Related papers: Dynamical patterns of p53 states driven by PML
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
A chain of connected genes with activation-repression links is analysed. It is shown that for various promoter activity functions (parametrised by Hill coefficient) the equations describing the concentrations of transcription factors, are…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
We studied in silico effects of structural stress in Mycoplasma pneumoniae, a genome-reduced model bacterial organism, by tracking the damage propagating on its metabolic network after a deleterious perturbation. First, we analyzed failure…
Mobile microscopic bodies, such as motile cells, can be modelled phenomenologically as ``active particles'' which can move against external forces by depleting an internal energy depot. The microscopic mechanisms underlying such ``active''…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
Dynamic mitigation is presented for filamentation instability and magnetic reconnection in a plasm driven by a wobbling electron sheet current. The wobbling current introduces an oscillating perturbation and smooths the perturbation. The…
Using DNA microarray and cluster analysis of expressed genes in a cloned line (M1-t-p53) of myeloid leukemic cells, we have analyzed the expression of genes that are preferentially expressed in different normal tissues. Clustering of 547…
Cell polarization is a critical process that separates molecular species into two distinct regions in prokaryotic and eukaryotic cells, guiding biological processes such as cell division and cell differentiation. Although several underlying…
Endothelial cells are responsible for the formation of the capillary blood vessel network. We describe a system of endothelial cells by means of two-dimensional molecular dynamics simulations of point-like particles. Cells' motion is…
Recent advances in mechanistic interpretability have revealed that large language models (LLMs) develop internal representations corresponding not only to concrete entities but also distinct, human-understandable abstract concepts and…
In this article, we will see a new approach to study the impact of a small microscopic population of cancer cells on a macroscopic population of healthy cells, with an example inspired by pathological hematopoiesis. Hematopoiesis is the…
Biological systems have the unique ability to self-organize and generate autonomous motion and work. Motivated by this, we investigate a 2D model colloidal network that can repeatedly transition between disordered states of low connectivity…
Pancreatic \b{eta}-cells secrete insulin in response to blood sugar levels to maintain glucose homeostasis. This vital insulin exocytosis is controlled by the cell's bursting behaviours, which are regulated by tight bidirectional coupling…
Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates…
In contrary to the common belief that only one strand of the pre-miRNA is active (usually the 5p one that is the more abundant) while the second one (miRNA*) is discarded, functional 5p and 3p have been observed for many miRNAs. Among those…
Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of a process known as spontaneous immortalization. In this process a generic series of cell state transitions occur in…
Cell migration is a fundamental process involved in physiological phenomena such as the immune response and morphogenesis, but also in pathological processes, such as the development of tumor metastasis. These functions are effectively…
We propose a statistical model of a large random network with high connectivity in order to describe the behavior of {\it E.\,coli} cells after exposure to acute stress. The building blocks of this network are feedback cycles typical of the…