Related papers: Pattern Formation Beyond Turing: Physical Principl…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
We study pattern formation in a chemotaxis model of bacteria and soil carbon dynamics as an example system where transient dynamics can give rise to pattern formation outside of Turing unstable regimes. We use a detailed analysis of the…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
The problem of pattern formation in a generic two species reaction--diffusion model is studied, under the hypothesis that only one species can diffuse. For such a system, the classical Turing instability cannot take place. At variance, by…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
In this paper we consider mathematical modeling of the dynamics of self-organized patterning of spatially confined human embryonic stem cells (hESCs) treated with BMP4 (gastruloids) described in recent experimental works. In the first part…
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…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
The work is devoted to the analysis of cell population dynamics where cells make a choice between differentiation and apoptosis. This choice is based on the values of intracellular proteins whose concentrations are described by a system of…
Among living organisms, there are species that change their patterns on their body surface during their growth process and those that maintain their patterns. Theoretically, it has been shown that large-scale species do not form distinct…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Spatio-temporal patterns emerging from an initial quiescent, uniform state is a phenomenon observed in many dynamical systems sustained far from thermodynamic equilibrium, the practical application of which has only recently begun to be…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Turing patterns are fundamental in biophysics, emerging from short-range activation and long-range inhibition processes. However, their paradigm is based on diffusive transport processes, which yields Turing patters that are less sharp than…
Dynamical reaction-diffusion processes and meta-population models are standard modeling approaches for a wide variety of phenomena in which local quantities - such as density, potential and particles - diffuse and interact according to the…
The biopolymers actin and microtubules are often in an ongoing assembling/disassembling state far from thermal equilibrium. Above a critical density this leads to spatially periodic patterns, as shown by a scaling argument and in terms of a…
Pattern formation is ubiquitous in nature and the mechanism widely-accepted to underlay them is based on the Turing instability, predicted by Alan Turing decades ago. This is a non-trivial mechanism that involves nonlinear interaction terms…
We consider the design of a pattern recognition that matches templates to images, both of which are spatially sampled and encoded as temporal sequences. The image is subject to a combination of various perturbations. These include ones that…
The patterns observed on the body surface of living organisms have traditionally been attributed solely to ecological strategies. However, this study investigates a fascinating phenomenon in Pelodiscus sinensis, where patterns formed on the…
We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing…