Related papers: Melting behavior and different bound states in thr…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
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…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
A barrier penetration model has been proposed to explain the spontaneous melting of the DNA oligomers into two separate single strands whereas the partially melted intermediate states are shown to be the bound state solution of the same…
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing,…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…
We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the…
The mass-imbalanced three-body recombination process that forms a shallow dimer is shown to possess a rich Efimov-St\"uckelberg landscape, with corresponding spectra that differ fundamentally from the homonuclear case. A semi-analytical…
In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
This review focuses on the force-induced unzipping transition of double-stranded DNA. It begins with a brief history of DNA melting, which emerged alongside the growth of the field of molecular biology, juxtaposed with the advancements in…
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
Ultracold gases of three distinguishable particles with large scattering lengths are expected to show rich few-body physics related to the Efimov effect. We have created three different mixtures of ultracold 6Li atoms and weakly bound 6Li2…