Related papers: Bio-Polymer Hairpin Loops Sustained by Polarons
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…
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 report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly…
Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…
Materials containing high densities of exceptionally displaceable ions (e.g. perovskites) have extremely large ratios of their static to high-frequency dielectric constants, > 2. Large polarons form in such materials as their electronic…
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
The velocity of polaron migration in the long poly-DNA chain (~40 base pairs) in an applied electric field has been studied within a polaron model. We found that the polaron velocity strongly depends on the polaron size. A small polaron…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
In the present study we revise the possible polaron contribution to the charge and energy transfer over long distances in biomolecules like DNA. The harmonic and the simple inharmonic ($U(x) = x^2/2 - \beta x^3/3$) lattices are considered.…
Conducting polymers have become standard engineering materials, used in manyelectronic devices. Despite this, there is a lack of understanding of the microscopicorigin of the conducting properties, especially at realistic device field…
A variational framework is developed to examine the equilibrium states of a semi-flexible polymer that is constrained to lie on a fixed surface. As an application the confinement of a closed polymer loop of fixed length $2\pi R$ within a…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…
Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study…
Organic semiconductors have the remarkable property that their optical excitation not only generates charge-neutral electron-hole pairs (excitons) but also charge-separated polaron pairs with high yield. The microscopic mechanisms…
We show by combining small-angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (cryo-TEM) that anionic silica nanoparticles (SiNPs) assemble into well-defined 1D cluster when mixed with a dilute solution of semiflexible…
Polarons, quasiparticles arising from electron-phonon coupling, are crucial in understanding material properties such as high-temperature superconductivity and colossal magnetoresistance. However, scarce studies have been performed to…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…