Related papers: A Spatial Filtering Approach to Biological Pattern…
The migratory dynamics of cells can be influenced by the complex micro-environment through which they move. It remains unclear how the motility machinery of confined cells responds and adapts to their micro-environment. Here, we propose a…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
Tissue dynamics play a crucial role in biological processes ranging from inflammation to morphogenesis. However, these noisy multicellular dynamics are notoriously hard to predict. Here, we introduce a biomimetic machine learning framework…
We propose a simple adaptive-network model describing recent swarming experiments. Exploiting an analogy with human decision making, we capture the dynamics of the model by a low-dimensional system of equations permitting analytical…
It is becoming increasingly appreciated that the signal transduction systems used by eukaryotic cells to achieve a variety of essential responses represent highly complex networks rather than simple linear pathways. While significant effort…
Dynamical patterns in complex networks of coupled oscillators are both of theoretical and practical interest, yet to fully reveal and understand the interplay between pattern emergence and network structure remains to be an outstanding…
Microscale fluid flows generated by ensembles of beating eukaryotic flagella are crucial to fundamental processes such as development, motility and sensing. Despite significant experimental and theoretical progress, the underlying physical…
This work proposes to model the space environment as a stochastic dynamic network where each node is a group of objects of a given class, or species, and their relationship is represented by stochastic links. A set of stochastic dynamic…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
Biological systems (among others) may respond to a large variety of distinct external stimuli, or signals. These perturbations will generally be presented to the system not singly, but in various combinations, so that a proper understanding…
This paper describes how realistic neuromorphic networks can have their connectivity fully characterized in analytical fashion. By assuming that all neurons have the same shape and are regularly distributed along the two-dimensional…
The symbiotic branching model describes the dynamics of a spatial two-type population, where locally particles branch at a rate given by the frequency of the other type combined with nearest-neighbour migration. This model generalizes…
We review the mathematical formalism underlying the modelling of stochasticity in biological systems. Beginning with a description of the system in terms of its basic constituents, we derive the mesoscopic equations governing the dynamics…
We introduce and analyze several aspects of a new model for cell differentiation. It assumes that differentiation of progenitor cells is a continuous process. From the mathematical point of view, it is based on partial differential…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
We show that when cells communicate by contact-mediated interactions, heterogeneity in cell shapes and sizes leads to qualitatively distinct collective behavior in the tissue. For inter-cellular coupling that implements lateral inhibition,…
The complex physics involved in atmospheric turbulence makes it very difficult for ground-based astronomy to build accurate scintillation models and develop efficient methodologies to remove this highly structured noise from valuable…
Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene…
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…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…