Related papers: Building multiscale models with PhysiBoSS, an agen…
Agentic AI systems have gained significant attention for their ability to autonomously perform complex tasks. However, their reliance on well-prepared tools limits their applicability in the medical domain, which requires to train…
Scalable manufacturing of human induced pluripotent stem cells (iPSCs) is essential for industrial-scale production of cell therapies and regenerative medicines. However, the 3D aggregate cultures used in manufacturing exhibit substantial…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
The advent of Large Language Models (LLMs) has significantly transformed tasks across Software Engineering. In the context of Business Process Management, LLMs are now being explored as tools to derive process models directly from textual…
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…
Despite the wealth of single-cell multi-omics data, it remains challenging to predict the consequences of novel genetic and chemical perturbations in the human body. It requires knowledge of molecular interactions at all biological levels,…
Von Neuman's work on universal machines and the hardware development have allowed the simulation of dynamical systems through a large set of interacting agents. This is a bottom-up approach which tries to derive global properties of a…
Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Agent-based modeling is indispensable for studying complex systems across many domains. However, existing simulation platforms exhibit two major issues: performance and modularity. Low performance prevents simulations with a large number of…
Large Language Models (LLMs) and Visual Language Models (VLMs) are attracting increasing interest due to their improving performance and applications across various domains and tasks. However, LLMs and VLMs can produce erroneous results,…
Agent-based modeling (ABM) is a powerful computational approach for studying complex biological and biomedical systems, yet its widespread use remains limited by significant computational demands. As models become increasingly…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Multi-agent approach has become popular in computer science and technology. However, the conventional models of multi-agent and multicomponent systems implicitly or explicitly assume existence of absolute time or even do not include time in…
Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a…
Mathematical models are indispensable to the system biology toolkit for studying the structure and behavior of intracellular signaling networks. A common approach to modeling is to develop a system of equations that encode the known biology…
Agent-based simulators (ABS) are a popular epidemiological modelling tool to study the impact of various non-pharmaceutical interventions in managing an epidemic in a city (or a region). They provide the flexibility to accurately model a…
Many models in natural and social sciences are comprised of sets of inter-acting entities whose intensity of interaction decreases with distance. This often leads to structures of interest in these models composed of dense packs of…
Agent-based modelling is a valuable approach for systems whose behaviour is driven by the interactions between distinct entities. They have shown particular promise as a means of modelling crowds of people in streets, public transport…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…