Related papers: Monte Carlo Simulation and Statistical Analysis of…
The paper presents an investigation of estimating treatment effect using different matching methods. The study proposed a new method which is computationally efficient and convenient in implication-'largest caliper matching' and compared…
To evaluate the feasibility of long duration, manned spaceflights, it is of critical importance to consider the selection and survival of multi-generational crews in a confined space. Negative effects, such as infertility, overpopulation…
This work aims at showing the relevance and the applications possibilities of the Fibonacci sequence, and also its q-deformed or quantum extension, in the study of the genetic code(s). First, after the presentation of a new formula, an…
Using the catalytic CO oxidation at RuO2(110) as a showcase, we employ first-principles kinetic Monte Carlo simulations to illustrate the intricate effects on temperature programmed reaction spectroscopy data brought about by the mere…
Ultracold neutrons (UCN) with kinetic energies up to 300 neV can be stored in material or magnetic confinements for hundreds of seconds. This makes them a very useful tool for probing fundamental symmetries of nature, by searching for…
Sequential Monte Carlo methods are a powerful framework for approximating the posterior distribution of a state variable in a sequential manner. They provide an attractive way of analyzing dynamic systems in real-time, taking into account…
Background: Hybridogenesis is a very interesting example of reproduction which seems to integrate the sexual and clonal processes in one system. In a case of frogs, described in the paper, two parental species - Rana lessonae and Rana…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
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…
The observation that phenotypic variability is ubiquitous in isogenic populations has led to a multitude of experimental and theoretical studies seeking to probe the causes and consequences of this variability. Whether it be in the context…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
The standard Penna ageing model with sexual reproduction is enlarged by adding additional bit-strings for love: Marriage happens only if the male love strings are sufficiently different from the female ones. We simulate at what level of…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
Simulation studies are used to evaluate and compare the properties of statistical methods in controlled experimental settings. In most cases, performing a simulation study requires knowledge of the true value of the parameter, or estimand,…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Permutation tests are amongst the most commonly used statistical tools in modern genomic research, a process by which p-values are attached to a test statistic by randomly permuting the sample or gene labels. Yet permutation p-values…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this paper we investigate these properties within an artificial genome model originally…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…
Requiring stability of genetic code against translation errors, modelised by suitable mathematical operators in the crystal basis model of the genetic code, the main features of the organisation in multiplets of the mitochondrial and of the…