相关论文: Dynamics of force-induced DNA slippage

The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…

A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…

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…

In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and…

The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…

Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…

A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…

A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…

We propose a simple nonlinear scaler displacement model to calculate the distribution of effect created by a shear stress on a double stranded DNA (dsDNA) molecule and the value of shear force $F_c$ which is required to separate the two…

This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…

Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…

DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…

Recent experimental data indicate that the elastic wormlike rod model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (Phys. Rev. Lett. 109, 228101, 2012)…

We numerically study stochastic resonance in the unzipping of a model double-stranded DNA by a periodic force. We observe multiple peaks in stochastic resonance in the output signal as the driving force frequency is varied for different…

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)…

A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…

We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…