Related papers: Elastic and Proton Dynamics of the DNA
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…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
In complex crystals close to melting or at finite temperatures, different types of defects are ubiquitous and their role becomes relevant in the mechanical response of these solids. Conventional elasticity theory fails to provide a…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
The eikonal model must be denoted as strongly preferable for the analysis of elastic high-energy hadron collisions. The given approach allows to derive corresponding impact parameter profiles that characterize important physical features of…
The pinning of an inhomogeneous elastic medium by a disordered substrate is studied analytically and numerically. The static and dynamic properties of a $D$-dimensional system are shown to be equivalent to those of the well known problem of…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
We analyze the elastic scattering of protons on a 4n system. This was used as part of the detection technique of a recent experiment [1] to search for the 4n (tetraneutron) as a bound particle. We show that it is unlikely that this process…
Elastic and inelastic cross section of proton-proton and electron-proton scattering are discussed. Special attention is given to elastic scattering and to the striking difference between the data of these two kinds of experiments. It is…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
Long length-scale structural deformations of DNA play a central role in many biological processes including gene expression. The elastic rod model, which uses a continuum approximation, has emerged as a viable tool to model deformations of…
We investigate the stability and geometrically non-linear dynamics of slender rods made of a linear isotropic poroelastic material. Dimensional reduction leads to the evolution equation for the shape of the poroelastica where, in addition…
We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link…
Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…