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A constitutive relation between stress and strain relative to a reference state is the basic assumption of elasticity theory. However, in living matter, force generation is governed by motor molecule activity, which does not depend on…
This article extends the preprint "Characterizing Agent-Based Model Dynamics via $\epsilon$-Machines and Kolmogorov-Style Complexity" by introducing diffusion models as orthogonal and complementary tools for characterizing the output of…
Agent-based models (ABMs) simulate complex systems by capturing the bottom-up interactions of individual agents comprising the system. Many complex systems of interest, such as epidemics or financial markets, involve thousands or even…
Epithelial tissues play a fundamental role in various morphogenetic events during development and early embryogenesis. Although epithelial monolayers are often modeled as two-dimensional (2D) elastic surfaces, they distinguish themselves…
Navigating topological transitions in cellular mechanical systems is a significant challenge for existing simulation methods. While abstract models lack predictive capabilities at the cellular level, explicit network representations…
Wounds in epithelial tissues compromise their vital role in homeostasis. A rapid and efficient wound healing encompasses different mechanisms, which includes the formation of a contractile actin-myosin cable around its edge, known as the…
The finite element simulation of dynamic wetting phenomena, requiring the computation of flow in a domain confined by intersecting a liquid-fluid free surface and a liquid-solid interface, with the three-phase contact line moving across the…
A novel locally statistical active contour model (ACM) for image segmentation in the presence of intensity inhomogeneity is presented in this paper. The inhomogeneous objects are modeled as Gaussian distributions of different means and…
Agentic AI is rapidly advancing in healthcare and biomedical research. However, in medical image analysis, their performance and adoption remain limited due to the lack of a robust ecosystem, insufficient toolsets, and the absence of…
This article concludes a three-part series developing a self-consistent theoretical framework of the electromechanics of lipid membranes at the continuum scale. Owing to their small thickness, lipid membranes are commonly modeled as…
We derive a continuum mechanical model to capture the morphological changes occurring at the pretumoral stage of epithelial tissues. The proposed model aims to investigate the competition between the bulk elasticity of the epithelium and…
Active nematics are a class of far-from-equilibrium materials characterized by local orientational order of force-generating, anisotropic constitutes. Traditional methods for predicting the dynamics of active nematics rely on hydrodynamic…
An introductory exposition of the virtual element method (VEM) is provided. The intent is to make this method more accessible to those unfamiliar with VEM. Familiarity with the finite element method for solving 2D linear elasticity problems…
We explore the recently-proposed Virtual Element Method (VEM) for numerical solution of boundary value problems on arbitrary polyhedral meshes. More specifically, we focus on the elasticity equations in three-dimensions and elaborate upon…
In various applications, such as virtual reality and gaming, simulating the deformation of soft tissues in the human body during interactions with external objects is essential. Traditionally, Finite Element Methods (FEM) have been employed…
In this paper, we introduce a novel convex formulation that seamlessly integrates the Material Point Method (MPM) with articulated rigid body dynamics in frictional contact scenarios. We extend the linear corotational hyperelastic model…
To understand cell migration, it is crucial to gain knowledge on how cells exert and integrate forces on/from their environment. A quantity of prime interest for biophysicists interested in cell movements modeling is the intracellular…
Collective cell migration plays a central role in tissue development, morphogenesis, wound repair and cancer progression. With the growing realization that physical forces mediate cell motility in development and physiology, a key…
Analog Content Addressable Memories (aCAMs) have proven useful for associative in-memory computing applications like Decision Trees, Finite State Machines, and Hyper-dimensional Computing. While non-volatile implementations using FeFETs and…
Collective cell migration is crucial in many biological processes such as wound healing, tissue morphogenesis, and tumor progression. The leading front of a collective migrating epithelial cell layer often destabilizes into multicellular…