Related papers: Efficient Monte Carlo Simulation of Biological Agi…
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…
An efficient Monte Carlo algorithm for the simulation of spin models with long-range interactions is discussed. Its central feature is that the number of operations required to flip a spin is independent of the number of interactions…
In this paper we consider a generalization to the asexual version of the Penna model for biological aging, where we take a continuous time limit. The genotype associated to each individual is an interval of real numbers over which Dirac…
Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of efficient methods for…
Our paper computationally explores the extinction dynamics of an animal species effected by a sudden spike in mortality due to an extreme event. In our study, the animal species has a 2-year life cycle and is endowed with a high survival…
Widespread population aging has made it critical to understand death rates at old ages. However, studying mortality at old ages is challenging because the data are sparse: numbers of survivors and deaths get smaller and smaller with age. We…
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…
Further to the proposal and application of a stochastic methodology and the resulting first exit time distribution function to life table data we introduce a theoretical framework for the estimation of the maximum deterioration age and to…
As the global population continues to age, there is an increasing demand for ways to accurately quantify the biological processes underlying aging. Biological age, unlike chronological age, reflects an individual's physiological state,…
The one-dimensional kinetic contact process with parallel update is introduced and studied by Monte Carlo simulations. This process is proposed to describe the plant population replication and epidemic disease spreading among them. The…
Monte Carlo simulations are based on the manipulation of random numbers to evaluate probable outcomes, with applicability in a variety of different fields. By assigning probabilities, which can be determined a priori, to various events, it…
This review deals with computer simulation of biological ageing, particularly with the Penna model of 1995.
Population annealing is a promising recent approach for Monte Carlo simulations in statistical physics, in particular for the simulation of systems with complex free-energy landscapes. It is a hybrid method, combining importance sampling…
We experiment with a massively parallel implementation of an algorithm for simulating the dynamics of metastable decay in kinetic Ising models. The parallel scheme is directly applicable to a wide range of stochastic cellular automata where…
How self-organized networks develop, mature and degenerate is a key question for sociotechnical, cyberphysical and biological systems with potential applications from tackling violent extremism through to neurological diseases. So far, it…
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…
Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…
I present a simplified analytical model that simulates the evolution of the binary population in a dynamically evolving globular cluster. A number of simulations have been run spanning a wide range in initial cluster and environmental…
Monte Carlo simulations are one of the major tools in statistical physics, complex system science, and other fields, and an increasing number of these simulations is run on distributed systems like clusters or grids. This raises the issue…
The long-time dynamics of the critical contact process which is brought suddenly out of an uncorrelated initial state undergoes ageing in close analogy with quenched magnetic systems. In particular, we show through Monte Carlo simulations…