Related papers: Determinative degree and nucleotide sequence analy…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
The $k$-th power of the adjacency matrix of a simple undirected graph represents the number of walks with length $k$ between pairs of nodes. As a walk where no node repeats, a path is a walk where each node is only visited once. The set of…
The possibility of prescribing local interactions between nano- and microscopic components that direct them to assemble in a predictable fashion is a central goal of nanotechnology research. In this article we advance a new paradigm in…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
A dual approach to defining the triangle sequence (a type of multidimensional continued fraction algorithm, initially developed in NT/9906016) for a pair of real numbers is presented, providing a new, clean geometric interpretation of the…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
Trace diagrams are structured graphs with edges labeled by matrices. Each diagram has an interpretation as a particular multilinear function. We provide a rigorous combinatorial definition of these diagrams using a notion of signed graph…
We present a framework for discriminative sequence classification where the learner works directly in the high dimensional predictor space of all subsequences in the training set. This is possible by employing a new coordinate-descent…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation…
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…
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
Quantum walks, both discrete (coined) and continuous time, form the basis of several quantum algorithms and have been used to model processes such as transport in spin chains and quantum chemistry. The enhanced spreading and mixing…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Topologically ordered materials may serve as a platform for new quantum technologies such as fault-tolerant quantum computers. To fulfil this promise, efficient and general methods are needed to discover and classify new topological phases…
In evolutionary policy search, neural networks are usually represented using a direct mapping: each gene encodes one network weight. Indirect encoding methods, where each gene can encode for multiple weights, shorten the genome to reduce…