Related papers: DNA sequence from the unzipping force? : one mutat…
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
The unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ is studied using Monte Carlo simulations. We obtain the dynamical order parameter, $Q$, defined as…
We consider force-induced unzipping transition for a heterogeneous DNA model with a long-range correlated base-sequence. It is shown that as compared to the uncorrelated situation, long-range correlations smear the unzipping…
The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
We present imaging and force spectroscopy measurements of DNA molecules adsorbed on functionalized mica. By means of Non-Contact mode AFM (NC-AFM) in Ultra High Vacuum (UHV), the frequency shift (\Delta f) versus separation (z) curves were…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
We introduce and test a method to predict the sequence of DNA molecules from in silico unzipping experiments. The method is based on Bayesian inference and on the Viterbi decoding algorithm. The probability of misprediction decreases…
We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…
We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on individual nucleotides are explored and related to model…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…