Related papers: Quantifying different modeling frameworks using to…
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…
Many complex systems can be modeled as multiagent systems in which the constituent entities (agents) interact with each other. The global dynamics of such a system is determined by the nature of the local interactions among the agents.…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Biological science produces large amounts of data in a variety of formats, which necessitates the use of computational tools to process, integrate, analyse, and glean insights from the data. Researchers who use computational biology tools…
Agent-based models, particularly those applied to financial markets, demonstrate the ability to produce realistic, simulated system dynamics, comparable to those observed in empirical investigations. Despite this, they remain fairly…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
In the present article we emphasize the importance of modeling time in the context of agent-based models. To this end, we present a (selective) survey of the Cellular Automata-literature on updating and draw parallels to the issue of agent…
Geophysical models of the atmosphere and ocean invariably involve parameterizations. These represent two distinct areas: Subgrid processes that the model cannot resolve, and diabatic sources in the equations, due to radiation for example.…
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…
Traffic models based on cellular automata have high computational efficiency because of their simplicity in describing unrealistic vehicular behavior and the versatility of cellular automata to be implemented on parallel processing. On the…
As zebrafish develop, black and gold stripes form across their skin due to the interactions of brightly colored pigment cells. These characteristic patterns emerge on the growing fish body, as well as on the anal and caudal fins. While…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
We introduce a new method based on cellular automata dynamics to study stochastic growth equations. The method defines an interface growth process which depends on height differences between neighbors. The growth rule assigns a probability…
Modern business and economic datasets often exhibit nonlinear, multi-scale structures that traditional linear tools under-represent. Topological Data Analysis (TDA) offers a geometric lens for uncovering robust patterns, such as connected…
Literature on the modeling and simulation of complex adaptive systems (cas) has primarily advanced vertically in different scientific domains with scientists developing a variety of domain-specific approaches and applications. However,…
The emergence of organized multiscale patterns resulting from convection is ubiquitous, observed throughout different cloud types. The reproduction of such patterns by general circulation models remains a challenge due to the complex nature…
Although tissues are usually studied in isolation, this situation rarely occurs in biology, as cells, tissues, and organs, coexist and interact across scales to determine both shape and function. Here, we take a quantitative approach…
Single-cell gene expression measurements encode variability spanning molecular noise, cell-to-cell heterogeneity, and technical artifacts. Mechanistic stochastic models provide powerful approaches to disentangle these sources, yet inferring…