Related papers: A modeling and simulation language for biological …

Membrane computing is a well-established and successful research field which belongs to the more general area of molecular computing. Membrane computing aims at defining parallel and non-deterministic computing models, called membrane…

Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…

Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…

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…

The response of cells during spreading and motility is dictated by several multi-physics events, which are triggered by extracellular cues and occur at different time-scales. For this sake, it is not completely appropriate to provide a cell…

In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…

Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…

In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…

Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…

Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…

Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…

The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…

Many computer models such as cellular automata and artificial neural networks have been developed and successfully applied. However, in some cases, these models might be restrictive on the possible solutions or their solutions might be…

Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…

Traditional top-down robotic design often lacks the adaptability needed to handle real-world complexities, prompting the need for more flexible approaches. Therefore, this study introduces a novel cellular plasticity model tailored for…

The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…

Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…

In this paper, we describe a computational model for motion events in natural language that maps from linguistic expressions, through a dynamic event interpretation, into three-dimensional temporal simulations in a model. Starting with the…

Models of areas of physics in terms of cellular automata have become increasingly popular. Cellular automata (CAs) support the modeling of systems with discrete state component values and enforce the comprehensive specification of the…

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…