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We introduce a stochastic agent-based model for the flocking dynamics of self-propelled particles that exhibit velocity-alignment interactions with neighbours within their field of view. The stochasticity in the dynamics of the model arises…
Transport networks play a key role across four realms of eukaryotic life: slime molds, fungi, plants, and animals. In addition to the developmental algorithms that build them, many also employ adaptive strategies to respond to stimuli,…
We study the effects of fast spatial movement of molecules on the dynamics of chemical species in a spatially heterogeneous chemical reaction network using a compartment model. The reaction networks we consider are either single- or…
Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learning theory, chemical reaction network theory, and statistical…
Active transport of biomolecular condensates and cell migration in collectives are fundamental to development, homeostasis, and processes such as cancer progression, wound healing, and infection response. Yet how these assemblies are…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
The relaxation of an elastic network, constructed by a contact map of a fractal (crumpled) polymer globule is investigated. We found that: i) the slowest mode of the network is separated from the rest of the spectrum by a wide gap, and ii)…
In this study, we performed comprehensive morphological investigations of the spontaneous formations of effective network structures among elements in coupled logistic maps, specifically with a delayed connection change. Our proposed model…
We study the formation of trails in populations of self-propelled agents that make oriented deposits of pheromones and also sense such deposits to which they then respond with gradual changes of their direction of motion. Based on extensive…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
Active solids combine internal active driving with elasticity to realize states with nonequilibrium mechanics and autonomous motion. They are often studied in overdamped settings, e.g., in soft materials, and the role of inertia is less…
This paper introduces a model of self-organization between communication and topology in social networks, with a feedback between different communication habits and the topology. To study this feedback, we let agents communicate to build a…
Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
Formation of spatial patterns of cells is a recurring theme in biology and often depends on regulated cell motility. Motility of M. xanthus depends on two motility machineries: the S-engine and A-engine. Moving M. xanthus cells can organize…
We show that driven dislocation assemblies exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials.…
We present a model for the time evolution of network architectures based on dynamical systems. We show that the evolution of the existence of a connection in a network can be described as a stochastic non-markovian telegraphic signal…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
Coarse-grained modeling in molecular simulations serves not only to extend accessible time and length scales beyond atomistic limits, but also to reduce high-dimensional chemical data to low-dimensional representations that expose the…
Cells are constantly exposed to diverse stimuli-chemical, mechanical, or electrical-that guide their movement. In physiological conditions, these signals often overlap, as seen during infections, where neutrophils and dendritic cells…