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Computer simulations offer a robust toolset for exploring complex systems across various disciplines. A particularly impactful approach within this realm is Agent-Based Modeling (ABM), which harnesses the interactions of individual agents…
Plasmodium of Physarum polycephalum is a single cell visible by unaided eye. During its foraging behavior the cell spans spatially distributed sources of nutrients with a protoplasmic network. Geometrical structure of the protoplasmic…
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…
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…
Using a Multi-agent systems paradigm, the present project develops, validates and exploits a computational $\textit{testbed}$ that simulates micro-biological complex systems, namely the aggregation patterns of the social amoeba…
Large Language Model (LLM) agents struggle with long-horizon software engineering tasks due to "Context Bloat." As interaction history grows, computational costs explode, latency increases, and reasoning capabilities degrade due to…
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources…
Recent advances in computing architectures and networking are bringing parallel computing systems to the masses so increasing the number of potential users of these kinds of systems. In particular, two important technological evolutions are…
We describe several techniques for using bulk matter for special purpose computation. In each case it is necessary to use an evolutionary algorithm to program the substrate on which the computation is to take place. In addition, the…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
A primary motivation for our research in digital ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
Recent advances in large language models (LLMs) transform how machine learning (ML) pipelines are developed and evaluated. LLMs enable a new type of workload, agentic pipeline search, in which autonomous or semi-autonomous agents generate,…
World models have recently attracted growing interest in Multi-Agent Reinforcement Learning (MARL) due to their ability to improve sample efficiency for policy learning. However, accurately modeling environments in MARL is challenging due…
This work examines the integration of large language models (LLMs) into multi-agent simulations by replacing the hard-coded programs of agents with LLM-driven prompts. The proposed approach is showcased in the context of two examples of…
We introduce a multicrossmodal LLM-agent framework motivated by the growing volume and diversity of materials-science data ranging from high-resolution microscopy and dynamic simulation videos to tabular experiment logs and sprawling…
Soft solids and their surface deformations control the response of many natural and artificial systems. Yet, their underlying properties are vigorously debated, particularly for polymer networks. While molecular-scale theories predict no…
The field of artificial intelligence has significantly advanced over the past decades, inspired by discoveries from the fields of biology and neuroscience. The idea of this work is inspired by the process of self-organization of cortical…
This article explores the dynamic influence of computational entities based on multi-agent systems theory (SMA) combined with large language models (LLM), which are characterized by their ability to simulate complex human interactions, as a…
Agent-based modelling (ABM), simulation (ABS), and distributed computation (ABC) are established methods. The Internet and Web-based technologies are suitable carriers. This paper is a technical report with some tutorial aspects of the…
This paper investigates the integration of cognitive agents powered by Large Language Models (LLMs) within the Scaled Agile Framework (SAFe) to reinforce software project management. By deploying virtual agents in simulated software…