相关论文: Electrostatic effects in DNA stretching

By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…

We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…

Conformation of single polyelectrolytes in tetravalent salt solutions is investigated under the framework of a coarse-grained model, using Langevin dynamics simulations. The chain size, studied by the radius of gyration, shows three…

A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…

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…

The force-extension relation for a semi-flexible polymer such as DNA confined in a nanoslit is investigated and it is found that both the effective persistence length and the form of the force-extension relation change as the chain goes…

Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…

For an understanding of DNA elasticity at high mechanical loads (F > 30 pN), its helical nature needs to be taken into account, in the form of coupling between the twist and stretch degrees of freedom. The prevailing model for DNA…

Two overall neutral surfaces with positive and negative charged domains ("patches") have been shown in recent experiments to exhibit long-range attraction when immersed in an ionic solution. Motivated by the experiments, we calculate…

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…

Within the cell, biopolymers are often situated in constrained, fluid environments, e.g., cytoskeletal networks, stretched DNAs in chromatin. It is of paramount importance to understand quantitatively how they, utilizing their flexibility,…

We study theoretically the entropic elasticity of a semi-flexible polymer, such as DNA, confined to two dimensions. Using the worm-like-chain model we obtain an exact analytical expression for the partition function of the polymer pulled at…

Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…

Stretched-exponential relaxation is a widely observed phenomenon found in ordered ferromagnets as well as glassy systems. One modeling approach connects this behavior to a droplet dynamics described by an effective Langevin equation for the…

Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…

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)…

Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…

Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…

Monte Carlo simulations and variational calculations using a Gaussian ansatz are applied to a model consisting of a flexible linear polyelectrolyte chain as well as to an intrinsically stiff chain with up to 1000 charged monomers. Addition…