Related papers: The bend stiffness of S-DNA
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…
Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…
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…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and 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 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…
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…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
Biological filaments such as DNA or bacterial flagella are typically curved in their natural states. To elucidate the interplay of viscous drag, twisting, and bending in the overdamped dynamics of such filaments, we compute the steady-state…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of…
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…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
We phenomenologically analyze short DNA rings' stability by discussing the second variation of its elastic free energy. Through expanding the perturbation functions as Fourier series, we obtain DNA rings' stability condition in a general…