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Mathematical models for systems of interacting agents using simple local rules have been proposed and shown to exhibit emergent swarming behavior. Most of these models are constructed by intuition or manual observations of real phenomena,…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
Reaching consensus in urban planning is a complex process often hindered by prolonged negotiations, trade-offs, power dynamics, and competing stakeholder interests, resulting in inefficiencies and inequities. Advances in large language…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
Agent-based models of disease transmission involve stochastic rules that specify how a number of individuals would infect one another, recover or be removed from the population. Common yet stringent assumptions stipulate interchangeability…
Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize a surface. Physically, swarming is a natural example of active particles that use energy to generate motion. Accordingly,…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
A cellular automata model that describes as limit cases of his parameters the spread of contagious diseases modeled by systems of ordinary or partial differential equations is developed. Periodic features of the behavior of human settlement…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
The design and engineering of molecular communication (MC) components capable of processing chemical concentration signals is the key to unleashing the potential of MC for interdisciplinary applications. By controlling the signaling pathway…
We propose a probabilistic framework for developing computational models of biological neural systems. In this framework, physiological recordings are viewed as discrete-time partial observations of an underlying continuous-time stochastic…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology. The biological nature of chemical signaling makes MC a promising methodology for interdisciplinary applications…
Complex systems have interested researchers across a broad range of fields for many years and as computing has become more accesible and feasible, it is now possible to simulate aspects of these systems. A major point of research is how…
The gradual accumulation of damage and dysregulation during the aging of living organisms can be quantified. Even so, the aging process is complex and has multiple interacting physiological scales -- from the molecular to cellular to whole…
We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model where agents who make decisions using either automatic or…