts as well as rewarding drift-induced optical flow as Dynamic Degree while not directly penalizing texture hardening or flow stagnation - motivating future task-specific benchmarks for static-camera nature-flow evaluation. Project page: https://minar09.github.io/steadyforcing/

We provide a concise framework for generalized ensemble theory through a matrix-based approach. By introducing an observation matrix, any discrete probability distribution, including those for non-equilibrium steady states, can be expressed as a generalized Boltzmann distribution, with observables and conjugate variables as the basis and coordinates in a linear space. In this framework, we identify the minimal sufficient statistics required for inferring the Boltzmann distribution. Furthermore, we show that the Hadamard and Vandermonde matrices are suitable observation matrices for spin systems and random walks. In master equation systems, the probability flux observation matrix facilitates the identification of detailed balance violations. Our findings provide a new approach to developing generalized ensemble theory for non-equilibrium steady-state systems.

Autoregressive learning of time-stepping operators provides an effective approach to data-driven partial differential equation (PDE) simulation, yet for conservation laws, they face a fundamental challenge: learned updates may violate global conservation over long rollouts. For the important subclass of mass-conservation-type equations, the problem is compounded by inherent physical bounds (e.g., nonnegativity or concentrations in [0,1]) whose violation further destabilizes predictions. We introduce FluxNet, which learns cumulative transport amounts representing the total conserved quantity redistributed between each cell and a configurable neighborhood over the full surrogate interval. A conservative update guarantees exact discrete conservation by construction; modular capacity-constrained transport heads (L, U, and D) enforce lower bounds, upper bounds, or near-zero dual-bound violations through architectural design. Unlike flux-rate surrogates that require temporal integration and thus inherit CFL constraints, FluxNet involves no such integration; configurable transport neighborhoods enable large-timestep prediction at full spatial resolution. Ghost cells extend the framework to non-periodic boundaries. Experiments on four benchmarks (1D convection--diffusion, 2D shallow water, 1D traffic flow, 2D Cahn--Hilliard) demonstrate exact conservation, structural bound preservation, architecture modularity, and superior stability over flux-rate surrogates at large temporal strides. The code is publicly available at: https://github.com/Lan-zs/FluxNet.

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.

Global solar photospheric magnetic maps play a critical role in solar and heliospheric physics research. Routine magnetograph measurements of the field occur only along the Sun-Earth line, leaving the far-side of the Sun unobserved. Surface Flux Transport (SFT) models attempt to mitigate this by modeling the surface evolution of the field. While such models have long been established in the community (with several releasing public full-Sun maps), none are open source. The Open Source Flux Transport (OFT) model seeks to fill this gap by providing an open and user-extensible SFT model that also builds on the knowledge of previous models with updated numerical and data acquisition/assimilation methods along with additional user-defined features. In this first of a series of papers on OFT, we introduce its computational core: the High-performance Flux Transport (HipFT) code (github.com/predsci/hipft). HipFT implements advection, diffusion, and data assimilation in a modular design that supports a variety of flow models and options. It can compute multiple realizations in a single run across model parameters to create ensembles of maps for uncertainty quantification and is high-performance through the use of multi-CPU and multi-GPU parallelism. HipFT is designed to enable users to easily write extensions, enhancing its flexibility and adaptability. We describe HipFT's model features, validations of its numerical methods, performance of its parallel and GPU-accelerated code implementation, analysis/post-processing options, and example use cases.

We present an online reinforcement learning (RL) algorithm for fine-tuning flow-matching policies in continuous-control problems. Our key insight is to view RL-based policy improvement as a transport of action densities towards regions of high reward, which naturally aligns with the transport formulation of flow matching models. Prior methods either approximate the current or optimal policy distribution or resort to distillation, which introduces biased gradients or sacrifices multimodal modeling capacity. In contrast, our approach for RL with Density Transport, which we name RLDT, constructs a transport field from a maximum-entropy RL objective using Stein Variational Gradient Descent (SVGD). Then, it finetunes a pretrained flow matching policy to align with this field. Training with this alignment objective is nontrivial because flow-matching policies generate actions via a multi-step process, making direct gradient-based optimization challenging. To overcome this challenge and stabilize training, we approximate policy actions from intermediate denoising steps via expected-target estimation. This allows the transport-field update to propagate into the network parameters without unstable backpropagation through time. Experimental results demonstrate that RLDT outperforms competitive baselines in reward quality and convergence speed. This performance holds across diverse continuous-control tasks, encompassing both dense and sparse rewards, as well as state- and vision-based long-horizon robot manipulation. The project webpage is https://rpfey.github.io/rldt/{https://rpfey.github.io/rldt/}.

Capillary-driven transport offers a simple, self-sustained alternative to externally pumped microfluidic systems, yet achieving precise control of such flows remains challenging. We experimentally and theoretically investigate capillary flow in rectangular microchannels when a liquid meniscus encounters a geometric step with varying channel width and height. Depending on the contact angle and step dimensions, the meniscus either pins or advances, defining distinct flow and no-flow regimes. Introducing a lateral offset between channel sidewalls provides an additional geometric control that enables reversible switching from a pinned to a flowing state, even for liquids with relatively high contact angles. We rationalize these transitions using numerical simulations and an energy-based scaling model that captures the balance between surface tension and Laplace pressure at the step. Finally, we demonstrate synchronization of capillary fronts in parallel microchannels by combining stepped and offset geometries. These results establish a simple, geometry-mediated mechanism for passive control and synchronization of capillary flows, expanding the design space for microfluidic systems.

Minibatch optimal transport coupling straightens paths in unconditional flow matching. This leads to computationally less demanding inference as fewer integration steps and less complex numerical solvers can be employed when numerically solving an ordinary differential equation at test time. However, in the conditional setting, minibatch optimal transport falls short. This is because the default optimal transport mapping disregards conditions, resulting in a conditionally skewed prior distribution during training. In contrast, at test time, we have no access to the skewed prior, and instead sample from the full, unbiased prior distribution. This gap between training and testing leads to a subpar performance. To bridge this gap, we propose conditional optimal transport C^2OT that adds a conditional weighting term in the cost matrix when computing the optimal transport assignment. Experiments demonstrate that this simple fix works with both discrete and continuous conditions in 8gaussians-to-moons, CIFAR-10, ImageNet-32x32, and ImageNet-256x256. Our method performs better overall compared to the existing baselines across different function evaluation budgets. Code is available at https://hkchengrex.github.io/C2OT

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.

Plasma modeling is central to the design of nuclear fusion reactors, yet simulating collisional plasma kinetics from first principles remains a formidable computational challenge: the Vlasov-Maxwell-Landau (VML) system describes six-dimensional phase-space transport under self-consistent electromagnetic fields together with the nonlinear, nonlocal Landau collision operator. A recent deterministic particle method for the full VML system estimates the velocity score function via the blob method, a kernel-based approximation with O(n^2) cost. In this work, we replace the blob score estimator with score-based transport modeling (SBTM), in which a neural network is trained on-the-fly via implicit score matching at O(n) cost. We prove that the approximated collision operator preserves momentum and kinetic energy, and dissipates an estimated entropy. We also characterize the unique global steady state of the VML system and its electrostatic reduction, providing the ground truth for numerical validation. On three canonical benchmarks -- Landau damping, two-stream instability, and Weibel instability -- SBTM is more accurate than the blob method, achieves correct long-time relaxation to Maxwellian equilibrium where the blob method fails, and delivers 50% faster runtime with 4times lower peak memory.

Accurately describing the distribution of CO_2 in the atmosphere with atmospheric tracer transport models is essential for greenhouse gas monitoring and verification support systems to aid implementation of international climate agreements. Large deep neural networks are poised to revolutionize weather prediction, which requires 3D modeling of the atmosphere. While similar in this regard, atmospheric transport modeling is subject to new challenges. Both, stable predictions for longer time horizons and mass conservation throughout need to be achieved, while IO plays a larger role compared to computational costs. In this study we explore four different deep neural networks (UNet, GraphCast, Spherical Fourier Neural Operator and SwinTransformer) which have proven as state-of-the-art in weather prediction to assess their usefulness for atmospheric tracer transport modeling. For this, we assemble the CarbonBench dataset, a systematic benchmark tailored for machine learning emulators of Eulerian atmospheric transport. Through architectural adjustments, we decouple the performance of our emulators from the distribution shift caused by a steady rise in atmospheric CO_2. More specifically, we center CO_2 input fields to zero mean and then use an explicit flux scheme and a mass fixer to assure mass balance. This design enables stable and mass conserving transport for over 6 months with all four neural network architectures. In our study, the SwinTransformer displays particularly strong emulation skill (90-day R^2 > 0.99), with physically plausible emulation even for forward runs of multiple years. This work paves the way forward towards high resolution forward and inverse modeling of inert trace gases with neural networks.

We propose a unified, few-step generative modeling framework based on cumulative flow maps for long-range transport in probability space, inspired by flow-map techniques for physical transport and dynamics. At its core is a cumulative-flow abstraction that connects local, instantaneous updates with finite-time transport, enabling generative models to reason about global state transitions. This perspective yields a unified few-step framework built on cumulative transport and cumulative parameterization that applies broadly to existing diffusion- and flow-based models without being tied to a specific prediction instantiation. Our formulation supports few-step and even one-step generation while preserving synthesis quality, requiring only minimal changes to time embeddings and training objectives, and no increase in model capacity. We demonstrate its effectiveness across diverse tasks, including image generation, geometric distribution modeling, joint prediction, and SDF generation, with reduced inference cost.

Chemical reaction networks can undergo nonequilibrium phase transitions upon variation of external control parameters like the chemical potential of a species. We investigate the flux in the associated chemostats that is proportional to the entropy production and its critical fluctuations within the Schlögl model. Numerical simulations show that the corresponding diffusion coefficient diverges at the critical point as a function of system size. In the vicinity of the critical point, the diffusion coefficient follows a scaling form. We develop an analytical approach based on the chemical Langevin equation and van Kampen's system size expansion that yields the corresponding exponents in the monostable regime. In the bistable regime, we rely on a two-state approximation in order to analytically describe the critical behavior.

We study the problem of the transformation of a given reactant species into an immiscible product species, as they flow through a chemically active porous medium. We derive the equation governing the evolution of the volume fraction of the species -- in a one-dimensional macroscopic description --, identify the relevant dimensionless numbers, and provide simple models for capillary pressure and relative permeabilities, which are quantities of crucial importance when tackling multiphase flows in porous media. We set the domain of validity of our models and discuss the importance of viscous coupling terms in the extended Darcy's law. We investigate numerically the steady regime and demonstrate that the spatial transformation rate of the species along the reactor is non-monotonous, as testified by the existence of an inflection point in the volume fraction profiles. We obtain the scaling of the location of this inflection point with the dimensionless lengths of the problem. Eventually, we provide key elements for optimization of the reactor.

Learning a transport model that maps a source distribution to a target distribution is a canonical problem in machine learning, but scientific applications increasingly require models that can generalize to source and target distributions unseen during training. We introduce distribution-conditioned transport (DCT), a framework that conditions transport maps on learned embeddings of source and target distributions, enabling generalization to unseen distribution pairs. DCT also allows semi-supervised learning for distributional forecasting problems: because it learns from arbitrary distribution pairs, it can leverage distributions observed at only one condition to improve transport prediction. DCT is agnostic to the underlying transport mechanism, supporting models ranging from flow matching to distributional divergence-based models (e.g. Wasserstein, MMD). We demonstrate the practical performance benefits of DCT on synthetic benchmarks and four applications in biology: batch effect transfer in single-cell genomics, perturbation prediction from mass cytometry data, learning clonal transcriptional dynamics in hematopoiesis, and modeling T-cell receptor sequence evolution.

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.