Related papers: Self-organization principles of intracellular patt…
We investigate the Susceptible-Infectious-Recovered contagion dynamics in a system of self-propelled particles with polar alignment. Using agent-based simulations, we analyze the outbreak process for different combinations of the spatial…
Biological circuits such as neural or gene regulation networks use internal states to map sensory input to an adaptive repertoire of behavior. Characterizing this mapping is a major challenge for systems biology, and though experiments that…
We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…
Self-organized criticality has been proposed to be a universal mechanism for the emergence of scale-free dynamics in many complex systems, and possibly in the brain. While such scale-free patterns were identified experimentally in many…
The spatial organization of individuals and their interactions in communities are important factors known to preserve diversity in many complex systems. Inspired by metapopulation models from ecology, we study opinion formation using a…
We give a description of cell diffusion in a soft tissue, paying special attention to the coupling of force, matter, and microforce balance laws through a suitable dissipation principle. To this end, we cast our framework into a multi-level…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
Active matter exhibits remarkable collective behavior in which flows, continuously generated by active particles, are intertwined with the orientational order of these particles. The relationship remains poorly understood as the activity…
Cell polarization is a critical process that separates molecular species into two distinct regions in prokaryotic and eukaryotic cells, guiding biological processes such as cell division and cell differentiation. Although several underlying…
The actin and microtubule cytoskeletons are vital structures for cell growth and development across all species. While individual molecular mechanisms underpinning actin and microtubule dynamics have been intensively studied, principles…
Self-organization phenomena in ensembles of self-propelled particles open pathways to the synthesis of new dynamic states not accessible by traditional equilibrium processes. The challenge is to develop a set of principles that facilitate…
Large networks of spiking neurons show abrupt changes in their collective dynamics resembling phase transitions studied in statistical physics. An example of this phenomenon is the transition from irregular, noise-driven dynamics to…
We investigate the self-organization of point-particles with short-range interactions modeled via simple 1D and 2D Hubbard-like models. We show how various properties emerge such as, boson-like ordering leading to topological structures in…
From a mathematical point of view self-organization can be described as patterns to which certain dynamical systems modeling social dynamics tend spontaneously to be attracted. In this paper we explore situations beyond self-organization,…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
We consider a reaction-diffusion system with discontinuous reaction terms modeled by non-ideal relays. The system is motivated by an epigenetic population model of evolution of two-phenotype bacteria which switch phenotype in response to…
We study the dynamics of pattern formation in a minimal model for active mixtures made of microtubules and molecular motors. We monitor the evolution of the (conserved) microtubule density and of the (non-conserved) nematic order parameter,…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Cytoskeletons are self organized networks based on polymerized proteins, actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality…