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Understanding the emergence of biological structures and their changes is a complex problem. On a biochemical level, it is based on gene regulatory networks (GRN) consisting on interactions between the genes responsible for cell…
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…
A central challenge in modeling neurodegenerative diseases is connecting cellular-level mechanisms to tissue-level pathology, in particular to determine whether pathology is driven primarily by cell-autonomous triggers or by propagation…
Many cellular processes rely on the cell's ability to transport material to and from the nucleus. Networks consisting of many microtubules and actin filaments are key to this transport. Recently, the inhibition of intracellular transport…
We study time-dependent density segregation of granular mixtures flowing over an inclined plane. Discrete Element Method (DEM) simulations in a periodic box are performed for granular mixtures of same size and different density particles…
Collective guidance of out-of-equilibrium systems without using external fields is a challenge of paramount importance in active matter, ranging from bacterial colonies to swarms of self-propelled particles. Designing strategies to guide…
We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin…
A race is held between ten species of organic gas molecules on a graphene substrate driven by thermal gradients via molecular dynamics. Fast conduction of the molecules is observed with selectivity for aromatic compounds. This selectivity…
Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary…
In one-dimensional, heterogeneous systems, the whole traffic dynamics depend strongly on the behavior of the leading vehicle. This result holds for a class of vehicular traffic models satisfying the following properties. The interactions…
Many biological active agents respond to gradients of environmental cues by redirecting their motion. Besides the well-studied prominent examples such as photo- and chemotaxis, there has been considerable recent interest in topotaxis, i.e.\…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
In both biological and artificial systems, concentration gradients can serve as a convenient mechanism for manipulating particles and generating motility. Particles that interact with a solute will move along its gradient; if they…
We consider one-dimensional asymmetric exclusion processes with a simple attractive interaction, where the distance between consecutive particles is not allowed to exceed a certain limit and investigate the consequences of this coupling on…
This paper deals with a model of cellular growth called "Epigenetic Tracking", whose key features are: i) distinction bewteen "normal" and "driver" cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the…
How does growth encode form in developing organisms? Many different spatiotemporal growth profiles may sculpt tissues into the same target 3D shapes, but only specific growth patterns are observed in animal and plant development. In…
By generalizing a class of models recently introduced to account for protracted transients in biological systems, we identify a novel mechanism for hyperuniformity. In this model, competition of particles over a shared resource guides the…
Diffusion processes are central to human interactions. One common prediction of the current modeling frameworks is that initial spreading dynamics follow exponential growth. Here, we find that, ranging from mobile handsets to automobiles,…
Mechanistic interpretability of biological foundation models has relied on selective feature sampling, pairwise interaction testing, and observational trajectory analysis. Each of these can introduce systematic bias. Here we present three…
Transport properties are among the defining characteristics of many important phases in condensed matter physics. In the presence of strong correlations they are difficult to predict even for model systems like the Hubbard model. In real…