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Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having 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…
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
In top-down multi-level design methodologies, design descriptions at higher levels of abstraction are incrementally refined to the final realizations. Simulation based techniques have traditionally been used to verify that such model…
When language models answer open-ended problems, they implicitly make hidden decisions that shape their outputs, leaving users with uncontextualized answers rather than a working map of the problem; drawing on multiverse analysis from…
Existing benchmarks for computational materials discovery primarily evaluate static predictive tasks or isolated computational sub-tasks. While valuable, these evaluations neglect the inherently iterative and adaptive nature of scientific…
Active nematics, formed from a liquid crystalline suspension of active force dipoles, are a paradigmatic active matter system whose study provides insights into how chemical driving produces the cellular mechanical forces essential for…
The extracellular matrix (ECM) is a highly complex structure through which biochemical and mechanical signals are transmitted. In processes of cell migration, the ECM also acts as a scaffold, providing structural support to cells as well as…
We present strategic portgraph rewriting as a basis for the implementation of visual modelling and analysis tools. The goal is to facilitate the specification, analysis and simulation of complex systems, using port graphs. A system is…
In this work, we present a computational formulation based on continuum mechanics to study the interaction of fluid membranes embedded with semiflexible filaments. This is motivated by systems in membrane biology, such as cytoskeletal…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Large language models (LLMs), in conjunction with various reasoning reinforcement methodologies, have demonstrated remarkable capabilities comparable to humans in fields such as mathematics, law, coding, common sense, and world knowledge.…
Metamaterials are artificial structures which have recently enabled the realization of novel electromagnetic components with engineered and even unnatural functionalities. Existing metamaterials are specifically designed for a single…
Software-defined metasurfaces are electromagnetically ultra-thin, artificial components that can provide engineered and externally controllable functionalities. The control over these functionalities is enabled by the metasurface…
Bioscientists frequently seek to visualize the biological systems they have empirically characterized and reported in the literature. Realizing such visualizations requires biological structure modeling, an inherently complex process that…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
With the increasing complexity of CPSs, their behavior and decisions become increasingly difficult to understand and comprehend for users and other stakeholders. Our vision is to build self-explainable systems that can, at run-time, answer…
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that…