arXiv subjects

Shabeeb Ameen

Publications and source records attributed to Shabeeb Ameen.

4 recordsLinked to original sources

arXiv2026

Training cell stress patterns in 3D cellular packings

The task of learning patterns is typically associated with systems that update parameters on fixed architectures, such as neural networks, where learning proceeds through continuous optimization. Here, we demonstrate that pattern learning can also emerge in reconfigurable cellular tissue, where both mechanical parameters and network topology evolve. Using a three-dimensional vertex model, we show that cellular packings can be trained to realize prescribed cell stress patterns through a contrastive learning algorithm to update hidden-cell shape indices. We find that learning is intrinsically collective, requiring coordinated, system-wide parameter adjustments, with learnability governed by an interplay between mechanical state, capacity, and training protocol. In particular, the rigidity of the tissue controls an effective exploration-exploitation tradeoff: fluid-like regimes enhance exploration through cellular rearrangements, while rigid regimes constrain dynamics and favor exploitation of existing configurations. These rearrangements introduce discontinuous learning dynamics, enabling the system to transition between distinct local minima in the cost function landscape. As the ratio of target cells to the total number cells in the packing or constraint load increases, learning becomes slower, more heterogeneous, and increasingly dependent on rare rearrangements that allow escape from geometrically constrained states. Finally, training cells in sequence, in contrast to parallel protocols, provides an alternative route that can be more robust but generally takes longer to train for the constraint loads studied. These results suggest a learning phase diagram governed by constraint load, cell packing rigidity, and training protocol. By enabling the training of localized internal states, this work positions tissues not only as adaptive materials, but as nonconventional AI platforms.

cond-mat.dis-nn↗

arXiv2026

Learning Associations in Reconfigurable Particle Packings via Local Cyclic Driving

We investigate associative-memory behavior in a reconfigurable particle packing programmed by purely local cyclic driving. The system is a two-dimensional bidisperse Lennard--Jones particle assembly with periodic boundaries evolved under athermal quasistatic relaxation. During training, a fixed set of input particles is driven cyclically while output particles are selected on-the-fly by a region-driving rule and driven according to a prescribed flow pattern; during retrieval, only the inputs are driven. Associative-memory performance is quantified by the cosine similarity between realized and target output displacement directions. Unlike physical learning systems with fixed architecture, learning here arises through emergent weight updates: localized rearrangements modify the contact network and reshape the effective mechanical couplings between inputs and outputs. Across task difficulty we identify three regimes. In an easy setting, the intrinsic mechanical response already produces coherent motion in the right-hand region under input-only driving, yielding high performance without training. In a hard setting, the desired mapping conflicts with the dominant collective drift, resulting in low baseline performance and only modest training gains; introducing intermittent relaxation cycles reduces train--retrieval mismatch and improves performance. In an intermediate quadrupolar task, repositioning the input--output geometry stabilizes the desired response and converts initially stochastic trajectories into reproducible learned motions. Together these results identify minimal physical ingredients for association-based functionality in athermally driven particulate media and motivate an association learning phase diagram for reconfigurable matter.

cond-mat.dis-nn↗

arXiv2026

Cell strain-stiffening drives cell breakout from embedded spheroids

Understanding how cells escape from embedded spheroids requires a mechanical framework linking stress generation within cells, across cells, and between cells and the surrounding extracellular matrix (ECM). We develop such a framework by coupling a 3D vertex model of a spheroid to a fibrous ECM network and deriving a 3D Cauchy stress tensor for deformable polyhedral cells, enabling direct cell-level stress quantification in three dimensions. We analyze maximum shear stress in solid-like and fluid-like spheroids: solid-like spheroids exhibit broader stress distributions and radial stress gradients, while fluid-like spheroids show lower stresses with weak spatial organization. Cell shape anisotropy is not generically aligned with principal stress directions, indicating that morphology alone is an unreliable proxy for mechanical state. We further demonstrate strain stiffening at the single-cell level, where elongation produces nonlinear increases in maximum shear stress, allowing boundary cells in otherwise low-stress, fluid-like spheroids to transiently generate forces sufficient to remodel the matrix. To connect strain-induced stress amplification to invasion modes, we introduce an extended 3D vertex model with explicit, tunable cell-cell adhesion springs. In this minimal mechanical framework, single-cell breakout results from strain stiffening combined with reduced adhesion, whereas multi-cell streaming additionally requires anisotropic adhesion strengthened along the elongation axis and weakened orthogonally. Together, these results identify distinct mechanical pathways coupling cell strain, stress amplification, and adhesion organization to spheroid invasion.

physics.bio-ph↗

arXiv2024

Enhanced extracellular matrix remodeling due to embedded spheroid fluidization

Tumor spheroids are in vitro three-dimensional, cellular collectives consisting of cancerous cells. Embedding these spheroids in an in vitro fibrous environment, such as a collagen network, to mimic the extracellular matrix (ECM) provides an essential platform to quantitatively investigate the biophysical mechanisms leading to tumor invasion of the ECM. To understand the mechanical interplay between tumor spheroids and the ECM, we computationally construct and study a three-dimensional vertex model for a tumor spheroid that is mechanically coupled to a cross-linked network of fibers. In such a vertex model, cells are represented as deformable polyhedrons that share faces. Some fraction of the boundary faces of the tumor spheroid contain linker springs connecting the center of the boundary face to the nearest node in the fiber network. As these linker springs actively contract, the fiber network remodels. By toggling between fluid-like and solid-like spheroids via changing the dimensionless cell shape index, we find that the spheroid rheology affects the remodeling of the fiber network. More precisely, fluid-like spheroids displace the fiber network more on average near the vicinity of the spheroid than solid-like spheroids. We also find more densification of the fiber network near the spheroid for the fluid-like spheroids. These spheroid rheology-dependent effects are the result of cellular motility due to active cellular rearrangements that emerge over time in the fluid-like spheroids to generate spheroid shape fluctuations. Our results uncover intricate morphological-mechanical interplay between an embedded spheroid and its surrounding fiber network with both spheroid contractile strength and spheroid shape fluctuations playing important roles in the pre-invasion stages of tumor invasion.

physics.bio-ph↗