Related papers: Generalized Poland-Scheraga model for DNA hybridiz…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
We give an overview of the state of the art of the analysis of disordered models of pinning on a defect line. This class of models includes a number of well known and much studied systems (like polymer pinning on a defect line, wetting of…
We had combined the Neukirch-Marko model that describes the extension, torque and supercoiling in single, stretched and twisted DNA of infinite contour length, with a form of the free energy suggested by Sinha and Samuels to describe short…
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,…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is…
DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
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…
In our report we consider two weakly coupled Schr\"odinger equations as a model of the interchain energy transport in the DNA double-helix. We use the reduction of the Yakushevich-type model considering the torsional dynamics of the DNA. In…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
We introduce a shell-model theory that combines traditional spherical states, which yield a diagonal representation of the usual single-particle interaction, with collective configurations that track deformations, and test the validity of…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…