Related papers: Simulation of stem cell survival in small crypts
A first step in exploring population structure in crop plants and other organisms is to define the number of subpopulations that exist for a given data set. The genetic marker data sets being generated have become increasingly large over…
The estimation of mutation probabilities and relative fitnesses in fluctuation analysis is based on the unrealistic hypothesis that the single-cell times to division are exponentially distributed. Using the classical Luria-Delbr\"{u}ck…
We have simulated the evolution of age structured populations whose individuals represented by their diploid genomes were distributed on a square lattice. The environmental conditions on the whole territory changed simultaneously in the…
Phenotype variations define heterogeneity of biological and molecular systems, which play a crucial role in several mechanisms. Heterogeneity has been demonstrated in tumor cells. Here, samples from blood of patients affected from colon…
The computational cost of a Monte Carlo algorithm can only be meaningfully discussed when taking into account the magnitude of the resulting statistical error. Aiming for a fixed error per particle, we study the scaling behavior of the…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
We review the background of the cluster algorithms in Monte Carlo simulation of statistical physics problems. One of the first such successful algorithm was developed by Swendsen and Wang eight years ago. In contrast to the local…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
This paper describes the Monte Carlo simulation developed specifically for the VCS experiments below pion threshold that have been performed at MAMI and JLab. This simulation generates events according to the (Bethe-Heitler + Born) cross…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
Computer simulations prove that we should spend more money on red wine than on medication. We optimise the problem of how to distribute a fixed amount of money between medication and food spendings, using the Penna ageing model.
When performing Monte-Carlo simulations, distributions are sometimes determined only for sub-intervals of the desired total range. In such cases, a frequent problem is to connect, or glue, individual distributions to obtain the final…
We deal with a small enough tumor section to consider it homogeneous, such that populations of lymphocytes and cancer cells are independent of spatial coordinates. A stochastic model based in one step processes is developed to take into…
Cells maintain a stable size as they grow and divide. Inspired by the available experimental data, most proposed models for size homeostasis assume size control mechanisms that act on a timescale of one generation. Such mechanisms lead to…
Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…
Population Monte Carlo (PMC) sampling methods are powerful tools for approximating distributions of static unknowns given a set of observations. These methods are iterative in nature: at each step they generate samples from a proposal…
An efficient Path Integral Monte Carlo procedure is proposed to simulate the behavior of quantum many-body dissipative systems described within the framework of the influence functional. Thermodynamic observables are obtained by Monte Carlo…
We developed a Monte Carlo simulation method to calculate incoherent Thomson scattering spectra in high temperature plasmas. The basic idea is to treat the entire scattering process as the superposition of individual photon-electron…