相关论文: A simple model for DNA denaturation

A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between…

A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…

An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent…

Sequence heterogeneity broadens the binding transition of a polymer onto a linear or planar substrate. This effect is analyzed in a real-space renormalization group scheme designed to capture the statistics of rare events. In the strongly…

Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the…

We present a precise equivalence of the Lifson-Poland-Scheraga model with wetting models. Making use of a representation of the former model in terms of random matrices, we obtain, in the limit of weak disorder, a mean--field approximation,…

We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…

We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…

Deformation twinning and martensitic transformations are displacive transformations; they are defined by high speed collective displacements of the atoms, the existence of a parent/daughter orientation relationship, and plate or lath…

In this paper we use a formal discrete-to-continuum procedure to derive a continuum variational model for two chains of atoms with slightly incommensurate lattices. The chains represent a cross-section of a three-dimensional system…

To establish a standard for the distinction of reptation from other modes of polymer diffusion, we analytically and numerically study the displacement of the central bead of a chain diffusing through an ordered obstacle array for times $t <…

We consider a pair of identical fermions with a short-range attractive interaction on a finite lattice cluster in the presence of strong site disorder. This toy model imitates a low density regime of the strongly disordered Hubbard model.…

We consider the large-time dynamics of one-dimensional processes involving adsorption and desorption of extended hard-core particles (dimers, trimers,\,$\cdots,k$-mers), while interacting through their constituent monomers. Desorption can…

We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…

We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…

Translocation of a single stranded DNA through genetically engineered $\alpha$-hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral…

Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…

There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…

Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…