Related papers: Converting a Systems Dynamic Model to an Agent-bas…
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…
Agent-based models provide a flexible framework that is frequently used for modelling many biological systems, including cell migration, molecular dynamics, ecology, and epidemiology. Analysis of the model dynamics can be challenging due to…
We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of…
There is great potential to be explored regarding the use of agent-based modelling and simulation as an alternative paradigm to investigate early-stage cancer interactions with the immune system. It does not suffer from some limitations of…
Single species population models and discrete stochastic gene frequency models are two standards of mathematical biology important for the evolution of populations. An agent based model is presented which reproduces these models and then…
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,…
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…
This thesis presents the theoretical, conceptual and methodological aspects that support the modeling of dynamical systems (DS) by using several agents. The modeling approach permits the assessment of properties representing order, change,…
Agent-based models capture heterogeneity among individuals in a population and are widely used in studies of multi-cellular systems, disease, epidemics and demography to name a few. However, existing frameworks consider discrete time-step…
In multicellular organisms, patterns of gene expression are established in response to gradients of signaling molecules. During fly development in early Drosophila embryos, the Bicoid (Bcd) morphogen gradient is established within the first…
The predetermination, formation and maintenance of the primary morphogenetic gradient (bicoid gradient) of the early Drosophila embryo involves many interrelated processes. Here we focus on a system-biological analysis of the processes of…
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…
Axes of polarity (and primary morphogenetic gradients) are established in the oocyte - early embryo through active transport and localization of maternal factors. It is the oocyte - syncytial embryo of Drosophila (D. melanogaster) that is a…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Von Neuman's work on universal machines and the hardware development have allowed the simulation of dynamical systems through a large set of interacting agents. This is a bottom-up approach which tries to derive global properties of a…
Agent-based modeling (ABM) is a powerful computational approach for studying complex biological and biomedical systems, yet its widespread use remains limited by significant computational demands. As models become increasingly…
Spatial agent-based models are increasingly used to investigate the evolution of solid tumours subject to localised cell-cell interactions and microenvironmental heterogeneity. Here we present a non-technical step by step guide to…
Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always…
Skin contraction is an important biophysical process that takes place during and after the recovery of deep tissue injury. This process is mainly caused by fibroblasts (skin cells) and myofibroblasts (differentiated fibroblasts) that exert…
In order to grasp the features arising from cellular discreteness and individuality, in large parts of cell tissue modelling agent-based models are favoured. The subclass of off-lattice models allows for a physical motivation of the…