Related papers: Mutation model for oligonucleotides fitting a Yule…
As input data distributions evolve, the predictive performance of machine learning models tends to deteriorate. In practice, new input data tend to come without target labels. Then, state-of-the-art techniques model input data distributions…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
I present an introduction to the field of Quantum Chromodynamics (QCD) with emphasis on nucleon spin structure and perturbative methods. After a somewhat comprehensive overview of perturbative QCD, including the systematics of…
We study the probability distribution function of the long-time values of observables being time-evolved by Hamiltonians modeling clean and disordered one-dimensional chains of many spin-1/2 particles. In particular, we analyze the return…
DNA inversion is an important mechanism by which bacteria and bacteriophage switch reversibly between phenotypic states. In such switches, the orientation of a short DNA element is flipped by a site-specific recombinase enzyme. We propose a…
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…
In several strongly correlated electron systems, defects, charge and local lattice distortions are found to show complex inhomogeneous spatial distributions. There is growing evidence that such inhomogeneity plays a fundamental role in…
Charge transfer is considered in systems composed of a donor, an acceptor and bridge sites of (AT) nucleotide pairs. For a bridge consisting of 180 (AT) pairs, three cases are dealt with: a uniform case, when all the nucleotides in each…
We consider a population model where individuals behave independently from each other and whose genealogy is described by a chronological tree called splitting tree. The individuals have i.i.d. (non-exponential) lifetime durations and give…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
A quantum spin model representing tautomeric mutation is proposed for any DNA molecule. Based on this model, the quantum mechanical calculations for mutational rate and complementarity restoring repair rate in the replication processes are…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
The Zipf distribution also known as scale-free distribution or discrete Pareto distribution, is the particular case of Power Law distribution with support the strictly positive integers. It is a one-parameter distribution with a linear…
Neutrino-nucleus scattering cross sections are critical theoretical inputs for long-baseline neutrino oscillation experiments. However, robust modeling of these cross sections remains challenging. For a simple but physically motivated toy…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
High fidelity state transfer is an important ingredient of distributed quantum information processing. We present and analyse results on perfect and quasi-perfect state transfer with linear spin chains incorporating non-uniform on-site…
Preferential attachment is a popular generative mechanism to explain the widespread observation of power law distributed networks. We introduce an alternative explanation for the phenomenon by allowing the link growth rates to vary across…
We analyse how the sampling dynamics of distributions evolve in score-based diffusion models using cross-fluctuations, a centered-moment statistic from statistical physics. Specifically, we show that starting from an unbiased isotropic…