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Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Occupancy of new habitats through dispersion is a central process in nature. In particular, long range dispersal is involved in the spread of species and epidemics, although it has not been previously related with cancer invasion, a process…
Identifying and characterizing mutational paths is an important issue in evolutionary biology and in bioengineering. We here introduce a generic description of mutational paths in terms of the goodness of sequences and of the mutational…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Locating the source that triggers a dynamical process is a fundamental but challenging problem in complex networks, ranging from epidemic spreading in society and on the Internet to cancer metastasis in the human body. An accurate…
Propagating fronts arising from bistable reaction-diffusion equations are a purely deterministic effect. Stochastic reaction-diffusion processes also show front propagation which coincides with the deterministic effect in the limit of small…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Epidemic spreading often occurs in spatially heterogeneous environments, yet how quenched heterogeneity reshapes its onset and critical dynamics remains poorly understood. The diffusive epidemic process, a minimal reaction-diffusion model…
Antimicrobial resistance is an emerging global health crisis that is undermining advances in modern medicine and, if unmitigated, threatens to kill 10 million people per year worldwide by 2050. Research over the last decade has demonstrated…
We study the onset of the propagation failure of wave fronts in systems of coupled cells. We introduce a new method to analyze the scaling of the critical external field at which fronts cease to propagate, as a function of intercellular…
The adoption of individual behavioural patterns is largely determined by stimuli arriving from peers via social interactions or from external sources. Based on these influences, individuals are commonly assumed to follow simple or complex…
A historical dispute in the conceptual underpinnings of evolution is the validity of the gene centered view of evolution. \cite{dawkins,lewontin} We transcend this debate by formalizing the gene centered view as a dynamic version of the…
We consider the dynamics of spatially-distributed, diffusing populations of organisms with antagonistic interactions. These interactions are found on many length scales, ranging from kilometer-scale animal range dynamics with selection…
In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in…
The study of microorganisms, or microbiology, has demonstrated significant development since its inception and is currently a key field of biological sciences that has a huge impact on modern society and scientific research. Over the…
Spreading processes on top of active dynamics provide a novel theoretical framework for capturing emerging collective behavior in living systems. I consider run-and-tumble dynamics coupled with coagulation/decoagulation reactions that lead…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…