Related papers: Simulation of stem cell survival in small crypts
We study the population profile in a simple discrete time model of population dynamics. Our model, which is closely related to certain ``bit-string'' models of evolution, incorporates competition for resources via a population dependent…
A revision of Stod\'o{\l}kiewicz's Monte Carlo code is used to simulate evolution of large star clusters. The survey on the evolution of multi-mass N-body systems influenced by the tidal field of a parent galaxy and by stellar evolution is…
We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…
Colorectal cancers are the third most common type of cancer. They originate from intestinal crypts, glands that descend from the intestinal lumen into the underlying connective tissue. Normal crypts are thought to exist in a dynamic…
Monte Carlo simulations are an important tool in statistical physics, complex systems science, and many other fields. An increasing number of these simulations is run on parallel systems ranging from multicore desktop computers to…
Apoptosis, or genetically programmed cell death, is a crucial cellular process that maintains the balance between life and death in cells. The precise molecular mechanism of apoptosis signaling and how these two pathways are differentially…
Single-cell experiments revealed substantial variability in generation times, growth rates but also in birth and division sizes between genetically identical cells. Understanding how these fluctuations determine the fitness of the…
We extend our study of a simple model of biological coevolution to its statistical properties. Staring with a complete description in terms of a master equation, we provide its relation to the deterministic evolution equations used in…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
The competition between cancer cells and immune system cells in inhomogeneous conditions is described at cell scale within the framework of the thermostatted kinetic theory. Cell learning is reproduced by increased cell activity during…
We present long Monte Carlo simulations of a simple model of biological macroevolution in which births, deaths, and mutational changes in the genome take place at the level of individual organisms. The model displays punctuated equilibria…
A numerical technique is introduced that reduces exponentially the time required for Monte Carlo simulations of non-equilibrium systems. Results for the quasi-stationary probability distribution in two model systems are compared with the…
Using a lattice model based on Monte Carlo simulations, we study the role of the reproduction pattern on the fate of an evolving population. Each individual is under the selection pressure from the environment and random mutations. The…
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
A Monte Carlo simulation of chemotactic bacteria is developed on the basis of the kinetic model and is applied to a one-dimensional traveling population wave in a microchannel. In this simulation, the Monte Carlo method, which calculates…
We outline the steps needed in to calibrate the Monte Carlo code in order to perform large scale simulations of real globular clusters. We calibrate the results against $N$-body simulations for $N = 2500$, 10000 and for the old open cluster…
All types of blood cells are formed by differentiation from a small self-maintaining population of pluri-potential stem cells in the bone marrow. Despite abundant information on the molecular aspects of division, differentiation, commitment…
A novel Monte Carlo technique of simulation of spatial fluorescence distribution within the human skin is presented. The computational model of skin takes into account the spatial distribution of fluorophores, which would arise due to the…
Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here we consider the…
We develop a classical Monte Carlo algorithm based on a quasi-classical approximation for a pseudospin S=1 Hamiltonian in real space to construct a phase diagram of a model cuprate with a high Tc. A model description takes into account both…