Related papers: Agent-Based Modeling of Intracellular Transport
Agent-based modelling is a valuable approach for systems whose behaviour is driven by the interactions between distinct entities. They have shown particular promise as a means of modelling crowds of people in streets, public transport…
Spatial patterns arising from the collective behavior of individual agents are present across biological systems. While agent-based models offer a natural framework for uncovering unknown agent (e.g., cell) interactions, these stochastic…
We propose a model to show the self-assembling of network-like structures between a set of nodes without using preexisting positional information or long-range attraction of the nodes. The model is based on Brownian agents that are capable…
Lattice-based random walk models are widely used to study populations of migrating cells with motility bias and proliferation. Crowding is typically represented by volume exclusion, where each lattice site can be occupied by at most one…
Intermediate filaments form an essential structural network, spread throughout the cytoplasm and play a key role in cell mechanics, intracellular organization and molecular signaling. The maintenance of the network and its adaptation to the…
In this paper, we analyze the behavior of a multi-agent system driven by the interactions of agents within a competitive environment. To achieve this, we describe the transition probabilities that underlie the system's stochastic nature. We…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
We find a statistical mechanism that can adjust orientations of intracellular filaments to cell geometry in absence of organizing centers. The effect is based on random and isotropic filament (de-)polymerization dynamics and is independent…
Perceiving the surrounding environment in terms of objects is useful for any general purpose intelligent agent. In this paper, we investigate a fundamental mechanism making object perception possible, namely the identification of…
Agent modeling is a critical component in developing effective policies within multi-agent systems, as it enables agents to form beliefs about the behaviors, intentions, and competencies of others. Many existing approaches assume access to…
We propose a stochastic model for intracellular transport processes associated with the activity of molecular motors. This out-of-equilibrium model, based on a generalized Langevin equation, considers a particle immersed in a viscoelastic…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
Modelling and computational methods have been essential in advancing quantitative science, especially in the past two decades with the availability of vast amount of complex, voluminous, and heterogeneous data. In particular, there has been…
Modeling how human moves in the space is useful for policy-making in transportation, public safety, and public health. Human movements can be viewed as a dynamic process that human transits between states (\eg, locations) over time. In the…
Pattern formation often occurs in confined systems, yet how boundaries shape patterning dynamics is unclear. We develop techniques to analyze confinement effects in nonlocal advection-diffusion equations, which generically capture the…
We introduce a multi-species lattice gas model for motor protein driven collective cargo transport on cellular filaments. We use this model to describe and analyze the collective motion of interacting vesicle cargoes being carried by…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
We investigate in detail a recent model of colliding mobile agents [Phys. Rev. Lett.~96, 088702], used as an alternative approach to construct evolving networks of interactions formed by the collisions governed by suitable dynamical rules.…
Agent-Based Models (ABMs) are powerful tools for studying emergent properties in complex systems. In ABMs, agent behaviors are governed by local interactions and stochastic rules. However, these rules are, in general, non-differentiable,…
Collectively coordinated cell migration plays a role in tissue embryogenesis, cancer, homeostasis and healing. To study these processes, different cell-based modelling approaches have been developed, ranging from lattice-based cellular…