Related papers: The bend stiffness of S-DNA
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…
We propose a new simple model for DNA denaturation bases on the pendulum model of Englander\cite{A1} and the microscopic model of Peyrard {\it et al.},\cite{A3} so called "combined model". The main parameters of our model are: the coupling…
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount…
We discuss in details a modified variational matrix-product-state algorithm for periodic boundary conditions, based on a recent work by P. Pippan, S.R. White and H.G. Everts, Phys. Rev. B 81, 081103(R) (2010), which enables one to study…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
Quantum transport for DNA conduction has widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works with concerning the electronic…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
The wormlike chain (WLC) model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for…
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…
Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It…
We consider a suspended elastic rod under longitudinal compression. The compression can be used to adjust potential energy for transverse displacements from harmonic to double well regime. As compressional strain is increased to the…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…
The interplay between global constraints and local material properties of chain molecules is a subject of emerging interest. Studies of molecules that are intrinsically chiral, such as double-stranded DNA, is one example. Their properties…
Self-positioned nanomembranes such as rolled-up tubes and wrinkled thin films have been potential systems for a variety of applications and basic studies on elastic properties of nanometer-thick systems. Although there is a clear driving…
Structural biology has long been dominated by the one sequence, one structure, one function paradigm, yet many critical biological processes - from enzyme catalysis to membrane transport - depend on proteins that adopt multiple…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…