Related papers: Agent-Based Modeling of Intracellular Transport
The use of oncolytic viruses as cancer treatment has received considerable attention in recent years, however the spatial dynamics of this viral infection is still poorly understood. We present here a stochastic agent-based model describing…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
Agent-based models are a natural choice for modeling complex social systems. In such models simple stochastic interaction rules for a large population of individuals can lead to emergent dynamics on the macroscopic scale, for instance a…
Most spreading processes require spatial proximity between agents. The stationary state of spreading dynamics in a population of mobile agents thus depends on the interplay between the time and length scales involved in the epidemic process…
Active matter, as other types of self-organizing systems, relies on the take-up of energy that can be used for different actions, such as active motion or structure formation. Here we provide an agent-based framework to model these…
Agent-based modeling is a computational dynamic modeling technique that may be less familiar to some readers. Agent-based modeling seeks to understand the behaviour of complex systems by situating agents in an environment and studying the…
Vascular networks play a key role in the development, function, and survival of many organisms, facilitating transport of nutrients and other critical factors within and between systems. The development of these vessel networks has been…
Immersive rooms are increasingly popular augmented reality systems that support multi-agent interactions within a virtual world. However, despite extensive content creation and technological developments, insights about perceptually-driven…
A large number of biological systems - from bacteria to sheep - can be described as ensembles of self-propelled agents (active particles) with a complex internal dynamic that controls the agent's behavior: resting, moving slow, moving fast,…
We present a novel model to simulate real social networks of complex interactions, based in a granular system of colliding particles (agents). The network is build by keeping track of the collisions and evolves in time with correlations…
Cell migration is frequently modelled using on-lattice agent-based models (ABMs) that employ the excluded volume interaction. However, cells are also capable of exhibiting more complex cell-cell interactions, such as adhesion, repulsion,…
In this paper, we develop a variational method to track and make predictions about a real-world system from continuous imperfect observations about this system, using an agent-based model that describes the system dynamics. By combining the…
In many biological systems, the movement of individual agents is commonly characterized as having multiple qualitatively distinct behaviors that arise from various biophysical states. This is true for vesicles in intracellular transport,…
Vesicle-mediated secretion of ions or molecules is a central mechanism of cellular communication, for example in processes such as neurotransmission or hormone release. These events are inherently stochastic: vesicle fusions lead to bursts…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
Intracellular transport of large cargoes, such as organelles, vesicles or large proteins, is a complex dynamical process that involves the interplay of ATP-consuming molecular motors, cytoskeleton filaments and the viscoelastic cytoplasm.…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
We consider a partial differential equation model for the growth of heterogeneous cell populations subdivided into multiple distinct discrete phenotypes. In this model, cells preferentially move towards regions where they feel less…
We propose an agent-based model of active flexible rods. Inspired by cytoskeletal flows, we introduce activity by an internal flow that contributes to the dissipative forces. The active force between our agents is central and reciprocal,…