Related papers: Maximum principle and mutation thresholds for four…
We examine a quintessence model with a modified exponential potential given by $V(\phi) = V_0(1+e^{-\lambda \phi})$. Unlike quintessence with a standard exponential potential, our model can yield an acceptable accelerated expansion at late…
The large discrepancy between the values of the free energy for DNA dinucleotides (or dimers) measured by different teams has raised a yet unsettled debate. Here the free energy is fitted by a three parameter empiric formula derived in the…
This paper develops a two gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by $ \sigma_{via} $, yields a…
Many analyses in high-energy physics rely on selection thresholds (cuts) applied to detector, particle, or event properties. Initial cut values can often be guessed from physical intuition, but cut optimization, especially for multiple…
A model-independent method to study the possible evolution of dark energy is presented. Optimal estimates of the dark energy equation of state w are obtained from current supernovae data from Riess et al. (2004) following a principal…
We investigate sampling laws for particle algorithms and the influence of these laws on the efficiency of particle approximations of marginal likelihoods in hidden Markov models. Among a broad class of candidates we characterize the…
The theory of quantum jump trajectories provides a new framework for understanding dynamical phase transitions in open systems. A candidate for such transitions is the atom maser, which for certain parameters exhibits strong intermittency…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
We consider a population evolving under mutation and selection. The genotype of an individual is a word of length $\ell$ over a finite alphabet. Mutations occur during reproduction, independently on each locus; the fitness depends on the…
An evolution equation for a population of strings evolving under the genetic operators: selection, mutation and crossover is derived. The corresponding equation describing the evolution of schematas is found by performing an exact coarse…
We have analyzed the relations between the mutational pressure, recombination and selection pressure in the bit-string model with sexual reproduction. For specific sets of these parameters we have found three phase transitions with one…
We introduce a new parameter to discuss the behavior of a genetic algorithm. This parameter is the mean number of exact copies of the best fit chromosomes from one generation to the next. We argue that the genetic algorithm should operate…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
Multiple testing problems are a staple of modern statistical analysis. The fundamental objective of multiple testing procedures is to reject as many false null hypotheses as possible (that is, maximize some notion of power), subject to…
The free energy of the Random Energy Model at the transition point between ferromagnetic and spin glass phases is calculated. At this point, equivalent to the decoding error threshold in optimal codes, free energy has finite size…
Time series data provided by single-molecule Forster resonance energy transfer (sm-FRET) experiments offer the opportunity to infer not only model parameters describing molecular complexes, e.g. rate constants, but also information about…
How mutations accumulate in genomes is the central question of molecular evolution theories, however our understanding of this process is far from complete. Drake's rule is a notoriously universal property of genomes from microbes to…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Point mutations can surely be dangerous but what is worst than to lose the reading frame?! Does DNA evolved a strategy to try to limit frameshift mutations?! Here we investigate if DNA sequences effectively evolved a system to minimize…