Related papers: Semiconservative Replication in the Quasispecies M…
Due to their algorithmic simplicity and high accuracy, force-based model coupling techniques are an exciting development in computational physics. For example, the force-based quasicontinuum approximation is the only known pointwise…
This work is concerned with the fundamental scaling laws of quasi-complementary sequence sets (QCSSs) by understanding how large the set size (denoted by $M$) can grow with the flock size ($K$) and the sequence length ($N$). We first…
A four-state mutation-selection model for the evolution of populations of DNA-sequences is investigated with particular interest in the phenomenon of error thresholds. The mutation model considered is the Kimura 3ST mutation scheme, fitness…
We study sharp peak landscapes (SPL) of Eigen model from a new perspective about how the quasispecies distribute in the sequence space. To analyze the distribution more carefully, we bring forth two tools. One tool is the variance of…
In biological cells, DNA replication is carried out by the replisome, a protein complex encompassing multiple DNA polymerases. DNA replication is semi-discontinuous: a DNA polymerase synthesizes one (leading) strand of the DNA continuously,…
We compare the integration error of Monte Carlo (MC) and quasi-Monte Carlo (QMC) methods for approximating the normalizing constant of posterior distributions and certain marginal likelihoods. In doing so, we characterize the dependency of…
We prove the quasi-optimal convergence of a standard adaptive finite element method (AFEM) for nonlinear elliptic second-order equations of monotone type. The adaptive algorithm is based on residual-type a posteriori error estimators and…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
The classical asymptotic theory for parametric $M$-estimators guarantees that, in the limit of infinite sample size, the excess risk has a chi-square type distribution, even in the misspecified case. We demonstrate how self-concordance of…
Mixture models have attracted significant attention due to practical effectiveness and comprehensive theoretical foundations. A persisting challenge is model misspecification, which occurs when the model to be fitted has more mixture…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
A particular case of the famous quasispecies model - the Crow-Kimura model with a permutation invariant fitness landscape - is investigated. Using the fact that the mutation matrix in the case of a permutation invariant fitness landscape…
We study the decay of survival probability at quantum phase transitions (QPT). The semiclassical theory is found applicable in the vicinities of critical points with infinite degeneracy. The theory predicts a power law decay of the survival…
Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is…
We examine the performance of efficient and AIPW estimators under two-phase sampling when the complete-data model is nearly correctly specified, in the sense that the misspecification is not reliably detectable from the data by any possible…
King and Roberts (2015, KR) claim that a disagreement between robust and classical standard errors exposes model misspecification. We emphasize that KR's claim only generally applies to parametric models: models that assume a restrictive…
The quasispecies theory is studied for dynamic replication landscapes. A meaningful asymptotic quasispecies is defined for periodic time dependencies. The quasispecies' composition is constantly changing over the oscillation period. The…
Using information-theoretic principles, we consider the generalization error (gen-error) of iterative semi-supervised learning (SSL) algorithms that iteratively generate pseudo-labels for a large amount of unlabelled data to progressively…
We study the semiclassical limit of the (generalised) KdV equation, for initial data with Sobolev regularity, before the time of the gradient catastrophe of the limit conservation law. In particular, we show that in the semiclassical limit…
In this paper we prove the existence of quasistatic evolutions for a cohesive fracture on a prescribed crack surface, in small-strain antiplane elasticity. The main feature of the model is that the density of the energy dissipated in the…