Related papers: Ternary and senary representations using DNA doubl…
Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA.…
We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT…
Since some years, non-overlapping sets of strings (also called cross-bifix-free sets) have had an increasing interest in the frame of the researches about Theory of Codes. Recently some non-overlapping sets of strings with variable length…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
Interfaces have long been known to be the key to many mechanical and electric properties. To nickel base superalloys which have perfect creep and fatigue properties and have been widely used as materials of turbine blades, interfaces…
The paper presents numerical simulations performed on dielectric properties of two-dimensional binary composites on eleven regular space filling tessellations. First, significant contributions of different parameters, which play an…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
Controlled deposition of DNA on graphene films obtained with the aid of mechanical splitting of graphite on a substrate with an epoxy sublayer is demonstrated. The DNA molecules are visualized using AFM.
The success of graphene for nanopore DNA sequencing has shown that it is possible to explore other potential single- and few-atom thick layers of 2D materials beyond graphene, and also that these materials can exhibit fascinating and…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Formation of random network of DNA strands is simulated on a two-dimensional triangular lattice. We investigate the size distribution of pores in the network. The results are interpreted within theory of percolation on Bethe lattice.
We consider the problem of developing interpretable and computationally efficient matrix decomposition methods for matrices whose entries have bounded support. Such matrices are found in large-scale DNA methylation studies and many other…
Deep neural networks (DNNs) transform stimuli across multiple processing stages to produce representations that can be used to solve complex tasks, such as object recognition in images. However, a full understanding of how they achieve this…
While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains…
Electronic DNA sequencing using two-dimensional (2D) materials such as graphene has recently emerged as the next-generation of DNA sequencing technology. Owing to its commercial availability and remarkable physical and conductive…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…