Related papers: Conformations of closed DNA
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
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…
We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
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…
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…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
This article proposes a model including thermal effects for closed supercoiled DNA. Existing models include an elastic rod. Euler's elastica, ideal elastic rods on a plane, have only two kinds of closed shapes, the circle and a…
We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…
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…
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…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…