Related papers: Monte Carlo Simulation and Statistical Analysis of…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
Cluster analysis has proved to be an invaluable tool for the exploratory and unsupervised analysis of high dimensional datasets. Among methods for clustering, hierarchical approaches have enjoyed substantial popularity in genomics and other…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
We study the dynamical evolution of globular clusters containing primordial binaries, including full single and binary stellar evolution using our Monte Carlo cluster evolution code updated with an adaptation of the single and binary…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences encoding these antibodies to find variants with improved…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
Generative quantum machine learning models are trained to deduce the probability distribution underlying a given dataset, and to produce new, synthetic samples from it. The majority of such models proposed in the literature, like the…
Partial clonality is widespread across the tree of life, but most population genetics models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
In this paper we consider a generalization to the asexual version of the Penna model for biological aging, where we take a continuous time limit. The genotype associated to each individual is an interval of real numbers over which Dirac…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
The use of the Monte Carlo technique in a reliable and inexpensive way without the need for a standard radioactive source in determining the detector efficiency is becoming widespread every passing day. It is important to model the detector…
A revision of Stod\{'o}{\l}kiewicz's Monte Carlo code is used to simulate evolution of large star clusters. A survey of the evolution of N-body systems influenced by the tidal field of a parent galaxy and by stellar evolution is presented.…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
Cancer cells are widely known to be protected from apoptosis, which is a major hurdle to successful anti-cancer therapy. Over-expression of several anti-apoptotic proteins, or mutations in pro-apoptotic factors, has been recognized to…
The application of machine learning to bioinformatics problems is well established. Less well understood is the application of bioinformatics techniques to machine learning and, in particular, the representation of non-biological data as…