Related papers: Conformations of Linear DNA
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
We reinvestigate the model originally studied by Neukirch and Marko that describes the extension, torque and supercoiling in single, stretched and twisted DNA molecules, which consists of a mixture of extended and supercoiled state, using…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
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 use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
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…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
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…
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…
The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent $\nu$ is topologically invariant and equal to the SAW…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
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…