Related papers: Building multiscale models with PhysiBoSS, an agen…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
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 simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events,…
Large Language Models (LLMs) show promise in biomedicine but lack true causal understanding, relying instead on correlations. This paper envisions causal LLM agents that integrate multimodal data (text, images, genomics, etc.) and perform…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited…
Agent-based modeling and simulation tools provide a mature platform for development of complex simulations. They however, have not been applied much in the domain of mainstream modeling and simulation of computer networks. In this article,…
When designing systems that are complex, dynamic and stochastic in nature, simulation is generally recognised as one of the best design support technologies, and a valuable aid in the strategic and tactical decision making process. A…
This work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performance analysis and include memory management, load balance, and…
How morphogenesis depends on cell properties is an active direction of research. Here, we focus on mechanical models of growing plant tissues, where microscopic (sub)cellular structure is taken into account. In order to establish links…
Computational models and simulations are not just appealing because of their intrinsic characteristics across spatiotemporal scales, scalability, and predictive power, but also because the set of problems in cancer biomedicine that can be…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
Agent-based modeling (ABM) is a well-established paradigm for simulating complex systems via interactions between constituent entities. Machine learning (ML) refers to approaches whereby statistical algorithms 'learn' from data on their…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
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 human brain is one of the most complex living structures in the known Universe. It consists of billions of neurons and synapses. Due to its intrinsic complexity, it can be a formidable task to accurately depict brain's structure and…
Realistic fine-grained multi-agent simulation of real-world complex systems is crucial for many downstream tasks such as reinforcement learning. Recent work has used generative models (GANs in particular) for providing high-fidelity…
The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…