Related papers: Stretching force dependent transitions in single s…
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…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
While slowly turning the ends of a single molecule of DNA at constant applied force, a discontinuity was recently observed at the supercoiling transition, when a small plectoneme is suddenly formed. This can be understood as an abrupt…
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…
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…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction…
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…
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition is of relevance to ongoing experimental and theoretical…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
When double stranded DNA is turned in experiments it undergoes a transition. We use an interacting self-avoiding walk on a three-dimensional fcc lattice weighted by writhe to relate to these experiments and treat this problem via…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…