Related papers: Simulation of stem cell survival in small crypts
We study time continuous branching processes with exponentially distributed lifetimes, with two types of cells that proliferate according to binary fission. A range of possible system dynamics are considered, each of which is characterized…
In this study, we present a stochastic simulation model designed to explicitly incorporate cell cycle length, overcoming limitations associated with classical compartmental models. Our approach employs a delay mechanism to represent the…
We have developed a new parallel supercomputer code based on Henon's Monte Carlo method for simulating the dynamical evolution of globular clusters. This new code allows us to calculate the evolution of a cluster containing a realistic…
We describe a Monte Carlo simulation study of the magnetic phase diagram of diluted magnetic semiconductors doped with shallow impurities in the low concentration regime. We show that because of a wide distribution of interaction strengths,…
In this paper we use a continuous model to describe the development of a single cell lineage following the committal of stem cells. Three separate controls are implemented in the model, namely the proliferative control of stem cells, the…
We study the effect of correlations in generation times on the dynamics of population growth of microorganisms. We show that any non-zero correlation that is due to cell-size regulation, no matter how small, induces long-term oscillations…
The sexual version of the Penna model of biological ageing, simulated since 1996, is compared here with alternative forms of reproduction as well as with models not involving ageing. In particular we want to check how sexual forms of life…
We study the effect of mutations in a simple model of colonization, based on Montecarlo simulations. When the population colonizes the whole available habitat, a maximum population density is reached, which depends on the mutation rate.…
An algorithm for Monte Carlo simulations is proposed in which the parameter controlling the strength of the transition becomes a dynamical variable and in which efficient transitions are achieved by cluster steps. It allows to avoid the…
We consider estimation of the structural distribution function of the cell probabilities of a multinomial sample in situations where the number of cells is large. We review the performance of the natural estimator, an estimator based on…
Population annealing Monte Carlo is an efficient sequential algorithm for simulating k-local Boolean Hamiltonians. Because of its structure, the algorithm is inherently parallel and therefore well suited for large-scale simulations of…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. We focus here on computational methods that promise to boost live-cell fluorescence microscopy,…
Voltage-gated ion channels are key molecules for the generation and propagation of electrical signals in excitable cell membranes. The voltage-dependent switching of these channels between conducting and nonconducting states is a major…
For high precision measurements of K decays, the presence of radiated photons cannot be neglected. The Monte Carlo simulations must include the radiative corrections in order to compute the correct event counting and efficiency…
Background: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. New method: Here we describe the…
We present a population control method with sampling and regulation steps for Monte Carlo particles involved in the numerical simulation of a transport equation. We recall in the first section the difficulties related to the variance…
The preliminary analyses on a multiscale model of intestinal crypt dynamics are here presented. The model combines a morphological model, based on the Cellular Potts Model (CPM), and a gene regulatory network model, based on Noisy Random…
Large-scale Monte Carlo simulations, together with scaling, are used to obtain the critical behavior of the Hastings long-range model and two corresponding models based on small-world networks. These models have combined short- and…
Modifying the Redfield model of sexual reproduction and the Penna model of biological aging, we compare reproduction with and without recombination in age-structured populations. In contrast to Redfield and in agreement with Bernardes we…