Papers

Neuroinflammation and glial scar formation in the central nervous system (CNS) emerge from coordinated signaling between neurons, astrocytes, oligodendrocytes and microglia. Conventional embryonic neuron-astrocyte-oligodendrocyte (NAO) TriCultures lack microglia and cannot model innate immune responses. Here, we introduce postnatal neuron-astrocyte-oligodendrocyte-microglia (NAOM) TetraCultures, in which resident microglia are retained from the original brain tissue and co-develop with other CNS cell populations from the onset of culture. Hippocampal and cortical cultures were maintained for 14 days in vitro and challenged with LPS, poly I or scratch injury. Only NAOM TetraCultures mounted robust, region- and stimulus-specific inflammatory responses. LPS induced marked TNF-\alpha and IL-1\beta secretion and increased IBA1 in hippocampal microglia, whereas poly I elicited IFN-\beta release without increasing IBA1. CD68 regulation differed between hippocampus and cortex, and microglial morphology showed pronounced amoeboid transitions after LPS. Astrocytes in NAOM TetraCultures expanded their territorial coverage after LPS, an effect absent in NAO TriCultures. Following scratch injury, IL-1\beta increased, microglia infiltrated lesion zones and astrocytes formed lesion borders. Thus, NAOM TetraCultures recapitulate key features of CNS immunity, glial scar formation and region-specific glial responses while providing a physiologically relevant microglia-containing model.

Cell viability assessment is a core requirement in cell culture systems, with critical applications in biopharmaceutical manufacturing and drug development. Conventionally, it is measured by adding membrane-impermeable dyes to a sample (a process called staining), which allows compromised cell membranes to be distinguished from intact ones. However, staining has several limitations: (a) chemical agents can perturb normal cellular processes of the cells being measured, (b) it is often ambiguous to assign viability to individual cells whose membrane integrity is only partially compromised. (c) photobleaching can undermine measurement accuracy over time when using fluorescent stains, and (d) staining cannot be performed in situ or in real time. Here, we show that (1) stained cells captured under brightfield imaging contain sufficient information to distinguish live and dead cells, and (2) cells captured under unstained brightfield imaging exhibit similar image features to their stained counterparts, enabling models trained on stained cells to generalize to unstained ones. We then report the development and validation of ViabiLens, an AI-assisted software for label-free cell viability analysis. The ViabiLens combines a cell detection model for localizing individual cells with a convolutional neural network (CNN) classifier for live/dead prediction, paired with an interactive UMAP-based viewer for visualizing and exploring individual cells across the sample. Evaluated on Chinese Hamster Ovary (CHO) cells spanning a wide range of viability conditions, ViabiLens achieves a mean absolute error of 2.68% on unstained samples against fluorescence-based reference measurements. We also release a benchmark dataset for label-free cell viability analysis to facilitate future research, available at https://amirrezavazifeh.github.io/ViabiLens-Project-Page/.

Discovering broadly neutralizing antibodies (bnAbs) from human natural immune repertoires remains a fundamental challenge in immunology, hindered by: the extreme rarity of bnAb, incomplete understanding of their cellular origins across pathogens, and the inability of existing computational tools to generalize across emerging viral threats. Here we present ImmuneAgent, a closed-loop AI system that integrates multimodal reasoning with continual meta-learning and wet-lab feedback to overcome these barriers. Applied to screen the natural BCR repertoires from vaccinated or infected cohorts, the system achieves a ~55% neutralization antibody discovery rate (60 of 110 cloned candidates) and a ~11% bnAb yield (12 of 110), substantially outperforming a state-of-the-art sequence-based neutralization predictor or cofolding models evaluated at the same cloning budget. Five ImmuneAgent-discovered antibodies conferred 100% in vivo protection against lethal influenza challenge, comparable to the clinical-stage therapeutic MEDI8852. The system recovered the cellular and structural determinants of bnAb activity and identified FCRL5+CD27+ atypical memory B cells as a conserved bnAb reservoir and hydrophobic interface enrichment as a cross-viral structural signature, which generalized to unseen antigens, discovering human metapneumovirus (hMPV) cross-neutralizing and human papillomavirus (HPV)-neutralizing antibodies without antigen-specific sorting. These results validate that ImmuneAgent is a generalizable framework for rapid therapeutic antibody discovery against emerging viral threats.

Phenotypic plasticity, the ability of cells to switch between states, is central to development, differentiation, and therapy resistance. Although it is modeled at several scales, from compartmental ODEs to phenotype-structured PDEs and single-cell stochastic equations, a framework connecting these descriptions is missing. We present such a framework. Starting from a general $n$-compartment ODE model encompassing nonlinear growth and linear transitions between phenotypes, we show, with a new, elementary and generalizable proof of a recent theorem, that under uniform competition, the long-term population distribution is solely governed by transition rates. All phenotypes become selectively neutral at saturation, and the imprint of fitness differences during growth fades at an explicit rate. Restricting transitions to neighboring states transforms the model into a discretization of a phenotype-structured reaction-diffusion-advection PDE. In this continuum model, diffusion and advection are identified from switching rates, and fitness remains asymptotically irrelevant. Interpreting the advection velocity as the negative gradient of an effective epigenetic potential transforms the PDE into a Fokker–Planck equation and converts single-cell trajectories into stochastic gradient descent (SGD) in the Langevin sense on the phenotypic landscape. Non-local transitions, such as mutations, are incorporated via an integro-differential term, yielding a unified model with reaction, gradient flow, diffusion, and jumps. State-dependent noise reshapes the effective landscape without altering the underlying potential. This gives cancer a route to elevated plasticity that static, single-cell snapshots cannot distinguish from a changed landscape. This framework provides a physical interpretation of Waddington's landscape, where cells perform SGD, and cancer corresponds to a corrupted landscape.

Predicting phenotypic and transcriptional responses to perturbations at single-cell resolution provides a powerful tool for probing biological systems. However, existing methods typically rely on fixed mappings learned during training, making it challenging to calibrate distribution shifts or adapt to novel perturbation conditions during inference. Here, we present scEGFlow, an energy-guided flow matching framework that dynamically bridges control and perturbed cellular states. scEGFlow models continuous transitions from control cell populations to perturbed states using conditional flow matching. It then applies condition-specific energy gradients to correct and steer these predictions, enabling flexible adjustments without retraining the flow model. Evaluations across benchmarks spanning imaging phenotypes and transcriptomic profiles show that scEGFlow outperforms existing methods in reconstructing response distributions under both seen and unseen perturbation conditions, faithfully preserving cellular manifold geometry and population heterogeneity. This advantage is notable when adapting to new conditions with only a few measured cells, consistently improving prediction accuracy. Furthermore, scEGFlow accurately recapitulates perturbation-induced up- and down-regulation patterns across consensus gene expression signatures, where energy guidance improves the agreement between predicted and observed regulatory directions. Ultimately, these findings demonstrate that scEGFlow provides a modular, generalizable, and steerable solution for single-cell perturbation modeling. By grounding generative flows in learned biological landscapes, this architecture establishes a new computational paradigm for navigating and manipulating cellular behavior in silico.

Ovarian follicle development has been modeled either by compartmental models, where developmental stages are represented by discrete compartments, or by physiologically structured population models (PSPMs), formulated as transport PDEs describing follicles along a continuous maturation variable. Compartmental models reproduce full-cycle hormonal and follicular dynamics but cannot describe cellular features. PSPMs capture multiscale behavior, yet lack a direct link to compartmental descriptions, making hormonal feedback difficult to incorporate. Here, we introduce a class of ODE systems derived as finite-dimensional reductions of PSPMs via a perturbative moment closure. These systems provide backbone approximations of the structured dynamics, retaining key nonlinear mechanisms governing recruitment, selection for dominance, and atresia while projecting maturation onto macroscopic variables. Zero- and first-order moments, derived from phenomenological assumptions regarding follicular maturation, allow us to realistically model follicle sizes and blood estradiol concentrations over one follicular wave. This application is supported by bovine data and likely generalizable to other mammalian species.

Confined cell migration is governed by nuclear and cellular deformation. In this work, we formulate a two-dimensional mathematical framework in which the cell and nuclear membranes are represented as evolving closed surfaces governed by force-balance laws incorporating surface tension, bending elasticity, and external mechanical interactions. Nuclear mechanics depends on several factors, including chromatin organization and compaction, which are regulated by epigenetic modifications. Molecular regulation at the nuclear periphery is described by a surface reaction-diffusion system posed on the evolving nuclear surface. We apply this coupled framework to an experimentally characterized lung cancer cell model in which the balance between the enzymes SETDB1 and SUV39H1 regulates the peripheral deposition of H3K9me3. Using experimentally measured mechanical parameters, we represent control (Ctrl) and SETDB1 knockout (SETDB1 KO) conditions, which display distinct H3K9me3 distributions, especially at the nuclear periphery. Numerical solutions obtained using the evolving surface finite element method qualitatively reproduce the changes in nuclear mechanics as well as part of the experimentally observed increase in the entry time in SETDB1 KO cells. The model therefore reproduces the direction of the experimental observations, while the residual difference between simulated and measured entry times indicates that the cellular response is multifactorial.

Receptor-mediated endocytosis requires a particle to approach the cell membrane to within a few nanometers before ligand–receptor binding can occur. Existing continuum models often start from an already established contact and do not explicitly describe how crowding particles on the extracellular side influence the distribution of the particle near the membrane. We examine entropic depletion forces as one possible nonspecific contribution to this initial approach. For ideal depletants, the Asakura–Oosawa excluded-volume construction gives an exact depletion potential for the planar geometry before contact. The potential and force vanish continuously at the onset of excluded-volume overlap. This interaction provides a possible contribution to membrane proximity before specific binding, while its extension to curved wrapping geometries requires additional approximation. Within a reduced continuum model, we combine depletion attraction, ligand–receptor binding, membrane deformation, and cytoskeletal viscoelastic dissipation. The viscoelastic contact is formulated through a hereditary integral and a standard linear solid. The kinetic model gives a conditional minimum ligand density for complete engulfment, a finite particle-size window, and a stiffness-dependent upper limit. When the stationary radius lies inside the domain of finite positive wrapping times, the estimated wrapping time has a minimum at a radius that decreases with increasing binding energy density. At fixed viscosity and other independent parameters, the same time approximation predicts slower wrapping as cell stiffness increases. The two positive roots defining the size window merge at a limiting parameter value, which characterizes closure of the admissible size interval. Depletion attraction is interpreted as one possible contribution to particle-membrane association

Simultaneous assessment of electrical excitation and mechanical contraction is essential for understanding cardiac cell function, yet these two processes are commonly measured with separate techniques or invasively. Here, changes in cellular electrical activity modulate local charge redistribution in optical microelectrodes and are converted into fluorescence signals, while cell contraction induces membrane displacement that contributes an additional mechanical component to the optical readout. By comparing recordings obtained in beating cells with those acquired after inhibition of contraction, we separate action-potential-associated electrostatic transduction from contractility-driven membrane motion. The approach offers a label-free route to support high-throughput in vitro assays for cardiotoxicity screening and electromechanical sensing. Concurrently, it unfolds the physical mechanisms governing membrane-based optical devices deployed in cardiac cell bioelectronics and mechanics.

Efferocytosis, the clearance of dying cells typically by macrophages, is essential for tissue homeostasis and the resolution of inflammation. Previous experiments by Ford et al. (Proc. R. Soc. B, 2019) showed that cannibalistic efferocytosis redistributes endogenous lipid from dying macrophages into the surviving population, but existing mathematical models do not reproduce the observed population dynamics and lipid distributions. Here, fifteen candidate models are compared, combining three mechanisms of apoptotic material uptake with five forms of the macrophage death rate. Model comparison is guided by the Akaike Information Criterion and qualitative agreement with the observed lipid distributions. Numerical solutions show that whole-cell uptake models predict internal maxima that are absent from the data, whereas nibbling uptake produces distributions that are too concentrated about their means. By contrast, intermediate "fragmented" uptake models provide substantially improved agreement when combined with either linear lipid-dependent or exponential time-dependent death rates. The fitted models predict that smaller fragments from dying cells are ingested at higher frequency than larger ones. This analysis provides new insight into how efferocytosis shapes the distribution of lipid within macrophage populations and highlights the importance of distribution-level data for distinguishing between mechanistic models that reproduce similar population-average dynamics.

We consider a minimal pressure-based model of heterogeneous cell populations consisting of proliferative and non-proliferative cells with different mobilities. The model is formulated as a system of reaction–cross–diffusion equations describing the spatio-temporal dynamics of the cell densities. The model is known to admit one-dimensional travelling wave solutions with strictly segregated components: non-proliferative cells occupy a finite region at the leading edge, while proliferative cells remain at the rear. However, the speed, parameter dependence, and stability of these waves remain poorly understood. In this work, we derive an almost explicit variational bound on the wave speed by reformulating the problem as a free-boundary problem for a generalised porous–Fisher equation. The estimates we obtain apply to general pressure laws and growth kinetics, agree closely with the results of numerical simulations, and become sharp in the incompressible limit, where we formally recover a fully explicit characterisation of the wave speed. We then analyse the stability of the waves to show that segregated waves are stable only when non-proliferative cells are more mobile than proliferative cells. Finally, motivated by numerical observations of finger-like protrusions, we investigate the stability of incompressible segregated circular waves through asymptotic shape-perturbation analysis. This yields explicit expressions for the pressure, interface velocity, and growth rates of angular modes, thereby making evident the destabilisation mechanisms that may lead to the emergence of fingering instability. Interestingly, we find that, in contrast with the one-dimensional case, the stability of such circular waves is not determined solely by the relative value of the mobility coefficients, and thus instabilities may arise irrespective of which cell type has the larger mobility.

The vertex model is widely used to describe the mechanics of epithelial tissues, but its conventional formulation assumes that all cells remain tightly packed and always share edges with their neighbors, making it difficult to represent local detachment or gap formation. Here, we propose a minimal extension of the vertex model that enables cell detachment by introducing a new topological transformation, T2-inverse, which acts as the inverse of the classical T2 transition. When the imbalance of forces acting on a vertex, quantified by a tension metric $T$, exceeds a threshold, the T2-inverse splits the vertex into multiple vertices and creates a closed polygon that is incorporated as a pseudo-cell. This operation allows the model to represent the emergence and propagation of local detachment events. Using this framework, we simulate the stretching of a cell sheet and show that force-induced local detachments can accumulate to produce macroscopic tissue rupture. These results demonstrate that the proposed model extends the capability of the vertex model to describe tissue-level breakdown processes, including detachment and tearing, and provides a foundation for studying a broader class of epithelial mechanical phenomena.

Agent-based models (ABMs) provide a natural framework for representing cell-level rules and spatial heterogeneity in bacterial infections, but their computational cost limits their use for macroscopic tissue-scale simulations and broad parameter exploration. We derive a deterministic coarse-grained description for a class of bacterial-infection ABMs in which immune cells and extracellular bacteria diffuse, immune cells ingest nearby bacteria, and intracellular bacterial loads evolve through prescribed birth and clearance processes. The first coarse-grained model is a semidiscrete reaction–diffusion system that retains a discrete internal state for each immune-cell bacterial load while representing cell and bacterial populations by continuum concentration fields. The key technical step is the derivation of state-dependent effective ingestion rates from the microscopic ABM parameters: these rates are obtained by solving an auxiliary diffusion problem around a single bacterium and computing the flux of immune cells into the interaction region. We then take a continuum limit in the internal state variable, yielding a state-structured reaction–diffusion system in which intracellular dynamics appear as advection and diffusion in state space. Numerical comparisons with ensemble-averaged ABM simulations show close agreement in biologically motivated parameter regimes. The resulting framework preserves the rule-based structure of the ABM while producing PDE models that are substantially more tractable for large-scale simulation and parameter studies.

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

In this study, we aim to theoretically investigate antipolar cell-cell adhesion, in which adhesion sites are located on the opposite side of the leading edge of migrating cells, as a candidate for irregularly polarized adhesion that induces disorder in collective cell migration. We employ the cellular Potts model to simulate the effects of antipolar adhesion on collective migration driven by cell motility. Antipolar adhesion induces a collective motility disorder, which exhibits a disordered configuration in the motility direction, even when collective motion occurs in the absence of adhesion. Consequently, antipolar adhesion inhibits collective migration. The effect is in contrast to that of polar adhesion, which accelerates the directional intercellular order of cell motility. At a specific motility strength, a depinning transition emerges from a collective motility disorder to a collective motion. The collective motility disorder can be physically explained by the cooperative effect between antipolar adhesion and motility persistence within the mean-field approximation.

Biased migration up chemical gradients and proliferation are fundamental drivers of collective invasion in several biological processes ranging from embryonic morphogenesis to cancer. Nonetheless, our understanding of how their interplay yields distinct invasion patterns remains incomplete. In this work, we propose a multiscale framework to systematically derive macroscopic hydrodynamic theories of cell invasion from a mesoscopic description of cells as biased self-propelled, interacting particles that proliferate. Our framework reveals how clump and stream invasion patterns emerge from the same kinetic equation under different asymptotic regimes of cell proliferation. Stream invasion is characteristic of cell populations in which proliferation balances cell motion. In contrast, clump invasion requires a separation of the hydrodynamic timescale of motion and the slower timescale of proliferation. By means of a multiple-scale approach, our analysis reveals that clump invasion is described as a slow evolution through a family of mass-dependent travelling-wave solutions. Overall, our work offers a novel approach to investigate multiscale regulation of cell invasion in systems where cell proliferation and collective invasion evolve on distinct timescales.

In this paper, we study a slow-fast model of Intracellular Calcium Concentrations (ICC) within a stochastic framework, where stochastic perturbations are introduced to capture the intrinsic randomness of such biological systems. We first analyse the three-dimensional single-cell model, based on the FitzHugh-Nagumo structure, and subsequently extend the analysis to a coupled two-cell six-dimensional setting. We prove existence and uniqueness of solutions and establish positivity of the calcium variable. We obtain explicit mean-square stability estimates around deterministic equilibria and quantify how they depend on the noise intensity. Numerical simulations for both the single-cell and coupled systems illustrate relevant qualitative behaviours and reveal additional dynamical features arising in the stochastic framework.

Gaucher disease (GD), the most common lysosomal storage disorder, alters red blood cell (RBC) mechanics and circulation, contributing to vascular occlusions, bone infarcts, and splenomegaly. However, the individual roles of GD-RBC biophysical properties in these processes remain unclear. Here, we present a combined computational-experimental investigation to quantitatively characterize GD-RBC biophysical properties and determine how specific mechanical parameters drive abnormal RBC behavior. Informed by experimental data, we independently quantify key RBC properties, including shear modulus (mu), surface-to-volume ratio (S/V), and bending modulus (k_c). Based on these parameters, we construct three GD-RBC subtypes (GD-RBC1-3) to systematically isolate their individual contributions. At the single-cell level, optical tweezers simulations show up to ~27% reduction in axial diameter and ~42% reduction in transverse compression. Tank-treading dynamics exhibit non-monotonic behavior, with rotation frequencies increasing by up to ~70% or decreasing under elevated bending rigidity. In confined flow, traversal times through microchannel constrictions increase by more than a factor of two, while splenic slit passage times rise from ~250 ms (control) to >1200 ms for the severe GD-RBC subtype, approaching a functional no-passage threshold. At the population level, viscosity simulations demonstrate that these alterations collectively elevate blood viscosity, with small fractions (~4.0%) of highly rigid cells disproportionately increasing flow resistance. Overall, this study provides a quantitative and mechanistic framework that disentangles the contributions of key RBC parameters to abnormal behavior in GD, linking cellular-scale biophysics to hematologic dysfunction and microvascular occlusion.

Cellular activity drives epithelial fluidization — a widespread phenomenon observed during tissue development, remodeling, and repair both in vivo and in vitro. Yet the physical origins and spatial organization of active forces vary widely across biological systems and are often represented by a single generic mechanism in theoretical models. Here, using an active vertex model, we systematically compare four modes of epithelial activity spanning subcellular to tissue scales: apolar motility, polar motility, fluctuating contractility, and mechanochemical regulation. Although all four mechanisms drive the same global transition from a solid-like rectangular tissue to a fluid-like circular morphology, they reach this state through distinct pathways — differing in the rates and topology of junctional rearrangements, cell elimination, and collective motion and leave distinguishable signatures in tissue architecture, cell dynamics, and mechanical relaxation. Among these observables, spatial velocity correlations directly capture the spatial organization of activity: their correlation length and functional form together resolve all four mechanisms. The robustness of these signatures across activity strengths suggests that spatial velocity correlations offer an experimentally accessible means of identifying the physical origin of epithelial activity from live-cell imaging alone.

Cells often estimate chemical concentrations from only a few diffusing molecules, whose stochastic motion limits sensing precision. We consider a perfect monitoring instrument that records the instantaneous molecular density throughout a finite region without perturbing the concentration field or distinguishing molecular identities. The standard Berg-Purcell estimator weights all positions uniformly. Here we derive the optimal spatial weighting within a large class of unbiased estimators for both concentration and gradient sensing. Variance minimization maps to an electrostatic problem. Surprisingly, although the instrument monitors the entire volume, the optimal estimator assigns all weight to its boundary, reducing the uncertainty in both concentration and gradient sensing. We extend the results to arbitrary geometries and spatial dimensions.

Cell unjamming in dense tissues is a complex but essential process in embryogenesis and cancer metastasis. Increasing evidence suggests that nuclear mechanics and density effects play a vital role in collective cell unjamming. However, state-of-the-art cell-shape-based theories fail to include nuclear and density effects, while computer models featuring rigid nuclei disagree with experimental observations of elongated nuclei promoting unjamming. Here, we introduce a computational model of confluent cells with explicitly deformable nuclei to study the dynamics of cell unjamming. Our simulations show an unjamming transition controlled by nuclear size and shape, reconciling conflicting theories of density-driven versus shape-driven mechanisms. We predict general relations connecting cellular and nuclear shape to collective cell motion, verified experimentally in distinct monolayers of MCF-10A and MDA-MB-436 breast cells, with striking accuracy. Our work establishes a rational connection between nuclear mechanics and tissue-scale rigidity transitions, highlighting the nucleus's key role in collective cell unjamming.

In bioreactor experiments, budding yeast can manifest stable metabolic oscillations. In some instances these oscillations involve the cell cycle and are associated with a dynamical phenomenon called temporal clustering. Since yeast divide asymmetrically, mother cells may be able to divide sooner than the smaller daughter cells. We show that asymmetric division plus positive feedback can result in stable temporal clustering. In this scenario, the cells self-organize into $p$ clusters of mother cells and $q$ clusters of daughter cells, $p \le q$. In simple numerical simulations of a population model with asymmetric division and positive feedback, we show that $p:q$ periodic arrangements form spontaneously from random populations of cells. Our main result is that these structures can be stable.