Related papers: A Phase-field Model for Apoptotic Cell Death
The kinetics of an initially undercooled solid-liquid melt is studied by means of a generalized Phase Field model, which describes the dynamics of an ordering non-conserved field phi (e.g. solid-liquid order parameter) coupled to a…
In this paper, we bring together our efforts in identifying and understanding nonequilibrium phase segregation driven by active processes in the living cell, with special focus on the segregation of cell membrane components driven by active…
Droplet formation has emerged as an essential concept for the spatiotemporal organisation of biomolecules in cells. However, classical descriptions of droplet dynamics based on passive liquid-liquid phase separation cannot capture the…
Biochemical processes in cells are governed by complex networks of many chemical species interacting stochastically in diverse ways and on different time scales. Constructing microscopically accurate models of such networks is often…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
The paper presents a computational stochastic model of virtual cells irradiation, based on Quasi-Markov Chain Monte Carlo method and using biophysical input. The model is based on a stochastic tree of probabilities for each cell of the…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control…
We propose a multiscale model of the invasion of the extracellular matrix by two types of cancer cells, the differentiated cancer cells and the cancer stem cells. We assume that the epithelial mesenchymal-like transition between them is…
The inverse geometric approach to the modeling of the growth of circular objects revealing required features, such as the velocity of the growth and fractal behavior of their contours, is presented. It enables to reproduce some of the…
We investigate the percolation properties of a two-state (occupied - empty) cellular automaton, where at each time step a cluster of occupied sites is removed and the same number of randomly chosen empty sites are occupied again. We find a…
The phase-field method is reviewed from the general perspective of converting a free boundary problem into a set of coupled partial differential equations. Its main advantage is that it avoids front tracking by using phase fields to locate…
We investigate the convergence of solutions of a recently proposed diffuse interface/phase field model for cell blebbing by means of matched asymptotic expansions. It is a biological phenomenon that increasingly attracts attention by both…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
Despite their potential to address crucial bottlenecks in computing architectures and contribute to the pool of biological inspiration for engineering, pathological biological mechanisms remain absent from computational theory. We hereby…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
Tumor angiogenesis concerns the development of new blood vessels supplying the necessary nutrients for the further development of existing tumor cells. The entire process is complex, involving the production and consumption of chemicals,…
We give a constructive method for realizing an arbitrary directed graph (with no one-cycles) as a heteroclinic or an excitable dynamic network in the phase space of a system of coupled cells of two types. In each case, the system is…
The TNF initiated processes are simulated using our integrative computational model with new quantitative proteomics data obtained on HeLa cell line. In spite of fact, that the model development is based on limited experimental information,…