Related papers: TYPE II DNA: when the interfacial energy becomes n…
A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base…
The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
We have studied the separation of a double stranded DNA (dsDNA), which is driven either by the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends…
We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
We investigate the relaxation dynamics of heat transport in superconductors, shaped by the interplay of diffusion, nonlinearity, and magnetic fields. Focusing on regimes near the critical temperature Tc, we analyze two classes of relaxation…
Gene regulation in higher eukaryotes involves a complex interplay between the gene proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive spatio-temporal expression. The experimental…
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…
We investigate the superconducting behaviour of Bi doped Pb. Pure lead shows type-I behaviour entering an intermediate state in a magnetic field. High dopings of Bi ($>$3%) lead to type-II behaviour showing a mixed state, where the magnetic…
As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount…
The electrical properties of DNA molecules are investigated by charge injection and electric force microscopy experiments. Prior to injection, DNA molecules exhibit a weak positively charged state. We probe the electrical behaviour of DNA…
Understanding the differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We develop a theoretical framework to quantify the underlying potential landscape and biological…
The universal behaviour of superconductors near the phase transition is described by the three-dimensional field theory of scalar quantum electrodynamics. We approximately solve the model with the help of non-perturbative flow equations. A…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
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 study a defect system of two parallel D5 probe branes in a large-N_c D3 background. Using the non-abelian DBI action, we study three different fields that can give rise to a superconducting phase transition: A vector (p-wave), a scalar…
Homogeneous nucleation of the new phase of one transition near a second phase transition is considered. The system has two phase transitions, we study the nucleation of the new phase of one of these transitions under conditions such that we…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…