Related papers: Simulation of stem cell survival in small crypts
Since the early 1970s, stellar population modelling has been one of the basic tools for understanding the physics of unresolved systems from observation of their integrated light. Models allow us to relate the integrated spectra (or…
The Simulation Argument has gained significant traction in the public arena. It has offered a hypothesis based on probabilistic analysis of its assumptions that we are likely to exist within a computer simulation. This has been derived from…
Two species with similar resource requirements respond in a characteristic way to variations in their habitat -- their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to…
Quantum Monte Carlo methods find fruitful application in large shell model problems. These methods reduce the imaginary-time many-body evolution operator to a coherent superposition of one-body evolutions in a fluctuating one-body field;…
The classical Luria-Delbr\"uck model for fluctuation analysis is extended to the case where cells can either divide or die at the end of their generation time. This leads to a family of probability distributions generalizing the…
Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly…
Using geometrical arguments it is shown that Cancer Stem Cells (CSC) must be confined inside solid tumors under natural situations. Aided by an agent-based model and percolation theory, the probability for a CSC to be at the border of a…
In previous papers of the series we used a combination of optical and near-infrared colours to derive constraints on the relative age structure in globular cluster systems. Here, we present the details, strength and limitations of our…
An agent-based computer simulation of death by inheritable mutations in a changing environment shows a maximal population, or avoids extinction, at so intermediate mutation rate of the individuals. Thus death seems needed to al for…
Monte Carlo optimizations of Number Partitioning and of Diophantine approximations are microscopic realizations of `Trap Model' dynamics. This offers a fresh look at the physics behind this model, and points at other situations in which it…
The many-body dynamics of a quantum computer can be reduced to the time evolution of non-interacting quantum bits in auxiliary fields by use of the Hubbard-Stratonovich representation of two-bit quantum gates in terms of one-bit gates. This…
We present the result of a survey of Monte Carlo simulations of globular clusters hosting two generations of stars including a large (f_b=50%) fraction of primordial binaries in both populations. The dynamical evolution of the two stellar…
This is a brief report on some recent large-scale Monte Carlo simulations for approximating the density of zeros in character tables of large symmetric groups. Previous computations suggested that a large fraction of zeros cannot be…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system…
Parallel Monte Carlo simulations often expose faults in random number generators
Bacteria populate the colon where they replicate and migrate in response to nutrient availability. Here I model the colon bacterial population as a sandpile model, the colon-pile. Sand addition mimics bacterial replication and grains…
Population Monte Carlo simulations in the form commonly referred to as population annealing can serve as a useful meta-algorithm for simulating systems with complex free-energy landscapes. In the present paper we provide an easily…
Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a…
We investigate methods for modelling metabolism within populations of cells. Typically one represents the interaction of a cloned population of cells with their environment as though it were one large cell. The question is as to whether any…