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Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
We study the emergence of the collective spatio-temporal macroscopic properties of the immune system, by representing individually the elementary interactions between its microscopic components (antibodies, antigens, cytokines). The results…
While recent advances in AI have transformed protein structure prediction, protein function is also strongly influenced by the thermodynamic and kinetic features encoded in its underlying free-energy surface. Here, we propose a…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction…
Microfluidics provides a powerful and versatile technology to accurately control spatial and temporal conditions for cell culturing and can therefore be used to study cellular responses to gradients. Here we use Lattice Boltzmann methods…
While it is commonly observed that the shape dynamics of mammalian cells can undergo large random fluctuations, theoretical models aiming at capturing cell mechanics often focus on the deterministic part of the motion. In this paper, we…
The movement of ionic solutions is an essential part of biology and technology. Fluidics, from nano- to micro- to microfluidics, is a burgeoning area of technology which is all about the movement of ionic solutions, on various scales. Many…
Hash Chemistry, a minimalistic artificial chemistry model of open-ended evolution, has recently been extended to non-spatial and cellular versions. The non-spatial version successfully demonstrated continuous adaptation and unbounded growth…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…
Self-propelled colloidal particles exhibit rich non-equilibrium phenomena and have promising applications in fields such as drug delivery and self-assembled active materials. Previous experimental and theoretical studies have shown that…
Chemical reactions-based microfluidic circuits are expected to provide new opportunities to perform signal processing functions over molecular domain. To realize this vision, in this article, we exploit and present the digital signal…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as…
Microfiltration technology is a widely used engineering strategy for fresh water production and water treatment. The major concern in many applications is the formation of a biological fouling layer leading to increased hydraulic resistance…
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…