Related papers: Agent-Based Modeling of Intracellular Transport

Agent-based models typically treat systems in isolation, discarding environmental coupling as either computationally prohibitive or dynamically irrelevant. We demonstrate that this neglect misses essential physics: environmental degrees of…

We give a description of cell diffusion in a soft tissue, paying special attention to the coupling of force, matter, and microforce balance laws through a suitable dissipation principle. To this end, we cast our framework into a multi-level…

In this work we introduce an approach for modeling and analyzing collective behavior of a group of agents using moments. We represent the group of agents via their distribution and derive a method to estimate the dynamics of the moments. We…

Based on symmetry consideration of migration and shape deformations, we formulate phenomenologically the dynamics of cell crawling in two dimensions. Forces are introduced to change the cell shape. The shape deformations induce migration of…

Predicting the motion of multiple agents is necessary for planning in dynamic environments. This task is challenging for autonomous driving since agents (e.g. vehicles and pedestrians) and their associated behaviors may be diverse and…

The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…

The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…

Living cells exhibit multi-mode transport that switches between an active, self-propelled motion and a seemingly passive, random motion. Cellular decision-making over transport mode switching is a stochastic process that depends on the…

We introduce a stochastic agent-based model for the flocking dynamics of self-propelled particles that exhibit velocity-alignment interactions with neighbours within their field of view. The stochasticity in the dynamics of the model arises…

We study the dynamics of individual agents in some kinetic models of wealth exchange, particularly, the models with savings. For the model with uniform savings, agents perform simple random walks in the "wealth space". On the other hand, we…

Exploring the collective behavior of interacting entities is of great interest and importance. Rather than focusing on static and uniform connections, we examine the co-evolution of diverse mobile agents experiencing varying interactions…

Reaction-diffusion systems have been proposed as a model for pattern formation and morphogenesis. The Fickian diffusion typically employed in these constructions model the Brownian motion of particles. The biological and chemical elements…

Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of…

Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…

Tumor-immune interactions are central to cancer progression and treatment outcomes. In this study, we present a stochastic agent-based model that integrates cellular heterogeneity, spatial cell-cell interactions, and drug resistance…

The rapidly growing field of network analytics requires data sets for use in evaluation. Real world data often lack truth and simulated data lack narrative fidelity or statistical generality. This paper presents a novel, mixed-membership,…

Starting from full-dimensional models of solute transport, we derive and analyze multi-dimensional models of time-dependent convection, diffusion, and exchange in and around pulsating vascular and perivascular networks. These models are…

This paper considers particle propagation in a cylindrical molecular communication channel, e.g. a simplified model of a blood vessel. Emitted particles are influenced by diffusion, flow, and a vertical force induced e.g. by gravity or…

In real-world systems, phase transitions often materialize abruptly, making it difficult to design appropriate controls that help uncover underlying processes. Some agent-based computational models display transformations similar to phase…