Related papers: Monte Carlo Simulation and Statistical Analysis of…
Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
The death of a biological population is an extreme event which we investigate here for a host-parasitoid system. Our simulations using the Penna ageing model show how biological evolution can ``teach'' the parasitoids to avoid extinction by…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
Genetic algorithm (GA) is inspired by biological evolution of genetic organisms by optimizing the genotypic combinations encoded within each individual with the help of evolutionary operators, suggesting that GA may be a suitable model for…
We present some results of simulations of population growth and evolution, using the standard asexual Penna model, with individuals characterized by a string of bits representing a genome containing some possible mutations. After about…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
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.
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…
A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Numerical simulations are performed on a stochastic model based on Monte Carlo damage simulation process and Markov Chain Monte Carlo techniques to investigate the formation and evaluation of isolated and multiple DNA damage and cellular…
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
The intensification and increased frequency of weather extremes is emerging as one of the most important aspects of climate change. We use Monte Carlo simulation to understand and predict the consequences of variations in trends (i.e.,…
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…
Stellar collisions have long been envisioned to be of great importance in the center of galaxies where densities of 1e6 stars per cubic pc or higher are attained. Not only can they play a unique dynamical role by modifying stellar masses…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…