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The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Recent work in the field of multi-agent systems has sought to use techniques and concepts from the field of formal methods to provide rigorous theoretical analysis and guarantees on complex systems where multiple agents strategically…
Biomaterial systems have allowed for the in vitro production of complex, emergent tissue behaviors that were not possible with conventional 2D culture systems allowing for analysis of the normal development as well as disease processes. We…
This is the first part of the comprehensive review, focusing on the historical development of Agent-Based Modeling (ABM) and its classic cases. It begins by discussing the development history and design principles of Agent-Based Modeling…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
Individual traffic significantly contributes to climate change and environmental degradation. Therefore, innovation in sustainable mobility is gaining importance as it helps to reduce environmental pollution. However, effects of new ideas…
Cell cell and cell matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response,…
Innovation diffusion has been studied extensively in a variety of disciplines, including sociology, economics, marketing, ecology, and computer science. Traditional literature on innovation diffusion has been dominated by models of…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Drug discovery is fundamentally a process of inferring the effects of treatments on patients, and would therefore benefit immensely from computational models that can reliably simulate patient responses, enabling researchers to generate and…
Agent-based models (ABMs) simulate complex systems by capturing the bottom-up interactions of individual agents comprising the system. Many complex systems of interest, such as epidemics or financial markets, involve thousands or even…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
Agent-based models (ABMs) and video games, including those taking advantage of virtual reality (VR), have undergone a remarkable parallel evolution, achieving impressive levels of complexity and sophistication. This paper argues that while…
During last decade, multi-level agent-based modeling has received significant and dramatically increasing interest. In this article we present a comprehensive and structured review of literature on the subject. We present the main…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
The diffusion model has recently emerged as a potent approach in computer vision, demonstrating remarkable performances in the field of generative artificial intelligence. Capable of producing high-quality synthetic images, diffusion models…
Dynamical systems theory describes how interacting quantities change over time and space, from molecular oscillators to large-scale biological patterns. Such systems often involve nonlinear feedbacks, delays, and interactions across scales.…