Related papers: Monte Carlo Simulation and Statistical Analysis of…

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…

This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…

We construct a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species posses genetic information, which is inherited according to the rules of the Penna model of genetic evolution.…

We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to…

Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…

The recently proposed full configuration interaction quantum Monte Carlo method allows access to essentially exact ground-state energies of systems of interacting fermions substantially larger than previously tractable without knowledge of…

Two important problems affect the ability of asexual populations to accumulate beneficial mutations, and hence to adapt. First, clonal interference causes some beneficial mutations to be outcompeted by more-fit mutations which occur in the…

The application of Genetic Programming to the discovery of empirical laws is often impaired by the huge size of the search space, and consequently by the computer resources needed. In many cases, the extreme demand for memory and CPU is due…

Neurons in the brain represent information in their collective activity. The fidelity of this neural population code depends on whether and how variability in the response of one neuron is shared with other neurons. Two decades of studies…

Monte Carlo computer simulations are virtually the only way to analyze the thermodynamic behavior of a system in a precise way. However, the various existing methods exhibit extreme differences in their efficiency, depending on model…

We have developed a new simulation code aimed at studying the stellar dynamics of a galactic central star cluster surrounding a massive black hole. In order to include all the relevant physical ingredients (2-body relaxation, stellar mass…

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.…

A deterministic model of an age-structured population with genetics analogous to the discrete time Penna model of genetic evolution is constructed on the basis of the Lotka-Volterra scheme. It is shown that if, as in the Penna model,…

When simulating biological populations under different evolutionary genetic models, backward or forward strategies can be followed. Backward simulations, also called coalescent-based simulations, are computationally very efficient. However,…

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…

Codon usage bias has a crucial impact on the translation efficiency and co-translational folding of proteins, necessitating the algorithmic development of codon optimization/harmonization methods, particularly for heterologous recombinant…

Monte Carlo simulation code has been developed and tested for studying the passage of charged particle beams and radiation through the crystalline matter at energies from tens of MeV up to hundreds of GeV. The developed Monte Carlo code…

We analyze the accuracy and sample complexity of variational Monte Carlo approaches to simulate the dynamics of many-body quantum systems classically. By systematically studying the relevant stochastic estimators, we are able to: (i) prove…

Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…

We provide an overview of Monte Carlo algorithms based on Markovian stochastic dynamics of interacting and reacting many-particle systems not in thermal equilibrium. These agent-based simulations are an effective way of introducing students…