Related papers: Entropic Penalties in Circular DNA Assembly
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
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…
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…
Self-assembling novel ordered structures with nanoparticles has recently received much attention. Here we use computer simulations to study a two-dimensional model system characterized by a simple isotropic interaction that could be…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
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…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models 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…
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…