Related papers: Bigraphical models for protein and membrane intera…

We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…

The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…

Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…

From multicellular tissues to bacterial colonies, three dimensional cellular structures arise through the interaction of cellular activities and mechanical forces. Simple bacterial communities provide model systems for analyzing such…

Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…

The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their…

Deep learning models have become fundamental tools in drug design. In particular, large language models trained on biochemical sequences learn feature vectors that guide drug discovery through virtual screening. However, such models do not…

Dialectical frameworks are a unifying model of formal argumentation, where argumentative relations between arguments are represented by assigning acceptance conditions to atomic arguments. Their generality allow them to cover a number of…

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…

Bigraphical Reactive Systems (BRSs) are a graph-rewriting formalism describing systems evolving in two dimensions: spatially, e.g. a person in a room, and non-spatially, e.g. mobile phones communicating regardless of location. Despite use…

Building multiscale biological models requires integrating independently developed submodels, which involves sharing variables and coordinating execution. Most existing tools focus on isolated mechanisms and numerical methods, but rarely…

Interaction nets are a graphical model of computation, which has been used to define efficient evaluators for functional calculi, and specifically lambda calculi with patterns. However, the flat structure of interaction nets forces pattern…

Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…

Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins, drugs) and edges represent relational ties among these objects (binds-to, interacts-with, regulates). This…

Currently, biological signaling is envisaged as a combination of activation and movement, triggered by local molecular interactions and molecular diffusion, respectively. However, we here suggest, that other fundamental physical mechanisms…

The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…

Starting from the concept of binary interactions between pairs of particles, a kinetic framework for the description of the action potential dynamics on a neural network is proposed. It consists of two coupled levels: the description of a…

Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…

Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…

Biological membranes and vesicles play a central role in living systems, forming dynamic interfaces that regulate cellular organization and function. Classical descriptions of membrane mechanics that are rooted in equilibrium statistical…