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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…
Cellular Agent-Based Models are commonly employed to describe a variety biological systems. Over the course of the past years, many modeling tools have emerged which solve particular research questions. In this short opinion piece, we argue…
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…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…
A complex system is made up of many components with many interactions. So the design of systems such as simulation systems, cooperative systems or assistance systems includes a very accurate modelling of interactional and communicational…
Agent-based cellular models simulate tissue evolution by capturing the behavior of individual cells, their interactions with neighboring cells, and their responses to the surrounding microenvironment. An important challenge in the field is…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in…
The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and…
Agent-based modelling and simulation offers a new and exciting way of understanding the world of work. In this paper we describe the development of an agent-based simulation model, designed to help to understand the relationship between…
Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
There are numerous scenarios in which populations of cells migrate in crowded environments. Typical examples include wound healing, cancer growth and embryo development. In these crowded environments cells are able to interact with each…
The article is devoted to the issues of using discrete simulation models for modeling some basic technological processes. In the scientific work, models in the form of multi-agent systems have been investigated, which allow us to consider a…
An agent-based model (ABM) is a computational model in which the local interactions of autonomous agents with each other and with their environment give rise to global properties within a given domain. As the detail and complexity of these…
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…
Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based…
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…
Discrete choice models (DCMs) have been widely utilized in various scientific fields, especially economics, for many years. These models consider a stochastic environment influencing each decision maker's choices. Extensive research has…
The study of system complexity primarily has two objectives: to explore underlying patterns and to develop theoretical explanations. Pattern exploration seeks to clarify the mechanisms behind the emergence of system complexity, while…